CA2116239C - Gene probe biosensor method - Google Patents
Gene probe biosensor method Download PDFInfo
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- CA2116239C CA2116239C CA002116239A CA2116239A CA2116239C CA 2116239 C CA2116239 C CA 2116239C CA 002116239 A CA002116239 A CA 002116239A CA 2116239 A CA2116239 A CA 2116239A CA 2116239 C CA2116239 C CA 2116239C
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
- G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
- G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
- G01N21/64—Fluorescence; Phosphorescence
- G01N21/645—Specially adapted constructive features of fluorimeters
- G01N21/648—Specially adapted constructive features of fluorimeters using evanescent coupling or surface plasmon coupling for the excitation of fluorescence
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6816—Hybridisation assays characterised by the detection means
- C12Q1/6825—Nucleic acid detection involving sensors
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
- G01N21/75—Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated
- G01N21/77—Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator
- G01N21/7703—Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated by observing the effect on a chemical indicator using reagent-clad optical fibres or optical waveguides
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10S435/00—Chemistry: molecular biology and microbiology
- Y10S435/81—Packaged device or kit
Abstract
The present invention relates to a method for the detection, identification and/or quantification of plant or animal tissues, microorganisms or cell free RNA or DNA and to detector apparatus adapted for performing said method. The method particularly uses Total Internal Reflection Fluorescence (TIRF) to measure hybridization of analyte RNA or DNA with RNA or DNA
that is associated with an evanescent wave detector waveguide.
that is associated with an evanescent wave detector waveguide.
Description
GENE PROBE BIOSENSOR METHOD_ The present invention relates a method for the detection, identification and/or quantification of plant or animal tissues, microorganisms or cell free RNA or DNA and to reagents and detector apparatus adapted for performing said method. The method particularly uses Total Internal Reflection Fluoresence (TIRF) to measure hybridization of analyte RNA or DNA with RNA or DNA that is associated with an evanescent wave detector waveguide.
Gene probe assays. using nucleic acid hybridization, are an alternative to immunoassays in the detection and identification of biological materials. The specificity of gene probes for their targets can be controlled much more.easily than is possible using protein-based binding phenomena and, when coupled with the polymerase chain reaction to pre-amplify the target material, extreme sensitivity can be obtained. Current techniques using gene probes are slow, taking from hours to days to produce a result. Biosensors offer an alternative route to fast gene probe assays, but the only reports so far on gene probe biosensor assays are those using surface plasmon resonance (Evans & Charles (1990); Abstracts of 1st World Congress on DNA probes and immunoassay; Pollard-Knight et al (1990) Ann. Biol.
Clin, 4$ 642-646).
Evanescent wave biosensors, which use the phenomenon of TIRF for detection (Sutherland & Dahne, (1987) J. Immunol.Meth., 7A, 253-265), have previously been used with proteins as,the biological recognition element. Antibodies have been used to detect the binding of fluorescent-labelled antigen (Eldefrawi et al (1991) Biosensors &
Bioelectronics, fa, 507-516) using acetyicholine receptors to study the binding of acetylcholine and cholinesterase inhibitors. Other groups (Poglitsch & Thompson (1990) Biochemistry, 2.q. 248-254) have measured the binding of antibody to Fc epitopes.
The present invention provides a method for carrying out gene probe assays with an evanescent wave biosensor and provides a TIRF waveguide which is adapted for carrying out said method when incorporated within an evanescent wave biosensor device.
Gene probe assays. using nucleic acid hybridization, are an alternative to immunoassays in the detection and identification of biological materials. The specificity of gene probes for their targets can be controlled much more.easily than is possible using protein-based binding phenomena and, when coupled with the polymerase chain reaction to pre-amplify the target material, extreme sensitivity can be obtained. Current techniques using gene probes are slow, taking from hours to days to produce a result. Biosensors offer an alternative route to fast gene probe assays, but the only reports so far on gene probe biosensor assays are those using surface plasmon resonance (Evans & Charles (1990); Abstracts of 1st World Congress on DNA probes and immunoassay; Pollard-Knight et al (1990) Ann. Biol.
Clin, 4$ 642-646).
Evanescent wave biosensors, which use the phenomenon of TIRF for detection (Sutherland & Dahne, (1987) J. Immunol.Meth., 7A, 253-265), have previously been used with proteins as,the biological recognition element. Antibodies have been used to detect the binding of fluorescent-labelled antigen (Eldefrawi et al (1991) Biosensors &
Bioelectronics, fa, 507-516) using acetyicholine receptors to study the binding of acetylcholine and cholinesterase inhibitors. Other groups (Poglitsch & Thompson (1990) Biochemistry, 2.q. 248-254) have measured the binding of antibody to Fc epitopes.
The present invention provides a method for carrying out gene probe assays with an evanescent wave biosensor and provides a TIRF waveguide which is adapted for carrying out said method when incorporated within an evanescent wave biosensor device.
Evanescent wave detectors exploit the TIRF phenomenon to provide a sensitive method for detecting reactions at the surface of waveguides.
The waveguide may take various forms but typically will be a prism, slab or fibre. The reaction to be used to measure the target molecule may be monitored, for example, through measuring the fluorescence changes on binding or desorption of fluorescent species or by the generation of fluorescent species by enzymic or chemical means.
Several patents have been published that cover the use of evanescent wave detectors with immunoa.ssay systems as the biological sensing element (eg. US 4582809) but the inherent limitations in the immuno-reagents have not allowed the full capabilities of the sensor to be exploited.
The present invention provides a method for the detection, identification and/or quantification of a material selected from plant or animal tissue, microorganisms and cell free RNA or DNA comprising:
(i) providing an oligonucleotide, complementarv to all or part of a.r:
cligonucleotide seauence characteristic of the RNA or DNA of the material, immobilised on the surface of an evanescent wave detector apparatus waveguide;
(ii) exposing the immobi lised cligonucleotide of step (i) to the sample, or DNA or RNA material derived therefrom, under conditions whereby DNA or RNA having the characteristic oligonucleotide sequence will hybridize with it;
(iii) associating the immobilised oligonucleotide of step (i) or the nucleic acid material derived from the sample with a fluorescently detectable agent, before, during or on completion of any hybridization with DNA or RNA as provided in step (ii), such that the fluorescently detectable agent becomes bound to the hybridized product but not to unhybridized immobilized oligonucleotide; and (iv) measuring the fluorescently detectable agent bound by step (iii) using the evanescent wave detector apparatus and relating the amount of that to the presence, identity and/or amount of the material, 2a characterised in that the characteristic sequence content is enriched by specific sequence amplification, the specific sequence ampli.fication being effected in solution, in contact with the evanescent wave detector apparatus waveguide.
The waveguide may take various forms but typically will be a prism, slab or fibre. The reaction to be used to measure the target molecule may be monitored, for example, through measuring the fluorescence changes on binding or desorption of fluorescent species or by the generation of fluorescent species by enzymic or chemical means.
Several patents have been published that cover the use of evanescent wave detectors with immunoa.ssay systems as the biological sensing element (eg. US 4582809) but the inherent limitations in the immuno-reagents have not allowed the full capabilities of the sensor to be exploited.
