CA2193501C - Luminescent lanthanide chelates and methods of use - Google Patents

Abstract

The invention provides lanthanide chelates capable of intense luminescence. The celates comprise a lanthanide chelator covalently joined to a coumarinlike or quinolone-like sensitizer. Exemplary sensitzers include 2- or 4-quinolones, 2or 4-coumarins, or derivatives thereof e.g. carbostyril 124 (7-amino-4-methyl-2-quinolone), coumarin 120 (7-amino-4-methyl-2-coumarin), coumarin 124 (7-amino-4-(trifluoromethyl)-2-coumarin), aminomethyltrimethylpsoralen, etc. The chelates form high affinity complexes with lanthanides, such as terbium or europium, through chelator groups, such as DTPA. The chelates may be coupled to a wide variety of compounds to create specific labels, probes, diagnostic and/or therapeutic reagents, etc. The chelates find particular use in resonance energy transfer between chelate-lanthanide complexes and another luminescent agent, often a fluorescent non-metal based resonance energy acceptor. The methods provide useful information about the structure, conformation, relative location and/or interactions of macromolecules.

Description

2~ 93~~J1 Luminescent Lanthanide Chelates and Methods of Use The research carried out in the subject application was supported in part by grants from the National Institutes of Health and the Office of Energy Research.
The government may have rights in any patent issuing on this application.
INTRODUCTION
Field of the Invention The field of this invention is luminescent lanthanide chelators.
Background Luminescent (including fluorescent and phosphorescent) markers find a wide variety of applications in science, medicine and engineering. In many situations, these markers provide competitive replacements for radiolabels, chromogens, radiation-dense dyes, etc. Improvements in fluorimetric instrumentation have increased attainable sensitivities and permitted quantitative analysis.
Perhaps the single-most significant limitation to the use of luminescent markers is generating an acceptable signal-to-noise ratio. Marker-dependent properties such as absorbtion and emission maxima, Stake's shift, quantum yield, etc. effect the ease of distinguishing signal from auto- or background fluorescence.
Hence, there is a continuous need to provide improved luminescent markers;

especially luminescent markers with long-lived luminescence and/or a large Stokes shifts with long wavelenght emmissions. Other useful and desireable properties include: easy and cost-effective synthesis; chemical stability, especially in an aqueous environment; convenient attachability to a wide variety of macromolecules including proteins and nucleic acids; efficient excitability by a convenient laser;
capable of intense luminescence; the capacity to perform as good luminescent resonance-energy transfer donors, enabling the determination of molecular distances beyond 100A; and usefulness as radiation-hardened ftuorophores in X-ray microscopy.
Relevant Literature Relevant patents include US Patent Nos 4,637,988 (1987) and 4,837,169 (1989).
DTPA-pAS-Tb is reported in Bailey et al. (1984) Analyst 109, 1449-1450.
For background papers on other lanthanide chelators, see Diamandis (1992) Analyst 117, 1879-1884, Canfi et al. (1989) Analyst 114, 1405-1406, Ando et al.
(1993) Biochimica et Biophysics Acta. 1102, 186-194, Georges and Ghazarian (1993) Analytica Chimica Acta, 276, 401-409, Mathis et al. (1993) Clin. Chem, 39, 1953 and Desai et al. '(1993) J. Am. Chem. Soc. 115, 11032, Seveus et al.
(1992) 13, 329-338, Saavedra and Picozza (1989) Analyst 114, 835-838, von Brenndorff et al. (1993) in Proceedings, 4th Intnl Conf on X-ray Microscopy, Chernogolovoka, Moscow District, Russia, Clark et al. (1993) Analytical Biochemistry 210, 1-6.
For an up-to-date review of Fluorescent Resonance Energy Transfer, see, Selvin (1994) Fluorescence Resonance Energy Transfer, in Biochemical Spectroscopy, a volume~of Methods in Enzymology, Academic Press, Ed. Kenneth Sauer, in press (copy attached).
SUMMARY OF THE INVENTION
The invention provides lanthanide chelates comprising a lanthanide chelator covalently joined to a polynuclear heterocyclic aromatic sensitizer of the general formula:

where X comprises an atom from periodic group 5 or 6. A single position 2-8 carbon atom of the sensitizer may be substituted with a linking group through which the sensitizer is covalently joined to the chelator.
This invention also provides a method of enhancing the luminescence of a lanthanide, the method comprising: forming a mixture of a lanthanide chelate as described above and a lanthanide capable of binding the chelate with an equilibrium constant of at least 109 M-1, whereby a luminescent lanthanide chelate-lanthanide complex is formed.
This invention also provides a method of detecting an analyte which may be present in a portion of a sample by luminescence, the method comprising the steps of:
contacting a sample portion with a luminescent complex of the above-described lanthanide chelate and a lanthanide capable of binding the chelate with an equilibrium constant of at least 109 M-1, wherein the chelate is covalently joined to a reagent capable of selectively binding the analyte;
2 0 incubating the sample portion under conditions wherein the reagent is capable of selectively binding the analyte;
exposing the sample portion to light at a first wavelength capable of inducing a first electronic transition in the chelate;
detecting an emission of light from the sample portion at a second wavelength wherein 2 5 the second wavelength is longer than the first wavelength and results from a second electronic transition in the chelate; ' wherein the detection of the emission of light correlates with the presence of the analyte sample protein.
This invention also provides a method of detecting the distance between a first 3 0 position and a second position in a portion of a sample by resonance energy transfer using a luminescent lanthanide chelate donor and an organic resonance energy acceptor, the method comprising the steps of:

3a exposing a sample portion comprising the donor located at the first position and the acceptor located at the second pos ition to light at a first wavelength capable of inducing a first electronic transition in the donor, wherein the donor comprises a complex of a lanthanide chelate as described above and a lanthanide capable of binding the chelate with an equilibrium constant of at least 109 M:-1, and wherein the spectral overlap of the donor emission and acceptor absorption is sufficient to enable energy transfer from the donor to the acceptor as measured by detectable quenching of donor luminescence intensity or lifetime or detectable 1 o increase in acceptor luminescence intensity or lifetime;
detecting at least one of:
the intensity of a first emission of light from the sample portion at a second wavelength, wherein the second wavelength is longer than the first wavelength and results from a second electronic transition in the donor, wherein the intensity of the first emission of light inversely correlates with the distance between the first and second positions of the sample portion; and the intensity of a second emission of light from the sample portion at a third wavelength, wherein the third wavelength is longer than the first wavelength and results from an electronic transition in the acceptor, wherein the intensity of the second emission of light 2 o correlates with the distance between the first and second positions of the sample portion.

In preferred chelates, the sensitizes has a first position 2-8 carbon atom substituted with an oxygen atom through a double covalent bond, a second position 2-8 carbon atom, different than the first position 2-8 carbon atom, substituted with a linking group through which the sensitizes is covalently joined to the chelator, and a substituted third position 2-8 carbon atom, different from the first and second position 2-8 carbon atoms. Frequently, the first position 2-8 carbon atom is the position 2 or 4 carbon atom, the second carbon atom is the position 7 carbon atom, the sensitizes and cheiator are linked through an amine or carboxyl group, and/or the third position 2-8 carbon atom is the position 4 carbon and is substituted with a hydrocarbon or halogen substituted hydrocarbon. Exemplary sensitizers include or 4-quinolones, 2- or 4- coumarins, or derivatives thereof e.g. carbostyril 124 (7-amino-4-methyl-2-quinolone), coumarin 120 (7-amino-4-methyl-2-coumarin), coumarin~ 124 (7-amino-4=(trifluoromethyl)-2-coumarin), aminomethyltrimethylpsoralen, etc.
The chelates axe capable of forming high affinity complexes with lanthanides, such as terbium or europium, through chelator groups, such as DTPA.
Typically, the chelators comprise a plurality of structurally constrained anionic groups such as carboxylate or phosphonate groups. Solutions of chelate-lanthanide complexes are capable of intense luminescence. The chelates may be coupled to a wide variety of compounds to create specific labels, probes, diagnostic and/or therapeutic reagents, etc.
Chelate-lanthanide complexes are useful as detectable labels in a wide variety of applications. Generally, the methods involve contacting a sample portion with a luminescent complex; exposing the sample portion to light at a first wavelength capable of inducing a first electronic transition in the chelate;
and detecting an emission of light from the sample portion at a second wavelength that is longer than the first wavelength and results from a second electronic transition in the chelate. Specific analytes in the sample may be detected by coupling the chelate to a reagent capable of analyte selectively binding.
The chelates also find use in resonance energy transfer between chelate-lanthanide complexes and another luminescent agent, often a fluorescent non-metal 5 based resonance energy acceptor. For example, by coupling the chelate-lanthanide complex donor to one atom and the acceptor to a second atom, the distance between two atoms can be measured. Generally, the spectral overlap of the donor emission and acceptor absorption is sufficient to enable energy transfer from donor to acceptor as measured by detectable quenching of donor luminescence intensity of lifetime or detectable increase in acceptor luminescence.
Where the atoms are on the same molecule, the methods provide useful information about the structure or conformation of the molecule. For example, the methods are used to monitor the status of a polymerase chain reaction by coupling the donor and acceptor to separated atoms of a diagnostic oligonucleotide. As the concentration of target DNA increases, the percentage of diagnostic oligonucleotides hybridized to target DNA increases which in turn increases the mean distance between the labelled atoms. This increased mean distance is detected as a decrease in energy transfer between the donor and acceptor.
Where the atoms are on different molecules, the methods provide useful information on the interactions or relative locations of the two molecules.