The present invention provides a method for the detection, identification and/or quantification of a material selected from plant or animal tissue, microorganisms and cell free RNA or DNA comprising:
(i) providing an oligonucleotide, complementarv to all or part of a.r:
cligonucleotide seauence characteristic of the RNA or DNA of the material, immobilised on the surface of an evanescent wave detector apparatus waveguide;
(ii) exposing the immobi lised cligonucleotide of step (i) to the sample, or DNA or RNA material derived therefrom, under conditions whereby DNA or RNA having the characteristic oligonucleotide sequence will hybridize with it;
(iii) associating the immobilised oligonucleotide of step (i) or the nucleic acid material derived from the sample with a fluorescently detectable agent, before, during or on completion of any hybridization with DNA or RNA as provided in step (ii), such that the fluorescently detectable agent becomes bound to the hybridized product but not to unhybridized immobilized oligonucleotide; and (iv) measuring the fluorescently detectable agent bound by step (iii) using the evanescent wave detector apparatus and relating the amount of that to the presence, identity and/or amount of the material, 2a characterised in that the characteristic sequence content is enriched by specific sequence amplification, the specific sequence ampli.fication being effected in solution, in contact with the evanescent wave detector apparatus waveguide.
3' In one preferred form of the present invention the fluorescently detectable agent is a fluorescently detectable intercalating dye capable of being incorporated into the duplex of the hybridization product. In this form of the method the dye is one that does not bind to the unhybridized immobilised oligonucleotides. Such method of determining the'presence of hybridization product is ideally used with immobilised sequences of sufficient length in themselves to provide specific hybridization under the hybridization conditions used. The sample so analysed may be unaltered in DNA/RNA content, or may have had this enriched by specific sequence amplification, eg. polymerase chain reaction amplification (PCR) or ligase chain reaction (LCR).
In a second preferred form the fluorescently detectable agent is a fluorescently detectable oligonucleotide whiph is capable of -.~ hybridizing with the hybridized characteristic sequence or which is capable of acting as a specific sequence amplification primer, eg.
such as a polymerase chain reaction primer, to yield fluorescently detectable amplification product, which is detectable using evanescence when hybridized to the waveguide immobilised oligonucleotide.
In a preferred embodiment of the second form, using detectable oligonucleotide. the present invention provides a method for the detection, identification and/or quantification of a material selected from plant or animal tissue. microorganisms or cell free RNA or DNA comprising:
(i) providing an oligonucleotide, complementary to part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected, immobilised on the surface of an evanescent detector apparatus waveguide;
(ii) providing a fluorescently detectable oligonucleotide complementary to all or part of the remainder of the characteristic sequence;
(iii) exposing the immobilised oligonucleotide from (i) to a solution comprising material to be investigated, or DNA or RNA material derived therefrom, under conditions whereby characteristic oligonucleotide sequence will hybridize with it;
(iv) replacing the solution of material from (iii) with a solution comprising the fluorescently detectable complementary oligonucleotide from (ii) and (v) measuring the amount of bound fluorescently detectable oligonucleotide using the evanescent wave detector apparatus and relating that to the presence, identity and/or amount of target material in the sample.
In a further preferred embodiment the present-invention provides a method for the detection, identification and/or quantification of, plant or animal tissues, microorganisms or cell free RNA and DNA
comprising:
(i) providing an oligonucleotide, complementary to part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected, immobilised on the surface of an evanescent wave detector apparatus waveguide;
(ii) providing a fluorescently detectable oligonucleotide identical to all or part of the remainder of the characteristic sequence;
(iii) performing a specific sequence amplification reaction on a sample of the material under investigation using the fluorescently detectable oligonucleotide of step (ii) as-one of the primers, to thereby amplify any of the characteristic sequence present while incorporating fluorescently detectable-agent therein;
(iv) exposing the waveguide immobilised complementary oligonucleotide of step (i) to the reaction mixture from step (iii) under conditions whereby hybridization of the amplification product with said immobilised oligonucleotide will occur;
(v) measuring any fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide using the evanescent wave.detector and relating that to the amount of amplified material initially present in the sample.
Preferably and conveniently the specific amplification reaction of step (iii) is a polymerase chain reaction, but other such reactions such as the ligase chain reaction may usefully be employed, as will be clear to those skilled in the art.
In all of the embodiments of the invention the waveguide is preferably situated within a temperature controllable environment, eg. within a temperature regulated chamber, such that the stringency of the hybridization of the complementary sequences to the target RNA or DNA
may be controlled, or such that the polymerase chain,reaction denaturation, hybridization and extension temperature cycles might be carried out.
-:' _ The fluorescently detectable complementary oligonucleotides may be provided in a number of forms, eg. as an oligonucleotide tagged either with a fluorescent label, with a moiety to which a fluorescent species can be bound or with an enzyme or catalyst capable of generating fluorescent species. Thus step measuring steps may require additional steps prior to the basic fluoresence detection step, eg:
exposure of the moiety to which a fluorescent species may be bound to such species or by exposure to substrate for the enzymp or catalyst reaction.
The complemetary sequence of step (i) may be of sufficient length to specifically bind the target RNA or DNA whilst leaving enough unbound target RNA or DNA sequence to bind the detectable oligonucleotide of step (iii). Typically the immobilised sequence will comprise about half of the length of the target sequence, but increasing the length of target sequence will allow lesser proportions to be used.
In a preferred embodiment employing the detectable oligonucleotide, the detectable sequence of will be complementary to all or almost all of the remainder of the target sequence but this may similarly be a reduced portion as target characteristic sequence length increases.
Advantageously the immobilised oligonucleotide is complementary to a sequence toward or at one end of the target sequence while the WO 93/06241 PCI'/6B92/01698 6 I i3 fluorescently detectable sequence is complementary to a sequence toward of at the other end. Thus restriction endonucleases may be conveniently employed prior to the hybridization for the purpose of cleaving the RNA or DNA of the sample material in order to allow easier access to these ends of the characteristic target sequence.
Similarly in the second preferred embodiment the detectable sequence need only be long enough to be useful as a PCR primer of the necessary specificity but may be longer. It will be appreciated that both PCR
primers may be fluorescently detectable thus increasing the potential fluorescence provided at the waveguide surface and thus the efficacy corresponding evanescent effect. In all cases preferred reagent baselengths are 5-30, more preferably 10-25, eg. 15-20 bases.
It will be realised by the man skilled in the art that. the complementary sequences need not be complemetary at every base-pair where they hybridize. Thus a man skilled in the art will readily determine the stringency requirements for statistically acceptable use of mismatched oligomers eg. 90% complementary sequences and will be able to obtain usable results by adjusting the hybridization temperature accordingly where such mismatched sequences are used.
The requirements for precise complementary sequence usage will vary with the uniqueness of the sequence for which the user is assaying.
Thus a sequence that shares a high percentage of bases with other potentially present sequences will require use of a more completely complementary sequence than a sequence that is relatively distinct.
Thus where the sequence being assayed for is not fully elucidated or is variable, the skilled man may be able to determine statistically acceptable oligomers for steps (i) and (iii).
A second aspect of the present invention provides an assay kit for use in the method of the invention comprising:
(1) an oligonucleotide complementary to all or part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected and (2) a fluorescently detectable oligonucleotide complementary or identical to part or all of the remainder of the characteristic sequence.
The options for the components (1) and (2) are those which are set out above, these components being optionally supplemented in the kit by those reagents necessary for immobilisation of the oligomer (1) on the waveguide; examples of suitable reagents being those referred to in the discussion of methods below.
A third aspect of the invention provides a waveguide suitable for use in an evanescent wave biosensor characterised in that it comprises, immobilised upon its surface, an oligonucleotide which is complementary to all or part of an oligonucleotide sequence which is characteristic of the RNA or DNA sequence of the material which is to be detected. Furthermore kits comprising such waveguides are provided for use in the method of the invention.
In a fourth aspect of the present invention is provided an evanescent wave detector biosensor characterised in that it comprises a waveguide which has, immobilised upon its surface, an oligonucleotide which is complementary to all or part of an oligonucleotide sequence which is characteristic of the RNA or DNA sequence of the material which is to be detected. Such waveguide may eg. be a prism, slab or fibre.
In all of the aspects of the invention, it will be realised that more than one characteristic sequence may be targeted simultaneously by employing more than one type of immobilised oligonucleotide and associated fluorescently detectable binding agent in the method and apparatus used to carry it out.
Advantages of the present method over analogous immunoassay systems include:
(a) denser packing of the immobilised component on the waveguide surface allowing greater sensitivity and dynamic range and making the construction of multispecificity surfaces easier;
(b) the binding between the analyte and the immobilised and derivatised oligonucleotides can be regulated by adjusting the hybridization conditions and the lengths of the oligonucleotides, thus permitting the specificity and sensitivity of a given test to be finely adjusted to suit requirements;
WO 93/06241 PCI'/GB92/01698 (c) immunoassays are limited by availability of reagents, stability of reagents, antigenic variability; masking of antigenic sites, and the dissociation constants of the antibody/antigen complexes. Gene probe assays are pontentially superior in all these respects;
(d) fluorescent'immunoassays suffer from interference from environmental contaminants and non-specific binding while the higher temperatures required for gene probe assays (ie. above 60 C rather than 37 C) will reduce unwanted adsorption of contaminants on the detector surface;
(e) as a result of the lower dissociation constants obtainable with nucleic acid complexes compared with immune complexes the full sensitivity of evanescent wave detector technology can be realised.
The samples to be investigated may be as found in the environment (eg.
for free RNA or DNA oligonucleotides) or may be pretreated such as by cell lysis techniques, DNA/RNA concentration or amplification (eg. as by polymerase chain reaction using Taq polymerase) or by restriction enzyme mediated degredation (eg. to provide more manageable sized oligonucleotides).
The potential of the method. kits and apparatus of the present invention will now be illustrated by way of example only with reference to the following Figures and Experiments; further embodiments will occur to the skilled man in the light of these.
Figures Figure 1: shows the principal elements of the evanescent wave detector used in the Examples.
Figure 2: shows the voltage/time relationship obtained on hybridization of a fluorescein-labelled 20-mer with a complementary sequence covalently coupled to an optic fibre waveguide.
Figure 3: shows concentration/response curves showing specific hybridization of complementary and control oligonucleotides;
WO 93i06241 PG'I/GB92/01698 signal(mV/min) plotted against nM concentration oligomer.
Figure 4: shows the effect of flow rate of sample solution throught the temperature controlled chamber containing the waveguide on the hybridization signal; signal (mV/min) is plotted against flow rate (mi/min).
Figure 5: shows the influence of temperature on the rate of hybridization; signal (mV/min) is plotted against temperature C for a 50ng/mi sample of a fluorescein labelled 20-mer.
Figure 6: shows a pH profile of oligonucleotide hybridization on the optic fibre waveguide; signal (mV/min) plotted against pH.
0.~O Figure 7: shows binding from 8nM solutions of oligomers complementary to the proximal or distal ends of a covalently coupled 204 base oligonucleotide.
Figure 8: shows a diagrammatic scheme of the molecular basis of the two of the embodiments of the method of the present invention.
dEMODS, Since oligonucleotides are long-chain molecules with lengths that can be comparable to the depth of the evanescent zone, studies were carried out which hybridized short, fluorescein-labelled oligonucleotides to either end of a 204-base oligomer, a fragment amplified from protective antigen gene of Bacillus anthracis, tethered at one end to the waveguide surface to examine the influence of probe length on detection.
Materials:
Glutaraldehyde, 3-aminopropyl triethoxysilane (APTS). Tween 20, Ficoll, formamide, polyvinyl pyrrolidone. bovine serum albumin fraction V(BSA), horse radish peroxidase labelled streptavidin (HRP-SA), 2,2.-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) ~rati.~.. ,.,.tiK.:... ,.., ..,,,,.. .. . :,._.:...< >,...,. , ......., .......y , . ...,,._..,. ... _. ... ... .. _ _._.. _ 2~16 2 (ABTS), sodium chloride and trisodium citrate were obtained from the Sigma Chemical Company, Poole. UK. Sodium dihydrogen orthophosphate, disodium hydrogen orthophosphate, sodium dodecyl sulphonate (SDS), hydrogen peroxide, hydrochloric acid, and acetone were AR grade from BDH. Poole, UK. Ammonium hydroxide was obtained from Aldrich, Gillingham. Dorset, UK and ethanol from Hayman Ltd.. Witham, Essex, UK. Streptavidin immobilised on agarose beads was obtained from Pierce and Warriner. Chester, UK. Synthetic DNA oligonucleotides with C6-linked fluorescein-, amino- or biotin-modified ends were purchased from British Bio-Technology Ltd, Abingdon, UK are listed in Table 1.
Table 1 Oligonucleotides Used.( 5' to 3') -:' .
ID No. Sequence 4946 CACC'1TGTGGACTGI'ITGGA-amino 4947 TCCAAACAGTCCACAACGTG-fluorescein 4949 CAACACACCTTAACAC-amino 4950 GTGTTAAGGTGTGTTG-fluorescein 5453 Amino-CTTTAATTGTCGCGAGTGTT
5805 Fluorescein-AACACTCGCGACAATTAAAG
6097 Biotin-AATTCAAGTACGGTCGCAAT
5452 Fluorescein-AAZTCAAGTACGGTCGCAAT
The fibre optic evanescent wave device, (prototype No.19), and 1mm x 65mm quartz optic fibres were purchased from ORD, North Salem. New Hampshire, USA. See Figure 1. A six watt tungsten filament source (1) provides light which is passed through three collimating lenses (2) interspaced by a 485mm blue filter (3) and a 0.8mm pinhole mask (4) to impinge upon a 50:50 beam splitting device (5) which intermittently directs light through a focussing lens (6) and into the oligonucleotide bearing waveguide (7). Fluorecsent light derived from any bound, eg. hybridized or intercalated, fluorescent materiai responding to the incoming light is redirected out of the waveguide (7) via the lens (6) and is allowed to pass through the beam splitting device toward a 530 nm green filter (8). From here light passes through a shutter assembly (9) and a focussing lens (10) whereafter it impinges upon a detector device (11) connected to a measuring device such as a voltmeter (not shown).