DESCRIPTION OF SPECIFIC EMBODIMENTS
We have synthesized a series of new chemical compounds which bind to lanthanide elements including terbium and europium, and efficiently sensitize them, i.e. allow them to be excited efficiently and subsequently luminesce efficiently.
The compounds also enable convenient coupling to macromolecules. We call these compounds lanthanide chelates.
The importance of the invention is several-fold: First, our lanthanide chelates can be used as non-isotopic replacements for radioactive labels.
Second, they can be used as alternatives to conventional fluorescent dyes, especially in imaging applications, with the potential for increased contrast. This increasal contrast arises because the lanthanide luminescence is extremely long (0.6-2.3 millisecond). If one 'uses a pulsed excitation source and gated (time-resolved) detection, the intense autofluorescence (background) will decay away, with the labels still emitting. Such autofluorescence currently prevents fluorescent images of many tissue samples. Third, because the chelates are all excited in the same spectral region, two color imaging is possible. Fourth, the lanthanide chelates can be used as extremely efficient donors in luminescent energy transfer analyses.
This use enables measurements of distances beyond 100A, distances currently not measurable with standard fluorescence energy transfer techniques, but of importance in structural biology and medicine.
Our chelates have a number of important advantages: 1. They are easy to synthesize and attach to macromolecules; 2. They are efficiently excited by a nitrogen laser (at 33~nm); 3. Some of of them (e.g. DTPA-cs124) can sensitize W096/00901 ~ ~ ~ } ~ ~ ~ PCTIU595I08319 both terbium and europium; 4. The lanthanide luminescence from the chelates are extremely intense; for example, the terbium chelate exemplified below luminesces approximately sixty-five times more intensely than DTPA-paraaminosalycilate (DTPA-pAS) when excited at 337 nm; 5. They are chemically stable; 6. They can be used to label nucleic acids and proteins under chemical conditions used in automated synthesizers (e.g. creating phosphoramidites in DNA/RNA technology or protein technology); 7. They are extremely good resonance energy transfer donors. An important element in the success of our chelates in energy-transfer is the fact that there is very little spectral or temporal overlap between the sensitizer's emission and the lanthanide's emission. In contrast, DTPA-pAS has very significant temporal and spectral overlap and provides a poor energy transfer donor; and, 8. They are useful as radiation-hardened fluorophores in X-ray microscopy.
Our lanthanide chelates comprise a polynuclear heterocyclic aromatic sensitizer of the general formula:
~. vxJ
where X comprises an atom from periodic group 5 or 6.
Suitable sensitizers may include a variety of additional structure including structures where the above general formula comprises a structurally minor portion of the sensitizer. Generally, at least one of the position 2-8 carbon atoms, preferably position 2 or 4, is oxidized, preferably to a carbonyl (i.e. double bonded to an oxygen atom). Positions are conventionally numbered: counter-clockwise from the heteroatom which is position number 1. Frequently, another posirion 2-carbon atom, preferably the other 2 or 4 position, is substituted (i.e. a hydrogen atom is replaced) with a group comprising an alkyl, vinyl, oxy (including hydroxyl, alkoxy, carboxyl), carbonyl or substituted nitrogen (e.g. nitro-, amino including substituted amines, etc.), cyano, acetate, etc. group, or a derivative thereof, particularly halide derivatives. Exemplary sensitizers include rhodamine 560, 575 and 590, fluoresceins, 2- or 4.-qainolones, 2- or 4- coumarins, or WO 9blD0901 ~ ~ ~ ~ ~ U ~ PCTIIfS95lidR319 derivatives thereof e.g. coumarin 445, 450, 49U, 500 and 503, 4-trifluoromethylcoumarin (T'FC), 7-diethyl-amino-cumarin-3-carbohydrizide, etc., and especially carbostyril 124 (7-amino-4-methyl-2-quinolone), coumarin 120 (7-amino-4-methyl-2-coumarin), coumarin 124 (7-amino-4-(trifluoromethyl)-2-coumarin), aminomethyltrimethylpsoralen:
15 ~~
~paslBon 1 position A wide variety of derivatives of the above general formula may be used as sensitizers, so long as the resultant chelate provides the requisite lanthanide binding and luminescence enhancement. By enhanced luminescence is meant that a solution of the chelate complexed with a lanthanide, when exposed to light at a wavelength, the complexed lanthanide emits light of greater intensity or lifetime WO 9b100901 ~ 1 9 ~ J ~ ~ PCTlUS95108319 than an identical sample absent the chelate. The enchancemcnt is usually at least 503&, preferably at least 500%, mare preferably at least 5000%, most preferably at least 50,000 greater intensity under at least one set of conditions (e.g.
specified concentration, solvent system, etc.) e.g. see conditions described herein.
To effectively excite the resident lanthanide, the chelates generally provide absorbtion maxima between 150 and 750 nm, usually between 200 and 650 nm, more usually between 250 and 550 nm, most usually between 300 and 450 nm.
Generally, detected emissions are at least 50 nm, usually at least 100 nm, more usually at least 150 nm greater than the incident light. For example, preferred detected emissions for terbium and europium are 492 and 546 nm and 617 and 695 nm, respectively. Extinction coefficients generally exceed 5,000, usually $,000, more usually 11,000.
The selection of particular chelator-sensitizer combinations is dependent on the intended application. Criteria include the selected lanthanide, sources of potential background fluoresence, quenching agents, the incident light source, etc.
Functionally, suitable chelates for a given lanthanide are identified by coupling a candidate sensitizer to a chelator such as DTPA, complexing with the lanthanide, and identifying complexes capable of enhanced lanthanide luminescent. Assay details are described below.
The chelates are capable of forming high affanity complexes with lanihanides, such as terbium or europium. The chelates bind at least one lanthanide, preferably at least one of terbium and europium, with an equilibrium constant of at least 106 M'', preferably at least 10g hl-', more preferably at least 10'° Ma under at least one set of conditions described herein. A wide variety of structural moieties can be used to provide the requisite lanthanide binding affinity, so long as the resultant chelate provides the requisite luminescence. However, the lanthanide is usually ionically bound by anionic groups such as carboxylate or phosphonate groups.
Frequently, the chelates comprise one or more structurally distinct chelator portions. Typically, these chelator portions comprise a plurality of structurally constrained anionic groups such as carboxylate or phosphonate groups. In a preferred embodiment, these portions are selected from compounds which themselves are capable of functioning as lanthanide cheIators with the W096/n09d1 { ~ ~ PCTlUS95108319 aforementioned binding affinities. For example, such chelator portions include EDTA, DTPA, DOTA, N'I'A, HDTA, etc. and their phosphonate analogs such as DTPP, EDTP, HDTP, NTP, etc. The chelate's lanthanide affinity may also be a cooperative (synergistic) result of the interaction of a plurality of functional groups.
S Far example, one ar more amino acids moieties, e.g. glycine, of the chelate can be structurally positioned to bind vacant coordination sites of the lanthanide to enhance overall binding affinity.
Where the cheIate comprises a structurally distinct chelator portion, it is usually cavalently joined to the sensitizes portion, typically through a linking 10 group. Any linking group thak is capable of cavalently Linking the sensitizes with the chelator and does not preclude requisite lanthanide binding and luminescence may be used. Thus, the linking group may comprise a wide variety of structures.
Frequently, the linking group comprises a nitrogen, carboxyl, carbonyl or alcohol group or a nitrogen or carboxyl derivative and is covalently joined to a position 2-8 carbon atom in the general formula. The linking group is often covalently joined to one of the position 2-8, frequently position 7, carbon atoms above. Common linking groups are aliphatic and aromatic amines, which may be primary or secondary, carboxyls and suIfhydryls. The chelator and sensitizes are frequently joined through an amide, anhydride, disulfide, thin-urea, thioether, etc.
band.
The chelates may be synthesized in any convenient way. Many of the disclosed sensitizers and chelators sensitizers are commercially available -others are synthesized or modifed from commercial starting materials according to conventional methods. The two may be coupled by any convenient chemistry, though they are most often directly coupled through functional groups as described herein. For example, same of the preferred chelates are based on a ruction between an anhydride (e.g. of diethylenetriaminepentaacetic acid, caDTPA) and a sensitizes (the DTPA acts as the chelator, binding the lanthanide tightly and preventing radiationless deactivation by water, and the organic compound acts as a sensitizes, allowing efficient excitation of the lanthanide). These chelates may be made by a modification of the procedure of Bailey et al (1984) Analyst 109, .1449-1450, where an amine-containing sensitizers replace pAS. The anhydride of DTPA
are separately dissolved in an anhydrous organic solvent, typically dry dimethylsulfoxide. The anhydride and selected sensitizes are then mixed and 21 ~~'~v ~
WO 96/00901 PCTlUS95108319 allowed to react for approximately an hour. The anhydride reacts with the amine on the sensitizes to form a stable amide bond.
Where desired, the chelate may be coupled to an analyte-specific reagent, organic polymer, macromolecule (esp, biomolecules like nucleic acids and proteins), etc in any convenient way. For example, for covalent coupling to a protein (or other amine containing macromolecule), the chelate can be originally formed using the dianhydride of DTPA. After coupling to the sensitizes, the mixture is then added to the amine-containing macromolecule, either in an organic solvent or in an aqueous solvent. The second dianhydride then reacts with the amines) on the macromolecule, forming another amide bond. The reactivity of the amine is sufficiently great that this reaction can be done in an aqueous medium (even though water competes for reaction with the anhydride).