The output voltage from the voltmeter is conveniently connected to a Pharmacia model 482 chart recorder. Optic fibres were held in a jacketed flow cell constructed from glass capillary tubing with stainless steel end caps and silicone gaskets. Temperature was controlled by circulating water from a water bath through the glass jacket. The temperature was monitored using a thermocouple. Optic fibres were cleaned and then covalent coupling with glutaraldehyde was carried out using a method based on that described by Tijssen,(1985), Practice and theory of enzyme immunoassays: page 322 to 323 of Vol 15 of Laboratory Techniques in Biochemistry and Molecular Biology. Ed:
Burdon and van Knippenburg: Pub. Elsevier.
Fibres were silanised in a 2% solution of APTS in acetone for 24 hrs at room temperature, washed with acetone, dried at 50 C, immersed in 1% glutaraldehyde in water for 1 hour, washed in PBS and finally left overnight at 4 C in a l0ug/mi solution of oligonucleotide with an aminoterminal. To perform an assay an optic fibre with immobilised oligonucleotide was rinsed in deionised water, blotted dry and inserted into the flow cell. When optimised, the following conditions, adapted from Anderson & Young,(1985) Nucleic acid hybridization - a practical approach Ed. Hames and Higgins; IRL
Press, Oxford, pp 73-111, were used. The temperature of the water jacket was adjusted to 65 C.
Prehybridisation solution, (250m1 20xSSC, plus 50m1 100x Denhardt's solution, 50m1 O.1M phosphate buffer and lml Tween*20 added to 600m1 sterile deionised water, final pH 6.8) was pumped using a peristaltic pump over the fibre in the 25u1 flow cell at 0.5ml/min until a steady baseline was obtained. The fluorescein end-labelled target oligonucleotide, in prehybridization solution, was then introduced at the same flow rate and hybridization was followed as the increase in output on thc chart recorder. After a few minutes prehybridization solution was switched back into the flow cell and the temperature raised to 80 C. After 10 to 15 minutes all the bound oligonucleotide *Trade-mark had desorbed and the temperature was lowered to 65 C ready for another run.
Initially only short (16- to 20-mer) oligonucleotides were attached to the fibres. To investigate the use of longer probes an amino-ended 204-mer was synthesised using PCR on the target sequence with one primer, a 20-mer, end-labelled with an amino-group - oligo.5453 - and the other primer. also a 20-mer, end-labelled with biotin oligo.1222.
Unincorporated amino-labelled primer was removed using streptavidin immobilised on agarose beads to pull out double-stranded PCR product from unincorporated amino-ended primer. The amino-labelled 204-base strand was released from the complementary strand and the beads by heating at 95 C for 10 minutes followed by quick chilling in a water/ice mixture and then removing the beads by centrifugation. The amount of the 204-mer produced was sufficient for a 0.85pg/mi solution to be used for coupling to fibres.
Assay of oligomers:
In initial 20-mer experiments high levels of target and control oligonucleotides were used. A 200nM (lpg/ml) solution of fluorescein -labelled oligonucleotide control (oligo.4950) was introduced at lml/min and 60 C into the flow cell containing a fibre with .oligo.4946 immobilised. There was an immediate shift in baseline of 80mV whereafter the output remained constant until prehybridisation solution was reintroduced when the output returned to its'previous level. In contrast, when oligo.4947 which was complementary to oligo .4946 on the fibre was introduced at 16onM, (also 1pg/ml), a continuously rising signal was obtained with an initial slope of about 350mV/min. A plateau was reached after 14 minutes at an output 1,140mV above the baseline level. The output fell again when prehybridization solution at 90 C was passed through the flow cell.
To confirm that binding was specific, the control oligo.4950 was shown to bind to an optic fibre with its complement, oligo.4949, covalently coupled to the surface.
The time course of hybridization of 8nM fluorescein-labelled oligo.4947 to immobilised oligo.4946 is shown in Figure 2 and a concentration/response curve for fluorescein-labelled oligo.4950 hybridizing to immobilised oligo.4949 with oligo.4947 as a control is given in Figure 3. The slopes of the curves were measured 1 minute after sample entered the flow cell.
Results from the optimisation of conditions are shown in Fiqures 4-6.
The effect of flow rate was evaluated witn 50ng/mi solutions of oligo.4947. The results are shown in Figure 4. The dependence of the rate of hybridization on temperature and pH were evaluated and the results are shown in Figures 5 & 6.respectively. Maximum rates of binding were observed at 65 C and pH6.8.
The binding curves of 50nM solutions of fluorescein-labelled oligonucleotides complementary to either the proximal or distal ends of a 204-base oligonucleotide covalently coupled at one end to the -' waveguide surface are shown in Figure 7. There was little difference between responses with both showing a rapid rise to a plateau level of 48mV (proximal) or 56mV (distal) after about three minutes followed by a slight fall in output when prehybridisation solution was reintroduced into the flow cell. Concentration/response curves using initial slopes for hybridization of the two oligonucleotides showed little difference between them. (results not shown). Oligo.4947 at 500nM as a control did not bind to the 204-mer.
Detection was in the nanomolar range with a linear relationship between the slope of the response and concentration : similar to results obtained using immunoassays with this biosensor.
For assays that require high sensitivity, the following equipment improvements and enhancement techniques are conveniently made:
Labelled oligomers are made using oligonucleotides labelled with multiple fluorophores or fluorescent beads. or fluorescent intercalating dyes are used to detect hybridization;
The biosensor assay may is combined with a DNA amplification technique such as PCR which could be performed on the sample, prior to,the hybridization on the waveguide, preferably using fluorophore-labelled primers (as in one of the preferred embodiments of the method of this invention above) to improve detection of product. It would also be ~~= 1 ~~~~(~
aJ 14 possible directly to monitor PCR reactions using the biosensor. The 60 seconds or so taken for the biosensor assays is orders of magnitude faster than conventional gene probe assays and still much faster than.
rapid, tests that take about 1 hour to perform. (Engleberg,(1991) ASM
News 57_ (4) 183-186).
The easy recycling of the detector surface through removal of bound nucleic acids by heating obviates one of the problems encountered with immunoassays on this system and renders it, with the 60 second response period, useful in military or other critically hazardous environments requiring rapid identification. Several optic fibres were found to be usable over periods of several days with no loss in response.
- r Both 5' and 3' B.-labelled oligonucleotides were used with this factor had no apparent effect on the results. Oligonucleotides were also bound to the proximal and distal ends of a 204-base oligonucleotide.
The length of this could have been from 7Onm, (using the value of 3.4nm for the pitch of double-stranded DNA which has 10 bases per helical), to 200nm. (using the inter-bond distances of the -0-P-0-C-C-C- repeats along the backbone of the molecule). The depth of the evanescent zone defined as the distance taken for the light intensity to fall to 1/e of its initial value would have been around 100nm. comparable to the length of the 204-mer. Since similar signals were obtained for the hybridisation of distal and proximal fluorescein-labelled oligonucleotides, (slightly higher signals were obtained for the di8L8l oligonucleotide), the orientation of the long oligonucleotide strands was presumably not,perpendicular to the wave guide surface.