Alternatively, a bifunctional linker can be used to couple the chelate and the macromolecule. For example, a suitable linker may comprise both a thiol reactive group (e.g. maleinide, acetyl halide, etc.) and an amine reactive group (e.g.
thiourea, isothiocyanate, etc.). For instance, the mono-anhydride of DTPA may be coupled to a protein by reacting with 3-(2-pyridyldithio)propionyl hydrazide (PDPH).
Chelate-lanthanide complexes are useful as detectable labels in a wide variety of applications. Generally, the methods involve contacting a sample portion with a luminescent complex of a chelate and a lanthanide; exposing the sample portion to light at a first wavelength capable of inducing a first electronic transition in the chelate; and detecting, advantageously with a time delay to minimisze the detection of shorter-lived background luminescence, an emission of light from the sample portion at a second wavelength that is longer than the first wavelength and results from a second electronic transition in the chelate.
Specific anaIytes in the sample may be detected by coupling the chelate to a reagent capable of analyte selectively binding.
The methods are adaptable to a wide variety of samples including biological samples and extracts (such as physiological fluids, nucleic acid and/or proteinaceous solutions, microbial cultures, ete.), environmental samples (such as water sources), industrial, especially chemical reagents, products and wastes, etc.
The chelates may be free in solution or restrained in a variety of ways. For WO ~6I00901 ~ ~ ~ ~ ~ ~ ~ PCTIUS95I08319 IL
example, the chelates may be preferentially partitioned in or on one phase, solid or liquid, such as adsorbed onto a solid surface or membrane or retained within a bead (e.g. latex microspheres). Thus, the methods are useful in conjunction with sorting (e.g. cell sorting), chromatography, electrophoretic, osmotic and centrifugal separations. Heat and organo-stable chelates are selected for applications involving elevated temperature (e.g. distillations, combustions, etc.) and organic extractions.
The first wavelength (that of the incident light) is selected to optimize the ultimate signal-to-noise ratio of the lanthanide emission. Frequently, fhe incident light is provided in a form to minimize background absorption. Useful sources include lasers (e.g. nitrogen, helium-cadmium, dye lasers, etc.) and arc lamps (e.g.
high-pressure, mercury, xenon, quartz, etc.). Nitrogen lasers are particularly preferred because their 337 nm emission frequency is close to a lanthanide absorbtion maximum. Similarly, the second wavelength is selected to optimize signal-to-noise ratio and in view of the available instrumentation.
The subject chelates may be coupled to a wide variety of compounds to create specific labels, probes, diagnostic andlor therapeutic reagents, etc.
Examples include biomolecules such as proteins (antibodies, enzymes, receptors, etc.), nucleic acids (RNA, DNA, etc.), bioactive molecules (drugs, toxins, etc.);
solid subtrates such as glass or polymeric beads, sheets, fibers, membranes (e. g.
nylon, nitrocellulose), slides (e. g. glass, quartz) and probes; etc.
Many of our chelates are particularly amenable to what we term Luminescence Resonance Energy Transfer, or LRET. LRFT is a generalized version of Fluorescent Resonance Energy Transfer, or FRET, a widely used technique in polymer science, biochemistry and structural biology. FRET can be used to measure the distances between two points that are labelled with fluorescent dyes and separated by approximately 10-75A. The technique is valuable because measurements can be made under physiological (or other) conditions with near-Angstrom resolution and with the exquisite sensitivity of fluorescence measurements. FRET relies on a distant-dependent transfer of energy from one fluorescent dye -- the donor - to another absorbing or fluorescent dye -- the acceptor. The donor and acceptor are site-specifically placed at the two points that one wishes to measure the distance between.

~1 '~:~~~~~
WO 96100901 PCTIUS95lD8319 While lanthanides do not fluoresce, the use of our chelates permits them to be efficiently excited. A non-fluorescent quantum transition of the lanthandide can then effect a non-radiative energy transfer to a suitable and appropriately distanced acceptor. To effect transfer, an acceptor absorbtion must overlap a lanthanide emission. The chelate - acceptor pair is selected for optimal overlap: for longer distance measurements, greater overlap is preferred. Since the lanthanides have lifetimes on the order of a millisecond, the signal-to-noise ratio of sensitized emission of the acceptor in LRET is improved by emission detection through time resolution (pulse delay) or phase modulation. Energy transfer can be detected by donor quenching or, preferably acceptor luminescence.
By using luminescent lanthanide chelators as donors (instead of conventional dyes), and conventional fluorescent dyes as acceptors, we have improved the signal to background of LRET by approximately 100-fold. This improvement allows measurements beyond 100A, a distance currently unmeasurable using small, conventional fluorescent dyes. This distance regime is important in many biological problems. Using lanthanide chelators as donors also makes distance measurements more accurate, because the chelators minimize the uncertainty in the orientation-dependence of energy transfer. We have also demonstrated the first lifetime measurement of the sensitized emission of the acceptor, a LRET
measurement which eliminates problems associated with non-specific or incomplete labelling.
A wide variety of acceptors are useful with our chelate donors. Generally, the selected acceptor will have an absorbance maximum at a wavelength between nm and 250 nm longer than that of the donor chelate. Exemplary acceptors 25 include xanthene dyes such as fluoresceins and rhodamines, coumarins, benzimide dyes, phenanthridine dyes, ethidium dyes, acridine dyes, cyanine dyes such as thiazole orange, thiazole blue, CyS, Cy5.5, Cy3, etc., carbazole dyes, phenoxazine dyes, porphyrin dyes, quinolone dyes, pycobillyc proteins, e.g.
allophycocyanin, R-phycoerythrin, B-phycoerythrin, Bodipy dyes, etc. The acceptors generally emit in the visible or infrared ranges.
LRET is particularly useful to obtain structural and kinetic information about macromolecules in solution, in real time. For example, double-end labeled oligonucleotides provide detectable LRET signalling when hound by nucleic acid .,~~,;
wo 9sroovat ~ 1 ~ J ~ a i ~'~S9srox3m binding proteins, e.g. transcription factors. Accordingly, the methods are used to screen for potential therapeutics that alter the structure or interactions of biomolecules; far example, anti-viral agents are sceened far the ability to alter viral transcription factor-induced alterations in nucleic acid conformation.
The general LRET-based method of detecting the distance between a first position and a second position in a portion of a sample involves: exposing a sample portion comprising the donor lanthanide-chelate complex located at the first position and the acceptor located at the second position to Tight at a first wavelength capable of inducing a first electronic transition in the danar. The spectral overlap of the donor emission and acceptor absorption is sufficient to enable energy transfer from the donor to the acceptor as measured by detestable quenching of donor luminescence intensity or lifetime or detectable increase in acceptor luminescence intensity or lifetime. Then the intensity of a first emission of light from the sample portion at a second wavelength is detected wherein the second wavelength is longer than the first wavelength and results from a second electronic transition in the donor, wherein the intensity of the first emission of light correlates with the distance between the first and second posifions. In other words, the closer the positions, the greater the energy transfer and the greater the donor quenching. Alternatively, one can detect the intensity of a second emission of light from sample partian at a third wavelength, wherein the third wavelength is longer than the first wavelength and results from an electronic transition in the acceptor, wherein the intensity of the second emission of light inversely correlates with the distance between the first and second portions of the sample portion. In ether wards, the closer the positions, the greater the energy transfer and the greater the acceptor luminescence.
This general method has broad application whenever the static or dynamic distance between to positions, e.g. two atoms or molecules, is of interest. In one specific embodiment, the method is used to monitor the status of a polymerase chain reaction. Here, the sample portion comprises a target nucleic acid strand comprising a first strand portion and a diagnostic nucleic acid strand labeled proximal to one end with the acceptor and proximal to' the other end with the donor (i.e. comprising a first atom covalently joined to the donor and a second atom covalently joined to the acceptor, the first and second atoms being separated by a WO 96!00901 ~ J PCTlUS95108319 second strand portion). The first and second strand portions are sufficiently complementary to hybridize under annealing conditions, and the second strand portion is of sufficient length to provide a detectable difference in the aggregate energy transfer from the donor to the acceptor when the first and second strand 5 portions are hybridized as compared with the aggregate energy transfer from the donor to the acceptor when the fast and second strand portions are not hybridized.
The detectable difference is measured as at least one of a detectable quenching of donor luminescence or detectable increase in acceptor luminescence, and the distance between the first and second atoms indicates whether the nucleic acid 10 strands have hybridized. Thus, as the reaction proceeds, the stepwise increase in the amount of target nucleic acid is reflected in a stepwise decrease in energy transfer.
The following examples are offered by way of illustration and not by way of limitation.
EXAMPLES
Example 1.
In this example, we exemplify the technique of luminescent resonance energy transfer (LRET) by introducing a luminescent teibium chelate as a donor, and an organic dye, tetramethylrhodamine, as acceptor. The results are consistent with a Forster theory of energy transfer, provided the appropriate parameters are used. The use of lanthanide donors, in general, and this pair, in particular, has many advantages over more conventional FRET pairs which rely solely on organic dyes. The distance at which SOgo energy transfer occurs (Ro) is large, 65A;
the donor lifetime is single exponential and long (millisecond), making lifetime measurements facile and accurate; uncertainty in the orientation factor (rc2) which creates uncertainty in measured distances is minimized by the donor's multiple electronic transitions and long lifetime; the sensitized emission of the acceptor can be measured with little or no interfering background, yielding a > 25 fold improvement in signal to background over standard donor-acceptor pairs. These improvements are expected to make distances greater than 100A measurable via LRET. We also report measurement of the sensitized emission lifetime, a L i '~ :.~ ~a WO )6/00901 PCrlU5951p8319 measurement which is completely insensitive to total concentration and incomplete labeling.