Only a limited amount of the 204-mer, which was generated by PCR from a larger target sequence, was available for coupling to the optic fibres and this presumably led to the concentration on the waveguide surface beingrelativelylow. This would explain the rapid plateauing of the responses seen in Figure 7 compared to the continuing rise in signal over an equivalent timescale seen in Figure 2. (where the immobilised gene probe was at a higher concentration, being covalently coupled from a solution >100x more concentrated. If plateau height rather than rate of change of output were to be chosen as the measure 21.1~2 t'3 of binding then limiting the amount of immobilised probe would allow saturation to be more rapidly achieved.
The molecular basis of the invention is provided in Figure 8 wherein 8a-c and 8d-f refer to the first and second preferred embodiments of the method of the invention respectively. In 8a an oligonucleotide sequence (A) complementary to part of an oligonucleotide sequence characteristic of a target DNA sequence (B) has been immobilised upon an evanescent wave detector waveguide by the method described above.
In 8b the immobilised oligonucleotide is exposed under hybridization conditions to a solution of sample under investigtion and target DNA
sequence (B) therein hybridizes to sequence (A). In 8c the sample solution is replaced with a solution comprising a fluorescein labelled oligonucleotide (C) which is complementary to the unhybridized +-' remainder of the target oligonucleotide, also under hybridizing conditions, and this is similarly hybridized. On hybridization the fluorescein is caused to fluoresce by the light in the evanescent zone of the waveguide.
In 8d the complementary sequence (A) is immobilised upon an evanescent wave detector waveguide as before; in 8e a sample solution is treated under PCR conditions with two primers (D) and (E), each corresponding to a characteristic sequence at one of the two ends of the target characteristic sequence (B). The primer for the end of the sequence which is opposite to the end which hybridizes to the immobilized oligonucleotide (A) is labelled with fluorescein and thus a product of the reaction is fluorescein labelled target sequence (F). In 8f immobilised sequence (A) is exposed to the.sample solution under hybridization conditions wherein fluorescein labelled target sequence (F) is hybridized to the sequence (A) may be detected by the evanescent wave detector induced fluorescence.
In a preferred form of the method of Figures 8. particular to use with PCR or other specific amplification technique incorporating method, the immobilised oligonucleotide (A) is selected such that it is not capable of binding to the primers (D) and (E), thus excess of these will not result in a blocking of the immobilised site. Thus in this form olignucleotide (A') hybridizes to a portion of (F) more central in sequence (B) than primer (D) with the result that the non-fluorophor bearing end of (F) is as shown in Figure 8g.
The intercalating dye utilising embodiments of the method of the invention whilst not specifically exemplified herein, are carried out as illustrated best by Figures 8a and 8b wherein these steps are carried out in'the presence or with later addition of the dye.
Suitable dyes and conditions for their interaction are disclosed in the prior art, eg. Latt and Wohlleb; Chromosoma (Berl.) 52. 297-316 (1975), Jorgenson et al, Chrmosoma (Berl.) 68, 287-302 (1978) and Jennings and Ridler; Biophysics of Structure and Mechanism. 10, 71-79. (1983).
.:- _
In a second preferred form the fluorescently detectable agent is a fluorescently detectable oligonucleotide whiph is capable of -.~ hybridizing with the hybridized characteristic sequence or which is capable of acting as a specific sequence amplification primer, eg.
such as a polymerase chain reaction primer, to yield fluorescently detectable amplification product, which is detectable using evanescence when hybridized to the waveguide immobilised oligonucleotide.
In a preferred embodiment of the second form, using detectable oligonucleotide. the present invention provides a method for the detection, identification and/or quantification of a material selected from plant or animal tissue. microorganisms or cell free RNA or DNA comprising:
(i) providing an oligonucleotide, complementary to part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected, immobilised on the surface of an evanescent detector apparatus waveguide;
(ii) providing a fluorescently detectable oligonucleotide complementary to all or part of the remainder of the characteristic sequence;
(iii) exposing the immobilised oligonucleotide from (i) to a solution comprising material to be investigated, or DNA or RNA material derived therefrom, under conditions whereby characteristic oligonucleotide sequence will hybridize with it;
(iv) replacing the solution of material from (iii) with a solution comprising the fluorescently detectable complementary oligonucleotide from (ii) and (v) measuring the amount of bound fluorescently detectable oligonucleotide using the evanescent wave detector apparatus and relating that to the presence, identity and/or amount of target material in the sample.
In a further preferred embodiment the present-invention provides a method for the detection, identification and/or quantification of, plant or animal tissues, microorganisms or cell free RNA and DNA
comprising:
(i) providing an oligonucleotide, complementary to part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected, immobilised on the surface of an evanescent wave detector apparatus waveguide;
(ii) providing a fluorescently detectable oligonucleotide identical to all or part of the remainder of the characteristic sequence;
(iii) performing a specific sequence amplification reaction on a sample of the material under investigation using the fluorescently detectable oligonucleotide of step (ii) as-one of the primers, to thereby amplify any of the characteristic sequence present while incorporating fluorescently detectable-agent therein;
(iv) exposing the waveguide immobilised complementary oligonucleotide of step (i) to the reaction mixture from step (iii) under conditions whereby hybridization of the amplification product with said immobilised oligonucleotide will occur;
(v) measuring any fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide using the evanescent wave.detector and relating that to the amount of amplified material initially present in the sample.
Preferably and conveniently the specific amplification reaction of step (iii) is a polymerase chain reaction, but other such reactions such as the ligase chain reaction may usefully be employed, as will be clear to those skilled in the art.
In all of the embodiments of the invention the waveguide is preferably situated within a temperature controllable environment, eg. within a temperature regulated chamber, such that the stringency of the hybridization of the complementary sequences to the target RNA or DNA
may be controlled, or such that the polymerase chain,reaction denaturation, hybridization and extension temperature cycles might be carried out.
-:' _ The fluorescently detectable complementary oligonucleotides may be provided in a number of forms, eg. as an oligonucleotide tagged either with a fluorescent label, with a moiety to which a fluorescent species can be bound or with an enzyme or catalyst capable of generating fluorescent species. Thus step measuring steps may require additional steps prior to the basic fluoresence detection step, eg:
exposure of the moiety to which a fluorescent species may be bound to such species or by exposure to substrate for the enzymp or catalyst reaction.
The complemetary sequence of step (i) may be of sufficient length to specifically bind the target RNA or DNA whilst leaving enough unbound target RNA or DNA sequence to bind the detectable oligonucleotide of step (iii). Typically the immobilised sequence will comprise about half of the length of the target sequence, but increasing the length of target sequence will allow lesser proportions to be used.
In a preferred embodiment employing the detectable oligonucleotide, the detectable sequence of will be complementary to all or almost all of the remainder of the target sequence but this may similarly be a reduced portion as target characteristic sequence length increases.
Advantageously the immobilised oligonucleotide is complementary to a sequence toward or at one end of the target sequence while the WO 93/06241 PCI'/6B92/01698 6 I i3 fluorescently detectable sequence is complementary to a sequence toward of at the other end. Thus restriction endonucleases may be conveniently employed prior to the hybridization for the purpose of cleaving the RNA or DNA of the sample material in order to allow easier access to these ends of the characteristic target sequence.