In FRET a fluorescent donor molecule transfers energy via a non-radiative dipole-dipole interaction to an acceptor molecule (which is usually a fluorescent molecule). FRET is a standard spectroscopic technique for measuring distances in the 10-70A range. Upon energy transfer, which depends ort the R~ distance between the donor and acceptor, the donor's lifetime and quantum yield are reduced, and the acceptor fluorescence is increased, or sensitized(1). FRET is frequently used in both polymer science and structural biology and has recently been used to study macromolecular complexes of DNA, RNA, and proteins (2-4).
Despite these successes, FRET has had a number of serious flaws which has limited its utility. First, the maximum distance which can be measured has been less than optimal far many biological applications. Second the lifetime of commonly used donor fluoraphores are short (typically a few nanoseconds) and multiexponentiai, making lifetime measurements difficult and of limited accuracy.
Third, the signal-to-background of the sensitized emission has been law due to interfering iluarescencx from the donor and from direct excitation of the acceptor.
Fourth, precise distances have been difficult to determine because the efficiency of energy transfer depends not only on the R-6 distance between the donor and acceptors, but also on their relative orientation, as expressed by the x2 factor. (The efficiency of energy transfer = I!(I+R°!Ro ), where Rpis a function of rr~ aee Appendix).
The luminescent lanthanide elements terbium and europium are attractive FRET donors because they potentially overcome many of these problems. Because lanthanide emission does not arise from a singlet to singlet transition, energy transfer using lanthanide donors is more accurately called luminescence resonance energy transfer (LRET:). The lanthanides have primarily been used in diffusion-enhanced FRET (5) and as isomarphous replacements in calcium-binding proteins (6-8). In addition, it~athis has used europium cryptates with the multichramophoric Allophycocanin to achieve an extremely large Ro of 90A (9). We have recently presented results showing numerous advantages of using a palycarboxylate-chelate of europium as a donor in conjunction with an organic dye such as CY-5 as the acceptor (10). Here we extend these results to the use of terbium as a donor.

~' 1 ~3 :~ ~ ;~F ~
WO 9G/0(1901 PC'flUS95108319 As a model system, we covalently attach donor and acceptor to the 5' ends of a series of double-stranded DNA oligomers of varying length. The use of DNA
in such a model system has been previously shown to be valid for energy transfer measurements between organic dyes (11).
Material and Methods Synthesis of Labeled DNA Oligomers. Complementary DNAs of 10,12,14 bases in length were synthesized using standard phosphoramidite procedures. An amino-group attached via a six-carbon linker (Glen Research) was incorporated at the 5' end. The acceptor sequence wasp that used by Clegg et al (11): 5'-CCA-CTC-TAG-G-3' (lObp); 5'-CCA-CTG-GCT-AGG-3' (l2bp); 5'-CCA-CTG-CTG-CTA-GG-3' (l4bp). The 5-isomer of Tetramethylrhodamine-isothiocyanate (Molecular Probes. T-1480: abbreviation: TMR) was attached via standard procedures and purifred by reverse phase HPLC. Extinction coefficients for TMR
attached to DNA were determined to be el~,= 33mM-'crrt' and else=93mh1'crri'.
The donor-strand consisted of complementary DNA labeled at the 5' end with a terbium chelate. The chelate is diethylenetriaminepentaacetic acid coupled to a laser dye, carbostyril 124 (DTPA-cs124). Details of the donor chelate synthesis will be presented elsewhere. Unlabelled DNA oligamers were also synthesized.
I3ybridization Conditions: Donor and acceptor strands were mixed in desired ratio in a DSO-based buffer containing lOmM Tris, pH 8.0, lOmM MgCI~, 150mM NaCI. Experiments were also performed in an Hz0-based buffer. Donor strand concentration was approximately 200nM. Oligomers were annealed by heating to 75°C and cooled to the final temperature (22°C or 5°C) over 15 minutes.
Spectroscopy: Absorption measurements were made on a Hewlett Packard 8452A spectrometer. Steady-state fluorescence measurements were on a SPEX
Fluorolog fluorimeter. Time-resolved and gated luminescence measurements were made on a laboratory-built spectrometer utilizing right-angle detection with a pulsed Laser-Photanics Nitrogen laser (Snsec pulse width, 40Hz repetition rate), a Gallium-arsenide photon-counting detecaor, a gated discriminator (Ortec 584) and a multichannel scalar with 2 sec time-resolution. Polarization studies were also conducted although energy-transfer experiments performed without an analyzer W096/UU9U1 ~ f '~ J ~ U ~ PCT/US95/U8319 is gave the same results as those using an analyzer. An analyzer was therefore routinely omitted. A temperature-regulated cuvette-holder and a quartz 3mmx3mm cuvette was used. Lifetime data was fit using TableCurve software (Jandel Scientific).
Results and Discussion The structure of the donor chelate, DTPA-cs124-Tb, and the model system used for energy transfer is shown below:
~+
(~3;~, ~vCt72-P-C C T~~~ T G
3'-GGA~~~AC
The donor-chelate has several important features. First, the chelate binds terbium (and europium) extremely tightly - titration with a 100 Fold excess of EDTA (Kb < 10")~'') is unable to displace a measurable amount of terbium. This is in agreement with ocher DTPA-based chelators (12) and ensures that there is no free terbium. Second, the chelate allows site-specitic attachment of terbium to macromolecules. Third, the chelate shields the terbium from non-radiative deexcitation mechanisms, likely resulting in a quantum yield for terbium luminescence near unity in D20 (see Appendix I). Finally, the covalent attachment WO 96!00901 ~ ~j 1 PCT1US95/OS319 of the laser dye carbostyril 124 overcomes the extremely low absorption cross-section of terbium (< 1 M~'cm') (6). The cs124 absorbs light (e32g=11,000 M-'crri '; Eg3g= 8,000 M-'crri') and because of its close proximity to the terbium, transfers energy to the lanthanide (13, 14).
Figure 1 shows the spectral characteristics of the terbium chelate and the tetramethylrhodamine which lead to efficient energy transfer and a large Ro of in D20 (60 A in HBO). Ro is calculated from standard equations (see appendix).
Here we mention two unusual aspects of using a lanthanide chelate as donor: 1) The efficiency of energy transfer can be adjusted, and hence Ra optimized for the particular system being measured, simply by varying, the ratio of Hx0 to Dz0 in the solvent. The H20/Dz0 ratio affects the efficiency of energy transfer by altering the lanthanide quantum yield (q") in our chelate (q,~~ 1 in DSO;
q"~0.6 in HZO; see Appendix 1) (15). 2) The orientation dependence of the energy transfer process is minimized because the terbium has multiple, degenerate, electronic transitions and is therefore an isotropic donor, even if stationary. This minimizes uncertainty in the measured distance due to orientation effects of +/-12% in the worst case(16).
Figure 1 also shows the highly spiked nature of the terbium emission.
Donor quenching can be measured without interference From acceptor emission at 492nm and 546nm. Similarly, the sensitized emission of the acceptor can be measured without significant interferencz from donor luminescence because terbium is nearly silent around 570nm, where TMR is at 70% of its emission maximum. The terbium signal at 570nm is 240x less than at its maximum, 546nm.
When measuring the sensitized emission, we can also eliminate the direct fluorescence of the acceptor by temporal discrimination. We use pulsed excitation, and collect data only after a 90 wsec delay, during which time direct fluorescence of the rhodamine has decayed away. (The acceptor fluorescence, with a lifetime of a few nanoseconds, decays rapidly; we also find a small component - probably either delayed fluorescence or a detector artifact - which decays away within the 90 .sec delay.) The donor, because of its millisecond lifetime, stays excited and capable of transferring energy at the end of the delay period. Consequently, any signal arising around 570nm after the delay is due only to sensitized emission, i.e.
fluorescence of the acceptor due to energy transfer.

2~ 9l~'~' W096100901 .~'.)f.! ~ PCTlUS95/08319 Figure 2A shows the results of an energy transfer experiment on a partially hybridized lOmer DNA. The average energy transfer is 77°k. The signal to background of the sensitized emission at 570nm is 54:1. By comparison, the signal to background for sensitized emission when using fiuorescein-rhodamine as 5 energy transfer pairs on the same DNA is approximately 1. Because the background is so small in our case, small signals become measurable, and hence distances much greater than 12o are expected to be possible. I-Iorrocks and Bruno, for example, have shown the ability to measure distances of 4Ro (lta=3.1A) utilizing the dark-background sensitized emission of tyrosine to terbium energy 10 transfer (6).
We can isolate the sensitized emission signal from donor luminescence even in regions where donor luminescence is significant. In a procedure analogous to that used by Clegg et al (11), we can subtract the donor luminescence at all wavelengths, leaving the sensitized emission signal. The efficiency of energy 15 transferred is then simply the area of the corr~ted sensitized emission, divided by the total corrected area:
efficiency of energy transfer = (falqA ) / (fR/q,, t fo) (1) where f" is the area under the sensitized emission curve, q,, is the fluorescence quantum yield of the acceptor, and fp is the area under the donor luminescence 20 cuwe. One can determine the quantum yield of the acceptor by a comparison with the donor quenching data. Based on a quantum yield of 0.174 for TMR (see Appendix I1), equation 1 yields an average energy transfer of 77~.
Figure 2B shows the lifetime data on a series of lOmer DNA oligomers.
The donor-only (single stranded DNA) signal is single exponential with a lifetime of 2.14msec. (A terbium labeled DNA oligomer hybridized to its complement is single exponential with a lifetime of 2.80m sec. The difference in lifetime between double-stranded and single-stranded terbium-only DNA is likely due to different radiative rates arising from different symmetries surrounding the terbium, rather than different quantum yields.) A titration with increasing amounts of acceptor strand shows bi-exponential donor quenching (curves B and C). The long-lifetime component corresponds to unhybridized, donor-only single stranded DNA; the short component corresponds to those terbium-strands that are hybridized with acceptor strands. As expected, increasing the amount of acceptor strand increases ~~r~, WO 9GI00901 ~ ' ~ ~ "I L , PCT/US95108319 the amplitude of the short component and decreases the amplitude of the long component, while leaving their lifetimes unchanged (compare curves B and C).
That the long-time component equals the donor-only signal is an important internal control which shows that intermolecular energy transfer is not significant.
The lifetime of the short component corresponds to an energy transfer in the donor-acceptor complex of 88% (1-331p,secJ2809psec). By comparison, the energy transfer an the same lOmer DNA with the same six-carbon linkers using fluorescein-TMR pair is 23% (11).
In calculating the efficiency of energy transfer based on the sensitized emission curve, we ignore the short time component since this is due to residual signal arising from the direct fluorescence of the acceptor. (No gate was used for this data). Multiple experiments show the long-time component is repeatable to within 10% in the worst case, and usually repeatable within a few percent. The short-time component, however, is highly variable since there is a very large, very short spike due to direct fluorescence which cannot be resolved.
At two-fold excess of acceptor strand, there is still a 10-12% unhybridized component. A similar phenomenon has been seen with dye-labelled oligomers (17) and in FRET experiments with europium substituted in our chelate (10}. In our case it does not appear to be a simple melting-temperature phenomenon since it is present at both 5°C and 22°C. The reason for this is under investigation. It is unlikely that this residual unquenched donor signal is due to fundamental lanthanide photophysics since this would require an uncoupled magnetic dipole transition, a situation which is not present since all terbium (and europium) luminescence arises from the same excited state (18, 19).
Figure 2B also shaves the lifetime of the sensitized emission at 570nm corresponding to the biexponential donor-quenching (curve B}. The sensitized emission decay can be accurately fit to the equation: y=33%exp(-t/45~sec) +
67%exp(-tJ326tcsec). The 45msec component corresponds to direct fluorescence from the acceptor or a detector artifact (which can be eliminated by gating}.
The 326usec component is due to energy transfer on the donor-acceptor complex, and agrees extremely well with the 329-331~csec donor quenching component. Note that after approximately 90 uses, the only species which contribute to the sensitized emission signal is the donor-acceptor complex - donor-only or acceptor-only do ~ ~ PCTIU595I08319 WO 9b1110901 not contibute. This significantly minimizes the problem of incomplete labeling.
The sensitized-emission lifetime signal is also insensitive to total concentration, to quantum yields, and to non-energy-transfer effects which can cause donor quenching.
Table 1 summarizes the lifetime and energy transfer data on donor-acceptor labelled DNA duplexes of 10,12, and l4bp length.
Table I
Lifetime Efficiency of Calculated Clegg et al.
(psec) energy transfer Distance (A) Distance (A) IOmer 336 0.88 46.6 55.5 l2mer 724 0.74 54.6 56.4 l4mer 1154 0.59 b1.2 61.0 Data. from multiple experiments show donor quenching and sensitized emission lifetimes for a given length DNA agree always within 10%, usually within a few percent. As expected, there is a decrease in energy transfer with increasing distances. For comparison we include the distances determined by Glegg et al. using f(uorescein-TMR (11). Both results are consistent with the DNA double-helix geometry, although differing salt conditions and donor-lifetimes lead to different dye positions, and hence different measured distances. We have fit our distances using the Clegg et al. model of the DNA helix and attached dyes.
With only three data points, it is not possible to resolve uniquely all the parameters in the model, but nevertheless, a good fit to their model is achieved if it is assumed that the terbium chelate andfor acceptor are fairly close to the DNA
helix.
This reduces the modulation seen in their FRET data, which arises because of the helical geometry of the DNA and the fact that their donor and acceptor are extended away from the helix (19A and 13A, respectively). This difference is qualitatively reasonable since the long-lifetime of our donor is expected to allow constrained diffusion of the donor and acceptor within the limits placed by the six-r, ~ ,- ~..
I~~J.>~u~
WO 96100901 PCfIUS95108319 carbon linkers, and because of the greater ionic strength used here, which minimizes charge repulsion.
In summary, the data are consistent with the geometry of the double-helix DNA if the energy transfer data are derived based on the dipole-dipole Forster-type mechanism. Numerous technical advantages of luminescence resonance energy transfer make this a technique well suited for measurements on biologically interesting macromolecules.
Appendix I
Calculation of Ro: Ra, the distance at which 50% of the donor's excited state energy is transferred to the acceptc:r, is calculated from standard equations (1}:
Ra = (8.79 x lOv J n2 n'° qU ) "d ~. (2) where q"is the luminescence quantum yield far donor emission fn the absence of IS acceptor, J is the spectral overlap of the. donor emission (fp) and acceptor absorption (eA) (J= f fDea)," dh), n is the index of refraction and kz is a geometric factor related to the relative angles of the tw°o dipoles. Here we evaluate each of the terms in equation 2 and discuss their uncertainty.
The index of refraction, n, varies from 1.33 for water to 1.39 for many organic molecules. We have used 1.33. A numerical integration leads to a J
overlap integral of 3.8x10'Snm'hM. This is an upper limit for J since the 546nm peak of terbium may arise from magnetic dipole, as well as electric dipole transitions (19), and the former do not significantly transfer energy (18}.
The fraction of magnetic dipole contribution can be calculated theoretically (20, 21}, or the problem avoided by using the 492nm line of terbium, which is known to be solely an electric dipole transition (20).
When using organic dyes in FRET, rcz is often a significant source of uncertainty and in the worst case, may vary from 0 to 4 (22). With terbium, however, emission arises from multiple electronic transitions which constrain r,~:l/3< rc2< 4/3. In addition, it is likely that the acceptor can undergo rotational motion during the millisecond donor-lifetime. This further constrains n~ and we assume rcz=2/3, corresponding to a random orientation rotating rapidly within the donor lifetime.

l?'~3~~i 1 The luminescence quantum yield of the terbium, qp, is difficult to accurately determine because of terbium's intrinsically low absorbance. q,~, however, is likely very close to 1 in Di0 (see helow). Note that when calculating Rn, it is important to use the terbium quantum yield (= 1 in Da0), not the S quantum yield of the entire chelate. 'fhe quantum yield of the entire chelate equals the lanthanide quantum yield times the fraction of energy absorbed by the cs124 that is transferred to the lanthanide.
Quantum yield of lanthanide emission: There are several lines of (indirect) evidence which argue qD ~ 1 in DxO. First, emission arises from 4f-4.f inner shell electrons which are shielded from the solvent and other sources of non-radiative deexcitation by the chelate. The 1.2 Hz0 molecules in the primary coordination sphere of the terbium in our chelate (data not shown) are the primary source of non-radiative deexcitation, but these are replaced by D20, which do not significantly deactivate terbium (I5, 23). The nonwater ligands, carboxylate groups and amine nitrogens are extremely inefficient at deactivating the terbium excited state (23). Via temperature studies (24), we have also looked for quenching effects of the cs124 and have found none.
A second line of evidence supporting qp = 1 in Dz0 comes from the work of Elbanowski and coworkers who directly measured the quantum yield of a 1:3 ZO mixture of terbium: EDTA in H20, and found a value of 0.54 (ZS). This measurement is difficult and of unknown accuracy, but nevertheless, it suggests a high quantum yield even in HZO, and the quantum yield in DSO is expected to be considerably higher. (There are probably 2 water molecules coordinated to the terbium in their complex (23)).
The third line of evidence comes from energy transfer experiments using terbium as a donor in thermolysin (8, 26), and as an acceptor in invertebrate calmodulin (6), where the assumption (sometime implicit) of unity quantum yield in DZO gives good agreement with x-ray crystallography data.
Appendix II
Calculating the fluorescence quantum yield of the acceptor: By comparing the donor-quenching lifetime data with the areas and using equation 1 it is possible to measure the quantum yield of the acceptor. This is a general and new method W09B100901 ~ 1 ~ ~ ~ ~ y PCTIUS95t08319 for measuring quantum yields of any dye whose absorption overlaps the emission of terbium (or europium). It has the advantage over more conventional methods of measuring quantum yields in that the measurement involves only one sample -the actual sample of interest - rather than comparing a reference to the sample.
5 T'o evaluate the quantum yield of TMR, we assume the unknown in equation 1 is q,, and take the average efficiency of energy transfer to be 77.6%, as determined from curve C (supra). Based on the integrated areas (620 for f,, and 1032 for f", in arbitrary units), this yields q,, = 0.174. By comparison, free tetramethylrhodamine in phosphate-buffered saline has a quantum yield of 0.25, as 10 measured by standard techniques (27).
Parenthetical references of Example 1.