Similarly in the second preferred embodiment the detectable sequence need only be long enough to be useful as a PCR primer of the necessary specificity but may be longer. It will be appreciated that both PCR
primers may be fluorescently detectable thus increasing the potential fluorescence provided at the waveguide surface and thus the efficacy corresponding evanescent effect. In all cases preferred reagent baselengths are 5-30, more preferably 10-25, eg. 15-20 bases.
It will be realised by the man skilled in the art that. the complementary sequences need not be complemetary at every base-pair where they hybridize. Thus a man skilled in the art will readily determine the stringency requirements for statistically acceptable use of mismatched oligomers eg. 90% complementary sequences and will be able to obtain usable results by adjusting the hybridization temperature accordingly where such mismatched sequences are used.
The requirements for precise complementary sequence usage will vary with the uniqueness of the sequence for which the user is assaying.
Thus a sequence that shares a high percentage of bases with other potentially present sequences will require use of a more completely complementary sequence than a sequence that is relatively distinct.
Thus where the sequence being assayed for is not fully elucidated or is variable, the skilled man may be able to determine statistically acceptable oligomers for steps (i) and (iii).
A second aspect of the present invention provides an assay kit for use in the method of the invention comprising:
(1) an oligonucleotide complementary to all or part of an oligonucleotide sequence characteristic of the RNA or DNA of the material to be detected and (2) a fluorescently detectable oligonucleotide complementary or identical to part or all of the remainder of the characteristic sequence.
The options for the components (1) and (2) are those which are set out above, these components being optionally supplemented in the kit by those reagents necessary for immobilisation of the oligomer (1) on the waveguide; examples of suitable reagents being those referred to in the discussion of methods below.
A third aspect of the invention provides a waveguide suitable for use in an evanescent wave biosensor characterised in that it comprises, immobilised upon its surface, an oligonucleotide which is complementary to all or part of an oligonucleotide sequence which is characteristic of the RNA or DNA sequence of the material which is to be detected. Furthermore kits comprising such waveguides are provided for use in the method of the invention.
In a fourth aspect of the present invention is provided an evanescent wave detector biosensor characterised in that it comprises a waveguide which has, immobilised upon its surface, an oligonucleotide which is complementary to all or part of an oligonucleotide sequence which is characteristic of the RNA or DNA sequence of the material which is to be detected. Such waveguide may eg. be a prism, slab or fibre.
In all of the aspects of the invention, it will be realised that more than one characteristic sequence may be targeted simultaneously by employing more than one type of immobilised oligonucleotide and associated fluorescently detectable binding agent in the method and apparatus used to carry it out.
Advantages of the present method over analogous immunoassay systems include:
(a) denser packing of the immobilised component on the waveguide surface allowing greater sensitivity and dynamic range and making the construction of multispecificity surfaces easier;
(b) the binding between the analyte and the immobilised and derivatised oligonucleotides can be regulated by adjusting the hybridization conditions and the lengths of the oligonucleotides, thus permitting the specificity and sensitivity of a given test to be finely adjusted to suit requirements;
WO 93/06241 PCI'/GB92/01698 (c) immunoassays are limited by availability of reagents, stability of reagents, antigenic variability; masking of antigenic sites, and the dissociation constants of the antibody/antigen complexes. Gene probe assays are pontentially superior in all these respects;
(d) fluorescent'immunoassays suffer from interference from environmental contaminants and non-specific binding while the higher temperatures required for gene probe assays (ie. above 60 C rather than 37 C) will reduce unwanted adsorption of contaminants on the detector surface;
(e) as a result of the lower dissociation constants obtainable with nucleic acid complexes compared with immune complexes the full sensitivity of evanescent wave detector technology can be realised.
The samples to be investigated may be as found in the environment (eg.
for free RNA or DNA oligonucleotides) or may be pretreated such as by cell lysis techniques, DNA/RNA concentration or amplification (eg. as by polymerase chain reaction using Taq polymerase) or by restriction enzyme mediated degredation (eg. to provide more manageable sized oligonucleotides).
The potential of the method. kits and apparatus of the present invention will now be illustrated by way of example only with reference to the following Figures and Experiments; further embodiments will occur to the skilled man in the light of these.
Figures Figure 1: shows the principal elements of the evanescent wave detector used in the Examples.
Figure 2: shows the voltage/time relationship obtained on hybridization of a fluorescein-labelled 20-mer with a complementary sequence covalently coupled to an optic fibre waveguide.
Figure 3: shows concentration/response curves showing specific hybridization of complementary and control oligonucleotides;
WO 93i06241 PG'I/GB92/01698 signal(mV/min) plotted against nM concentration oligomer.
Figure 4: shows the effect of flow rate of sample solution throught the temperature controlled chamber containing the waveguide on the hybridization signal; signal (mV/min) is plotted against flow rate (mi/min).
Figure 5: shows the influence of temperature on the rate of hybridization; signal (mV/min) is plotted against temperature C for a 50ng/mi sample of a fluorescein labelled 20-mer.
Figure 6: shows a pH profile of oligonucleotide hybridization on the optic fibre waveguide; signal (mV/min) plotted against pH.
0.~O Figure 7: shows binding from 8nM solutions of oligomers complementary to the proximal or distal ends of a covalently coupled 204 base oligonucleotide.
Figure 8: shows a diagrammatic scheme of the molecular basis of the two of the embodiments of the method of the present invention.
dEMODS, Since oligonucleotides are long-chain molecules with lengths that can be comparable to the depth of the evanescent zone, studies were carried out which hybridized short, fluorescein-labelled oligonucleotides to either end of a 204-base oligomer, a fragment amplified from protective antigen gene of Bacillus anthracis, tethered at one end to the waveguide surface to examine the influence of probe length on detection.
Materials:
Glutaraldehyde, 3-aminopropyl triethoxysilane (APTS). Tween 20, Ficoll, formamide, polyvinyl pyrrolidone. bovine serum albumin fraction V(BSA), horse radish peroxidase labelled streptavidin (HRP-SA), 2,2.-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) ~rati.~.. ,.,.tiK.:... ,.., ..,,,,.. .. . :,._.:...< >,...,. , ......., .......y , . ...,,._..,. ... _. ... ... .. _ _._.. _ 2~16 2 (ABTS), sodium chloride and trisodium citrate were obtained from the Sigma Chemical Company, Poole. UK. Sodium dihydrogen orthophosphate, disodium hydrogen orthophosphate, sodium dodecyl sulphonate (SDS), hydrogen peroxide, hydrochloric acid, and acetone were AR grade from BDH. Poole, UK. Ammonium hydroxide was obtained from Aldrich, Gillingham. Dorset, UK and ethanol from Hayman Ltd.. Witham, Essex, UK. Streptavidin immobilised on agarose beads was obtained from Pierce and Warriner. Chester, UK. Synthetic DNA oligonucleotides with C6-linked fluorescein-, amino- or biotin-modified ends were purchased from British Bio-Technology Ltd, Abingdon, UK are listed in Table 1.
Table 1 Oligonucleotides Used.( 5' to 3') -:' .
ID No. Sequence 4946 CACC'1TGTGGACTGI'ITGGA-amino 4947 TCCAAACAGTCCACAACGTG-fluorescein 4949 CAACACACCTTAACAC-amino 4950 GTGTTAAGGTGTGTTG-fluorescein 5453 Amino-CTTTAATTGTCGCGAGTGTT
5805 Fluorescein-AACACTCGCGACAATTAAAG
6097 Biotin-AATTCAAGTACGGTCGCAAT
5452 Fluorescein-AAZTCAAGTACGGTCGCAAT
The fibre optic evanescent wave device, (prototype No.19), and 1mm x 65mm quartz optic fibres were purchased from ORD, North Salem. New Hampshire, USA. See Figure 1. A six watt tungsten filament source (1) provides light which is passed through three collimating lenses (2) interspaced by a 485mm blue filter (3) and a 0.8mm pinhole mask (4) to impinge upon a 50:50 beam splitting device (5) which intermittently directs light through a focussing lens (6) and into the oligonucleotide bearing waveguide (7). Fluorecsent light derived from any bound, eg. hybridized or intercalated, fluorescent materiai responding to the incoming light is redirected out of the waveguide (7) via the lens (6) and is allowed to pass through the beam splitting device toward a 530 nm green filter (8). From here light passes through a shutter assembly (9) and a focussing lens (10) whereafter it impinges upon a detector device (11) connected to a measuring device such as a voltmeter (not shown).
The output voltage from the voltmeter is conveniently connected to a Pharmacia model 482 chart recorder. Optic fibres were held in a jacketed flow cell constructed from glass capillary tubing with stainless steel end caps and silicone gaskets. Temperature was controlled by circulating water from a water bath through the glass jacket. The temperature was monitored using a thermocouple. Optic fibres were cleaned and then covalent coupling with glutaraldehyde was carried out using a method based on that described by Tijssen,(1985), Practice and theory of enzyme immunoassays: page 322 to 323 of Vol 15 of Laboratory Techniques in Biochemistry and Molecular Biology. Ed:
Burdon and van Knippenburg: Pub. Elsevier.
Fibres were silanised in a 2% solution of APTS in acetone for 24 hrs at room temperature, washed with acetone, dried at 50 C, immersed in 1% glutaraldehyde in water for 1 hour, washed in PBS and finally left overnight at 4 C in a l0ug/mi solution of oligonucleotide with an aminoterminal. To perform an assay an optic fibre with immobilised oligonucleotide was rinsed in deionised water, blotted dry and inserted into the flow cell. When optimised, the following conditions, adapted from Anderson & Young,(1985) Nucleic acid hybridization - a practical approach Ed. Hames and Higgins; IRL
Press, Oxford, pp 73-111, were used. The temperature of the water jacket was adjusted to 65 C.
Prehybridisation solution, (250m1 20xSSC, plus 50m1 100x Denhardt's solution, 50m1 O.1M phosphate buffer and lml Tween*20 added to 600m1 sterile deionised water, final pH 6.8) was pumped using a peristaltic pump over the fibre in the 25u1 flow cell at 0.5ml/min until a steady baseline was obtained. The fluorescein end-labelled target oligonucleotide, in prehybridization solution, was then introduced at the same flow rate and hybridization was followed as the increase in output on thc chart recorder. After a few minutes prehybridization solution was switched back into the flow cell and the temperature raised to 80 C. After 10 to 15 minutes all the bound oligonucleotide *Trade-mark had desorbed and the temperature was lowered to 65 C ready for another run.
Initially only short (16- to 20-mer) oligonucleotides were attached to the fibres. To investigate the use of longer probes an amino-ended 204-mer was synthesised using PCR on the target sequence with one primer, a 20-mer, end-labelled with an amino-group - oligo.5453 - and the other primer. also a 20-mer, end-labelled with biotin oligo.1222.
Unincorporated amino-labelled primer was removed using streptavidin immobilised on agarose beads to pull out double-stranded PCR product from unincorporated amino-ended primer. The amino-labelled 204-base strand was released from the complementary strand and the beads by heating at 95 C for 10 minutes followed by quick chilling in a water/ice mixture and then removing the beads by centrifugation. The amount of the 204-mer produced was sufficient for a 0.85pg/mi solution to be used for coupling to fibres.
Assay of oligomers:
In initial 20-mer experiments high levels of target and control oligonucleotides were used. A 200nM (lpg/ml) solution of fluorescein -labelled oligonucleotide control (oligo.4950) was introduced at lml/min and 60 C into the flow cell containing a fibre with .oligo.4946 immobilised. There was an immediate shift in baseline of 80mV whereafter the output remained constant until prehybridisation solution was reintroduced when the output returned to its'previous level. In contrast, when oligo.4947 which was complementary to oligo .4946 on the fibre was introduced at 16onM, (also 1pg/ml), a continuously rising signal was obtained with an initial slope of about 350mV/min. A plateau was reached after 14 minutes at an output 1,140mV above the baseline level. The output fell again when prehybridization solution at 90 C was passed through the flow cell.
To confirm that binding was specific, the control oligo.4950 was shown to bind to an optic fibre with its complement, oligo.4949, covalently coupled to the surface.
The time course of hybridization of 8nM fluorescein-labelled oligo.4947 to immobilised oligo.4946 is shown in Figure 2 and a concentration/response curve for fluorescein-labelled oligo.4950 hybridizing to immobilised oligo.4949 with oligo.4947 as a control is given in Figure 3. The slopes of the curves were measured 1 minute after sample entered the flow cell.
Results from the optimisation of conditions are shown in Fiqures 4-6.
The effect of flow rate was evaluated witn 50ng/mi solutions of oligo.4947. The results are shown in Figure 4. The dependence of the rate of hybridization on temperature and pH were evaluated and the results are shown in Figures 5 & 6.respectively. Maximum rates of binding were observed at 65 C and pH6.8.
The binding curves of 50nM solutions of fluorescein-labelled oligonucleotides complementary to either the proximal or distal ends of a 204-base oligonucleotide covalently coupled at one end to the -' waveguide surface are shown in Figure 7. There was little difference between responses with both showing a rapid rise to a plateau level of 48mV (proximal) or 56mV (distal) after about three minutes followed by a slight fall in output when prehybridisation solution was reintroduced into the flow cell. Concentration/response curves using initial slopes for hybridization of the two oligonucleotides showed little difference between them. (results not shown). Oligo.4947 at 500nM as a control did not bind to the 204-mer.
Detection was in the nanomolar range with a linear relationship between the slope of the response and concentration : similar to results obtained using immunoassays with this biosensor.
For assays that require high sensitivity, the following equipment improvements and enhancement techniques are conveniently made:
Labelled oligomers are made using oligonucleotides labelled with multiple fluorophores or fluorescent beads. or fluorescent intercalating dyes are used to detect hybridization;
The biosensor assay may is combined with a DNA amplification technique such as PCR which could be performed on the sample, prior to,the hybridization on the waveguide, preferably using fluorophore-labelled primers (as in one of the preferred embodiments of the method of this invention above) to improve detection of product. It would also be ~~= 1 ~~~~(~
aJ 14 possible directly to monitor PCR reactions using the biosensor. The 60 seconds or so taken for the biosensor assays is orders of magnitude faster than conventional gene probe assays and still much faster than.
rapid, tests that take about 1 hour to perform. (Engleberg,(1991) ASM
News 57_ (4) 183-186).