1) Cantar and Schimmel, (1980) Biophysical Chemistry. (W. H. Freeman and Co., San Francisco}; 2) Clegg, (1992) Methods Enzymol. 211:353-388; 3) Selvin, (1994) Methods En~ymoJ. 246, (in press); 4) Coker et al., (1994) 15 Resonance Energy Transfer. (VCH Publishers, Inc.) (in press); S) Stryer et al., (1982) Annu. Rev, of Biophys. and Bloengin. 11:203-222; 6} Bruno et al., (1992) Biockem. 31:7016-7026; 7) Crance and Horrocks, (1.992) Biochenr. 31:7963-7969;
8) Horrocks, et al., (1975) Proc. Natl. Acad. Sci. USA 72:4764-4768; 9) Mathis, (1993) Clin. Chem. 39:1953-1959; lOj Salvin et al., (1994) JACS (in press);
11) 20 Clegg et al., (1993) Proc. Natl. Acarl. Sci., USA 90:2994-2998; I2) Oser et al., (1990) Anal. Biochemistry 191:295-301: 13) Abusaleh and Meares, (1984) P)rotochem. & Photobiol. 39:763-769; 14) Kirk et al., (1993) J. Phys. Chem.
97:10326-10340; IS) Horrocks et al., (1977) JACS 99:2378-2380; 16} Stryer, (1978) Ann. Rev. Biochent. 47:819-46; 17) Cooper and Hagerman, (1990) 25 Biochemistry 29:9261-9268; 18) Dexter, (1953) J. Chem. Phys. 21:836-850;
19) Bunzli, (1989) Luminescent Probes, ed. Bunzli, 7.-C.G., Choppin, G.R.
(Elsevier, New York), pp. 219-293; 20) Carnall et al., (1968) J. Chen:. Phys. 49:4412-4423;
21) Goriler-Walrand et al., (1991) J. Phys. Chem. 95:3099-3106; 22) Dale et al., (1979) Biophys. J. 26:161-194; 23) Hoirocks and S~sdnick, (1979) J. Am. Chem.
30, Soc. 101:334-350; 24) Alpha et al., (1990) P)totochem. and Photobiol.
52:299-306;
25) Elbanowski et al., (1989) Mnnat. Chem. 120:699-703; 26) Berner et al., (1975) Biochem. do Biophys. Res. Comrntm. 66:763-768; and 27) Waggoner, (1994} Hfethods Enzymol. 246 (in press).

Example 2.
In this example, we exemplify the technique of fluorescence resonance energy transfer (FRET) by introducing a europium chelate as donor and an organic dye, CY-5 as acceptor. The use of lanthanide donors, in general, and this pair, in particular, has many advantages over more conventional FRET pairs which rely solely on organic dyes. The Ro is large, 70A; the donor lifetime is single exponential and long (2.Smsec in D20); the orientation factor which creates uncertainty in measured distances is minimized by the donor's multiple electronic transitions and long lifetime; the sensitized emission of the acceptor can be measured with little or no interfering background, yielding a >50 fold improvement in signal to background over standard donor-acceptor pairs. This improvement in signal to background is expected to make distance measurements of greater than 10011 feasible. We also measure the sensitized emission lifetime, a measurement which is independent of total concentration and incomplete labeling.
We have used a luminescent europium chelate as donor and an organic dye, CY-5 as acceptor. This luminescence resonance energy transfer (F.RET) has several advantages over the more conventional FRET'. The distance at which 50l of the energy is transferred (R~) is large, 70A; the donor lifetime is single exponential and long (0.63msec in H20; 2.Smsec in D20), making lifetime measurements facile and highly accurate; the orientation dependence (x2) of energy transfer is minimized by the donor's multiple electronic transitions and long lifetime, limiting uncertainty in the measured distance due to orientation effects to +/-129& in the worst case'; the sensitized emission of the acceptor can be measured with little or no interfering background, yielding a >50 fold improvement in signal to background over standard donor-acceptor pairs and enabling distances several times R" to be measured'. We also measure the sensitized emission lifetime which, in our case, is independent of total concentration and incomplete labeling.
We have used both terbiums and europium as donors, and the results for europium are presented here. A schematic diagram of the donor-acceptor model system comprising double stranded DNA with europium chelate (donor) at one 5' end and CY-5 at other 5' end is shown below:

~~~7J~i WO 961011901 PCT/US95f08319 The europium chelate, (diethylenetriaminepentacetic acid-carbostyril 124-Eu: trivial name, DTFA-cs124-Eu) was made by a modification of the procedure of BaileytZ, starting with the dianhydride of DTFA (Sigma), carbostyril 124 (Aldrich), and the synthetic DNA base-protected and on the column to ensure that labelling occurs only at the 5' amino group. The cs124 effectively increases the absorption cross section of the europium to approximately $000 M-'cru' at 337nm, where we excited the donor with a pulsed Nitrogen laser. A 100-fold excess of EDTA did not remove any noticeable amount of europium from the DTPA-cs124 chelator.
The acceptor was 5' labeled with CY-5'3 (Biological Detection Systems) via standard methods. Unlabelled complementary DNA oligomers were made as controls. All DNA was reversed-phase HPLC purified. In this system, the double-stranded DNA oligomer serves as a rigid tether to establish a defined distance between the europium donor and the CY5 acceptor. The points of attachment of the donor and acceptor are separated by 42A, although the dye positions retain limited variability duo to the flexible six-carbon linkers used for attachment °'' Figure 3 shows the spectral characteristics which lead to the unusually large Ro of 70A in Dz0 (56A in Hz0). Ro is determined from standard equations) based on a calculated spectral overlap (J) of b.55 x10'3 Manm', an orientation factor (rcz) of 2/3, an index of refraction of 1.33, and a quantum yield for europium luminescence in DZO of one (0.25 in FI20)~. In calculating Ro it is important to use the quantum yield of the lanthanide emission, and not the quantum yield of the entire chelate, and to include in the spectral overlap (J) calculation only those PC1'IUS95108319 ~O 96100901 2$
transitions which are electric dipole. The europium emission at 6I7nm, which is used here for energy transfer, has been shown to be "forced" electric dipole9, and hence Fiirster's theory of energy transfer is applicable. The europium emission at 596nm cannot crouple to an acceptor because it is a magnetic dipole transition and so is not included in the spectral overlap calculation'°.
We can measure the sensitized emission of the acceptor without significant interference from either donor emission or direct acceptor fluorescence. At 668nm, europium is nearly silent (europium emission at 668nm is 125 times less than at its 617nm maximum) and by using pulsed-excitation and gating off the IO detector for 90msec, the direct fluorescence of the carbostyril sensitizer in the donor complex and the direct fluorescence of the CY-5 are completely eliminated, while the europium stays excited and capable of energy transfer".
Figure 4A shows such a dark-background sensitized emission experiment.
Here the ratio of donor to acceptor strands is approximately I:0.6; we intentionally add less acceptor than donor to show the ability of our system to analyze heterogeneous signals. The average fraction of energy transfer in figure 4A is 57~. The signal at 668 nm arises from sensitized emission of CY-5, i.e.
fluorescence due only to energy transfer. We calculate the signal/background at 668 nm to be 94:1 (where background is due to a small amount of europium luminescence), a factor of 50-100 improvement in signal/background over the sensitized emission signal from fluorescein-rhodamine, one of the best donor-acceptor pairs, attached to the same lOmer.
Figure 4B shows lifetime data corresponding to Figure 4A. The donor-only signal is single exponential with a lifetime of 2.52msec. The donor quenching signal fits a biexponent extremely well (r~=0.998): y = 633'oexp(-t/0.22msec) +
37 roexp(-t/2.40msec). The long-time component corresponds to the donor-only species. That the long-time component nearly equals the donor-only lifetime is an internal control which shows that intermolecular energy transfer is at most 5%.
The short time component arises from intramolecular energy transfer in the hybridized donor-acceptor complex and corresponds to 9I % quenching (1-0.22msec/2.52msec), and a donor-acceptor distance of 46A. (Fluorescein-rhodamine on the same DNA with C-6 linkers yields 2286 energy transfer'.) A
titration with increasing acceptor concentration increases the fraction of the short WO 96/00901 ~ ~ ~ ~~. ~ ~ Pt:TIU595/08319 time-component but does not change its lifetime, as expected. At two-fold excess of acceptor strand, a 10% camponent corresponding to donor-only signal remains, presumably due to unhybridized donor strands.
Figure 4B also shows the lifetime of the sensitized emission. The sensitized emission lifetime signal is fit to a biexponential (rz=0.999): y = 40%exp(-t159psec) + 60%exp(-t10.25msec). The short-time component is due to direct fluorescence of the acceptor and can be eliminated by gating the detector. The 0.25msec component is due to an energy transfer of 90 % (1-0.2512.52msec), in excellent agreement with the short-time component of the donor quenching. A
very small long-time component ( =1 %) can be seen due to direct donor fluorescence.
In summary, luminescence energy transfer yields results consistent with a FBrster theory assuming the appropriate parameters are used. Based on the large Ro, the ease and reproducibility of our lifetime measurements, and the excellent signal to background, distances significantly greater than 100A are measurable.
FOOTNOTED REFERENCES IN EXAMPLE 2.
(1) Cantor and Schimmel, (1980) Blophysieal Chemistry, W. H. Freeman and Co., San Francisco, Vol. 2; (2) Lanthanides in energy transfer have been used in diffusion enhanced FRET (Stryer, L., Thomas, D. D., Meares, C. F. (1982) In Annual Review of Biophysics and Bioengineering, L. J. Mullins, Ed., Annual Reviews, Inc., Palo Alto, CA, 11:203-222). They have also used been used with multichromophoric AlIophycocanin (Mathis, (1993) Clln. Chem. 39:1953) and as isomorphous replacements in calcium-binding proteins (Horrocks et al., Proc.
Nat.
Acad. Sci. USA (1975), 72:4764; Cronce and Horrocks, (1992) Biochem. 31:7963);
(3) Stryer, (1978) Ann. Rev. Binchcn:. 47:819-846; (4) The ability to measure energy transfer beyond Ro using sensitized emission has been shown by Bruno and Horrocks. They used terbium as the acceptor and tyrosine as the donor. With an Ro of 3A they measured out to 12A. (Bruno et al., (1992) Biachem. 31:7016);
(5) Selvin and Hearst, (1994) Proc. Natl. Acad. Sci, USA (submitted), (6) Cardullo et al., (1988) Proc. Natl. Acad. Sci., USA 85:8780; (7) Clegg et al., (1993) Proc.
Natl. Acad. Scl. USA 90:2994; (8) The exact quantum yield is difficult to determine although the long-lifetime and lack of radiationless deactivation mechanisms make it likely that the quantum yield is close to one in D20. This PGTIUS95l08319 assumption has given distances in agreement with x-ray crystallography studies (See ref 4). In HZO, the quantum yield is decreased because there are 1.3 water molecules in the primary coordination sphere of the lanthanide in our chelate (Horrocks and Sudnick, (1979) J. Am. Chem. Soc. 101:334); (9) Bunzli, J.-C.G.
5 (1989) In Lanthanide Probes in Life, Chemical and Earth Sciences, Theory oral Practice Luminescent Probes; BunzIi, J.-C.G. 8c Choppin, G.R. Ed., Elsevier, New York, pp. 219-293; (IO) Dexter, (1953) J. Chem. Phvs. 21:836; (11) Morrison has used gated integration to increase the signal to background of the sensitized emission with organic dyes. Morrison, (1988) Anal. Biochem.
174:101;
10 (12) Bailey et al., (i984) Analyst 109:1449; and (13) Mujumdar et al., (1993) Bloconf. Chem. 4:105.
Example 3. Terbium chelate -ftuorescein energy transfer.
This example employed a terbium chelate (Terbium-diethylenetriamine-15 pentaacetic acid coupled to carbostyril 124) transferring energy to fluorescein. The donor and acceptor are separated by an 8 mer DNA duplex oligonucleotide modified with a primary amine on the 5' end. The acceptor is attached to the S' end of a complementary oligonucleotide. The sensitized emission is measured with no background at around 520 nm. Furthermore, there is excellent overlap between 20 492 nm donor emission line and fluorescein absorbance, leading to a large Rfl. By using a pulsed excitation source and monitoring at 520 nm, any signal arises only from sensitized emission. The 8-mer oligonucleotide is used to rigidly separate the donor and acceptor, and the complex is immersed in a viscous sucrose solution to eliminate intermolecular interactions, though the sucrose solution is generally not 25 necessary when the oligonucleotide concentration is maintained below about 0.25 uM. Sensitized emission signal to background ratio at 520 nm is approximately 400:1. The extent of energy transfer based on both donor intensity quenching and the integrated sensitized emission area is 70%. Measurements of the unquenched donor lifetime (I.5 msec) in the absence of acceptor, and the sensitized emission 30 lifetime in the donor-acceptor complex (lifetime 250 usec), indicate a quenching of 85 ~ . The difference between the 70 and 85 °~ is due to the small fraction of unhybridized donor labeled DNA which cannot transfer energy.

w0 96100901 ~ C~1 ~ ~ ~ ~ PCTlUS95108319 Example 4. Assay for Enzymatic (1'roteolytic) Activity Fluorescence resonance energy transfer (FRET) has been used to study enzymatic activity where the distance between two labeled points changes as a function of this activity. In general, where FRET has been used, LRET can also be used, often with significant improvements. For example, Matayoshi et al.
(1990) Science 247:954-958, used FRET to measure HIV protease activity by labeling a substrate peptide with a donor and acceptor on either side of a protease bindinglcutting site. Because of the close proximity of the donor and acceptor, the donor fluorescence in the intact peptide was highly quenched. Upon addition of a protease, the peptide was cleaved, the donor and acceptor diffuse away from each other and the donor fluorescence increased approximately forty fold. The sensitivity of the assay is largely determined by the extent of donor quenching in the intact peptide. The lack of 100% quenching causes background fluorescence even in the absence of proteolytic activity. The authors note that they used a donor with a relatively long lifetime (tens of nanoseconds) because this helps increase donor quenching of the intact peptide. ('fhe reason is that the peptide is flexible and a long-lifetime allows the peptide time to flex such that the donor and acceptor come close together, resulting in donor quenching.) Replacing a standard fluorescent donor with a lanthanide chelate provides significantly reduced background, and hence, better sensitivity. The lanthanide chelate has a lifetime which is > 105 times longer than organic fluorophore, which leads to greater donor quenching due to the peptide flexibility. In addition, any residual donor luminescence can be discriminated against by using pulsed excitation and turning of the detector for some fraction of a millisecond after the pulse. If the donor is quenched by 9010 in the intact peptide, for example, the remaining 10% luminescence will have a lifetime 1/10 of the unquenched chelate, or approximately 100 usec. By gating off the detector for a few hundred microseconds, this residual donor luminescence is prevented from reaching the detector, while the unquenched luminescence which arises after proteolysis, which has approximately a millisecond lifetime, is relatively unaffected by the gating.
Lastly, the exceptional efficiency of energy transfer from the lanthanide chelates to acceptors allows the attachment points of the donor and acceptor to be placed W09610090I ~ ~ f~ ~ ~ ~ ~ PCI'IUS95l0$319 farther apart on the peptide than is possible with standard dyes. This is an important consideration when the binding site of the enzyme is large.
Example 5. Detection of genes and DNA sequences FRET has been used to detect specific DNA sequences, Morrison et al.
(1.989) Analytical Biochemistry 183:231-244, and Lee et al. (1993] Nucleic Acids Research 21:3761-3766. The primary advantage of using FRET in this application is that the technique is potentially sensitive (i.e. capable of detecting one or a few "target" DNA sequences), and can be done in a homogenous format. The same technique described by Lee et al. is now a commercially available product from Applied Biosystems known as "Taq-Man". In this application, a DNA probe complementary to the target DNA sequence is made with donor and acceptor attached. When the probe is intact and single-stranded, the donor is highly quenched because the acceptor is in close proximity. When the probe hybridizes to the target DNA, the probe is degraded by a specific endo or exonuclease. The donor is then free to diffuse away from the acceptor molecule, and donor fluorescence increases. If there is no target DNA, no specific degradation occurs and no specific increase in donor fluorescence occurs.
This system can also exploit amplification: there are many probe DNA
molecules and each 6me one binds, the probe in the double stranded product is hydrolyzed by the nuclease, and fluorescence increases. As soon as one probe molecule is degraded, another probe molecule can bind and the enzyme repeats the process. Hence, for only one target, the fluorescence from many probe molecules can be generated. A variety of exonucleases and endonucleases are compatible ZS with amplification; for example, Applied Biosystems utilizes Taq-palymerase, which has a 5' exonuclease activity. If the probe comprises RNA, RNAaseH may be used to exploit amplification.
In any of these FRET-based systems for DNA detection, replacing the organic dye donor with a lanthanide chelate improves the assay. The extent of donor quenching in the intact single-stranded probe is considerably greater because of the lanthanide's long-lifetime and efficient energy transfer. Any residual donor luminescence can he discriminated against with time-gating. The result is WO48/00401 ~ ~ t" '~ ~ ~ ~ PCTIUS451083t9 significantly decreased background (exactly analogous to the protease experiment outlined above).
Example 6. Lifetime-tailored Dyes As discussed above, the lanthanides can be used as luminescent labels in microscopy and detection in general. 13y using pulsed excitation and time-delayed detection, the lanthanide's long excited-state lifetime (milliseconds) enables signal to be isolated from background fluorescence, which tends to be of nanosecond duration. The long-lifetime, however, has the drawback that the signal intensity per molecule is necessary weak: a molecule with an excited state lifetime of 1 msec can emit at most 1,000 photonslsec. This is particularly significant at high illumination intensities, where the slow-emitting molecule may saturate. At low illumination intensity, the long lifetime is not deleterious because any one lanthanide is being excited at a rate less than the inverse of the lifetime.
Ideally, one would have a luminescent label in which the lifetime can be tailored to the optimal time-scale - long enough that background can be discriminated against, short enough that signal intensity is not significantly compromised. Since the background tends to have nanosecond lifetime, a probe with a microsecond lifetime, for example, would still have a thousand-times longer lifetime, enabling time-discrimination of the signal, but would potentially be able to emit 1,000 times more photonslsec than the millisecond lanthanide. Such lifetime-tailored dyes can be made by utilizing luminescence energy transfer between a Imthanide chelate (as donor) and a fluorescent acceptor. The signal will be the emission of the acceptor due to energy transfer. The lifetime of this emission (r) will equal the lifetime of the quenched donor and will be:
r = ra (1- E} (1) where ra is the lifetime of the lanthanide chelate in the absence of acceptor and E
is the fraction of energy transferred (also called the efficiency of energy transferred). The distance between the donor and acceptor (R) to achieve a given r can easily be calculated using the standard formula for FRET, Cantor et a1.
(19$0) Biophysical Chemistry, WH Freeman and Co, SF, a formula which has been shown to be applicable to LRET (Selvin et a1. (1994) PNAS USA 91:10024-10028;

wo ~sroosot ~ ~ ~ 3 5 ~ ~ rcr~tls~s~oa3is Selvin et al. J. Amer. Chem. Soc. 116:6029-6030; 5elvin et al. (1994) Methods in Enzymology, K Sauer, ed., Academic Press, Orlando):
E = 1I[1+(RIR~a] (2) where Ro can be calculated from the spectral properties of the donor and acceptor.
Combining equations 1 and 2 yields the lifetime as a function of distance between donor and acceptor:
r = ro I[I+(Ra/R)d] (3) if ro is 1.5 cosec, then with 909b energy transfer, the sensitized emission will decay with a lifetime of I~0 usec. With 99% energy transfer, the lifetime is 1S
uses. If a luminescent label with a lifetime of IS usec is desired, then the donor and acceptor should be placed such that 99~a energy transfer occurs. This corresponds to a distance of 0.465 x Ro. For Tb-chelate as donor, and tetramethylrhodamine as acceptor (Selvin, et al. 1995, supra), where Ra = 60A, this corresponds to 2$A.
A probe with a 1.5 uses lifetime can be achieved by placing donor and acceptor 0.316 Ra apart for 99.9°k energy transfer, or 19A for Tb-chelate and tetramethylrhodamine.
Note that lifetime-tailored dyes can be made to emit at many different colors. Any acceptor which can take energy from the luminescent lanthanide chelate are possible. The acceptor absorption need not overlap with the main emission line of the lanthanide; overlap with less intense emission lines can still yield very efficient energy transfer so long as the acceptor is placed sufficiently close. A donor/acceptor pair with an Ro of only 30A will still give 99.9 energy transfer at a distance of 9.SA. Further note that efficient energy transfer can arise even if the donor lanthanide has a relatively poor quantum yield for emission.
While Tb and Eu quantum yields tend to be fairly high in the appropriate chelate, other lanthanides and transition elements with significantly lower quantum yields, such as Pr, Nd, Sm, Dy, Ho, Er, Tm and Ru, Os, and Sm become useful donors as well. Finally, note that because the efficiency of energy transfer will in general be high (>90%) almost every photon which would have been emitted from the lanthanide, now gets emitted by the acceptor, but in a shorter period of time.
The only significant loss in photons arises from the non-unity quantum yield of the acceptor. This can be minimized by choosing acceptors with high quantum yields.

A wide variety of different linker molecules may be used to create thtse lifetime-tailored dyes. Generally, the subject linkers provide separation distances from about 4 to 60, preferably from about 9 to about 30A. The composition of the linker is selected based on the needs of the application, e.g. hydrophobic polymeric 5 linkers may be used to provide membrane permeable dyes. Peptides are readily synthesized to useful lengths, and their N- and C-termini can be used to attach the donor and acceptor. By introducing an internal aminophenylalanine (or a lysine), a reactive isothiocyanate is generated for attachment of the complex to a biological (or other) macromolecule. Peptides also have the advantage that the properties of 10 the peptide can be optimized for a particular application; for example, polyproline is very rigid and hydrophobic; polylysine is hydrophilic and highly positively charged; while polyglutamate or polyaspartate are hydrophilic and negatively charged. Other linkers include polymers such as polysaccharides, which have excellent solubility and reactivity, polyimides, and nucleic acids. The polymers 15 may be derivitized to provide improved attachment sites, e.g. a primary amine can be inserted into a nucleic acid strand and converted to an isothiocyanate group for attachment to macromolecules.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

Claims (21)

WHAT IS CLAIMED IS:

1. A lanthanide chelate comprising a lanthanide chelator covalently joined to a sensitizer, wherein said chelate is capable of binding a lanthanide with an equilibrium constant of at least 10 6 M-1, a complex of said chelate and said lanthanide is capable of enhanced lanthanide luminescence, and said sensitizer comprises a polynuclear heterocyclic aromatic compound of the general formula:
wherein X comprises an atom from periodic group 5 or 6, wherein a single position 2-8 carbon atom of said sensitizer is substituted with a linking group through which said sensitizer is covalently joined to said chelator.

2. A chelate according to claim 1, wherein a first position 2-8 carbon atom of said sensitizer is substituted with an oxygen atom through a double covalent bond, and a second position 2-8 carbon atom of said sensitizer, different than said first position 2-8 carbon atom, is substituted with a linking group through which said sensitizer is covalently joined to said chelator.

3. A chelate according to claim 2, wherein said linking group consists essentially of an amine or carboxyl group.

4. A chelate according to claim 2, wherein said first position 2-8 carbon atom is the position 2 or 4 carbon atom and said second carbon atom is the position 7 carbon atom.

5. A chelate according to claim 2, wherein a third position 2-8 carbon atom of said sensitizer, different from said first and second position 2-8 carbon atoms, is substituted.

6. A chelate according to claim 5, wherein said third position 2-8 carbon atom is the position 4 carbon and is substituted with a hydrocarbon or halogen substituted hydrocarbon.

7. A chelate according to claim 1, wherein said sensitizer comprises a 2- or 4-quinolone or a 2- or 4- coumarin.

8. A chelate according to claim 1, wherein said sensitizer comprises carbostyril 124 (7-amino-4-methyl-2-quinolone), coumarin 120 (7-amino-4-methyl-2-coumarin), coumarin 124 (7-amino-4-(trifluoromethyl)-2- coumarin), aminomethyltrimethylpsoralen.

9. A chelate according to claim 1, wherein a complex of said chelate and a lanthanide capable of binding said chelate with an equilibrium constant of at least 109 M-1 is capable of at least ten fold greater luminescence probability than is said lanthanide.

10. A chelate according to claim 1, wherein a first solution comprising complexes of said chelate and a lanthanide capable of binding said chelate with an equilibrium constant of at least 10 9 M-1 is capable of at least ten fold greater luminescence than is a second solution comprising said lanthanide, wherein said first and second solutions are identical except for the presence of said chelate in said first solution and absence of said chelate in said second solution.

11. A chelate according to claim 1, wherein said lanthanide is terbium or europium.

12. A chelate according to claim 1, wherein said chelator is capable of binding said lanthanide with an equilibrium constant of at least 10 10 M-1.

13. A chelate according to claim 1, wherein said chelator comprises a plurality of carboxylate or phosphonate groups.

14. A chelate according to claim 1, wherein said chelator comprises DTPA.

15. A chelate according to claim 1, wherein said chelate is covalently joined to a macromolecule.

16. A molecular label comprising a chelate according to claim 1 covalently joined to a analyte-selective reagent.

17. A method of enhancing the luminescence of a lanthanide, said method comprising: forming a mixture of a lanthanide chelate according to claim 1 and a lanthanide capable of binding said chelate with an equilibrium constant of at least 10 9 M-1, whereby a luminescent lanthanide chelate-lanthanide complex is formed.

18. A chelate according to claim 1, wherein said enhanced lanthanide luminescence is at least 50,000% greater intensity.

19. A method of detecting an analyte which may be present in a portion of a sample by luminescence, said method comprising the steps of:
contacting a sample portion with a luminescent complex of a lanthanide chelate according to claim 1 and a lanthanide capable of binding said chelate with an equilibrium constant of at least 10 9 M-1, wherein said chelate is covalently joined to a reagent capable of selectively binding said analyte;
incubating said sample portion under conditions wherein said reagent is capable of selectively binding said analyte;
exposing said sample portion to light at a first wavelength capable of inducing a first electronic transition in said chelate;
detecting an emission of light from said sample portion at a second wavelength, wherein said second wavelength is longer than said first wavelength and results from a second electronic transition in said chelate;
wherein the detection of said emission of light correlates with the presence of said analyte sample portion.

20. A method of detecting the distance between a first position and a second position in a portion of a sample by resonance energy transfer using a luminescent lanthanide chelate donor and an organic resonance energy acceptor, said method comprising the steps of:
exposing a sample portion comprising said donor located at said first position and said acceptor located at said second position to light at a first wavelength capable of inducing a first electronic transition in said donor, wherein said donor comprises a complex of a lanthanide chelate according to claim 1 and a lanthanide capable of binding said chelate with an equilibrium constant of at least 10 9 M-1, and wherein the spectral overlap of the donor emission and acceptor absorption is sufficient to enable energy transfer from said donor to said acceptor as measured by detectable quenching of donor luminescence intensity or lifetime or detectable increase in acceptor luminescence intensity or lifetime;
detecting at least one of:
the intensity of a first emission of light from said sample portion at a second wavelength, wherein said second wavelength is longer than said first wavelength and results from a second electronic transition in said donor, wherein the intensity of said first emission of light inversely correlates with the distance between said first and second positions of said sample portion; and the intensity of a second emission of light from said sample portion at a third wavelength, wherein said third wavelength is longer than said first wavelength and results from an electronic transition in said acceptor, wherein the intensity of said second emission of light correlates with the distance between said first and second postions of said sample portion.

21. A method according to claim 20 used to monitor the status of a polymerase chain reaction, wherein, said sample portion comprises a target nucleic acid strand comprising a first strand portion and a diagnostic nucleic acid strand comprising a first atom covalently joined to said donor and a second atom covalently joined to said acceptor, said first and second atoms being separated by a second strand portion, wherein said first and second strand portions are sufficiently complementary to hybridize under annealing conditions; said second strand portion is of sufficient length to provide a detectable difference in the aggregate energy transfer from said donor to said acceptor when said first and second strand portions are hybridized as compared with the aggregate energy transfer from said donor to said acceptor when said first and second strand portions are not hybridized, wherein said detectable difference is measured as at least one of a detectable quenching of donor luminescence or detectable increase in acceptor luminescence, and said distance between said first and second atoms indicates whether said nucleic acid strands have hybridized.