The easy recycling of the detector surface through removal of bound nucleic acids by heating obviates one of the problems encountered with immunoassays on this system and renders it, with the 60 second response period, useful in military or other critically hazardous environments requiring rapid identification. Several optic fibres were found to be usable over periods of several days with no loss in response.
- r Both 5' and 3' B.-labelled oligonucleotides were used with this factor had no apparent effect on the results. Oligonucleotides were also bound to the proximal and distal ends of a 204-base oligonucleotide.
The length of this could have been from 7Onm, (using the value of 3.4nm for the pitch of double-stranded DNA which has 10 bases per helical), to 200nm. (using the inter-bond distances of the -0-P-0-C-C-C- repeats along the backbone of the molecule). The depth of the evanescent zone defined as the distance taken for the light intensity to fall to 1/e of its initial value would have been around 100nm. comparable to the length of the 204-mer. Since similar signals were obtained for the hybridisation of distal and proximal fluorescein-labelled oligonucleotides, (slightly higher signals were obtained for the di8L8l oligonucleotide), the orientation of the long oligonucleotide strands was presumably not,perpendicular to the wave guide surface.
Only a limited amount of the 204-mer, which was generated by PCR from a larger target sequence, was available for coupling to the optic fibres and this presumably led to the concentration on the waveguide surface beingrelativelylow. This would explain the rapid plateauing of the responses seen in Figure 7 compared to the continuing rise in signal over an equivalent timescale seen in Figure 2. (where the immobilised gene probe was at a higher concentration, being covalently coupled from a solution >100x more concentrated. If plateau height rather than rate of change of output were to be chosen as the measure 21.1~2 t'3 of binding then limiting the amount of immobilised probe would allow saturation to be more rapidly achieved.
The molecular basis of the invention is provided in Figure 8 wherein 8a-c and 8d-f refer to the first and second preferred embodiments of the method of the invention respectively. In 8a an oligonucleotide sequence (A) complementary to part of an oligonucleotide sequence characteristic of a target DNA sequence (B) has been immobilised upon an evanescent wave detector waveguide by the method described above.
In 8b the immobilised oligonucleotide is exposed under hybridization conditions to a solution of sample under investigtion and target DNA
sequence (B) therein hybridizes to sequence (A). In 8c the sample solution is replaced with a solution comprising a fluorescein labelled oligonucleotide (C) which is complementary to the unhybridized +-' remainder of the target oligonucleotide, also under hybridizing conditions, and this is similarly hybridized. On hybridization the fluorescein is caused to fluoresce by the light in the evanescent zone of the waveguide.
In 8d the complementary sequence (A) is immobilised upon an evanescent wave detector waveguide as before; in 8e a sample solution is treated under PCR conditions with two primers (D) and (E), each corresponding to a characteristic sequence at one of the two ends of the target characteristic sequence (B). The primer for the end of the sequence which is opposite to the end which hybridizes to the immobilized oligonucleotide (A) is labelled with fluorescein and thus a product of the reaction is fluorescein labelled target sequence (F). In 8f immobilised sequence (A) is exposed to the.sample solution under hybridization conditions wherein fluorescein labelled target sequence (F) is hybridized to the sequence (A) may be detected by the evanescent wave detector induced fluorescence.
In a preferred form of the method of Figures 8. particular to use with PCR or other specific amplification technique incorporating method, the immobilised oligonucleotide (A) is selected such that it is not capable of binding to the primers (D) and (E), thus excess of these will not result in a blocking of the immobilised site. Thus in this form olignucleotide (A') hybridizes to a portion of (F) more central in sequence (B) than primer (D) with the result that the non-fluorophor bearing end of (F) is as shown in Figure 8g.
The intercalating dye utilising embodiments of the method of the invention whilst not specifically exemplified herein, are carried out as illustrated best by Figures 8a and 8b wherein these steps are carried out in'the presence or with later addition of the dye.
Suitable dyes and conditions for their interaction are disclosed in the prior art, eg. Latt and Wohlleb; Chromosoma (Berl.) 52. 297-316 (1975), Jorgenson et al, Chrmosoma (Berl.) 68, 287-302 (1978) and Jennings and Ridler; Biophysics of Structure and Mechanism. 10, 71-79. (1983).
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Claims (19)
1. A method for the detection, identification and/or quantification of a material selected from the group consisting of a plant or animal tissue, a microorganism and cell free RNA or DNA, comprising:
(i) providing an oligonucleotide, complementary to all or part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent wave detector apparatus;
(ii) exposing the immobilised oligonucleotide of step (i) to a solution of a sample of the material, or DNA
or RNA material derived therefrom, under conditions whereby the target RNA or DNA having the characteristic oligonucleotide sequence will hybridize with the immobilised oligonucleotide and form a hybridized product;
(iii) associating the immobilised oligonucleotide of step (i) or the DNA or RNA material derived from the sample, with a fluorescently detectable agent, before, during or on completion of any hybridization with the target RNA or DNA as provided in step (ii), such that the fluorescently detectable agent becomes bound to the hybridized product but not to the immobilised oligonucleotide with the target RNA or DNA; and (iv) measuring an amount of the fluorescently detectable agent bound by step (iii) using the evanescent wave detector apparatus and relating the amount to the presence, identity and/or amount of the material, wherein a content of the characteristic oligonucleotide sequence is enriched by a specific sequence amplification effected in a solution in contact with the evanescent wave detector apparatus waveguide.
(i) providing an oligonucleotide, complementary to all or part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent wave detector apparatus;
(ii) exposing the immobilised oligonucleotide of step (i) to a solution of a sample of the material, or DNA
or RNA material derived therefrom, under conditions whereby the target RNA or DNA having the characteristic oligonucleotide sequence will hybridize with the immobilised oligonucleotide and form a hybridized product;
(iii) associating the immobilised oligonucleotide of step (i) or the DNA or RNA material derived from the sample, with a fluorescently detectable agent, before, during or on completion of any hybridization with the target RNA or DNA as provided in step (ii), such that the fluorescently detectable agent becomes bound to the hybridized product but not to the immobilised oligonucleotide with the target RNA or DNA; and (iv) measuring an amount of the fluorescently detectable agent bound by step (iii) using the evanescent wave detector apparatus and relating the amount to the presence, identity and/or amount of the material, wherein a content of the characteristic oligonucleotide sequence is enriched by a specific sequence amplification effected in a solution in contact with the evanescent wave detector apparatus waveguide.
2. The method as claimed in claim 1, wherein the specific sequence amplification is conducted by polymerase chain reaction amplification (PCR) or ligase chain reaction (LCR).
3. The method as claimed in claim 1 or 2, wherein the fluorescently detectable agent is a fluorescently detectable oligonucleotide which is capable of hybridizing with the characteristic oligonucleotide sequence hybridized in step (ii).
4. The method as claimed in claim 1 or 2, wherein the fluorescently detectable agent is capable of acting as a primer of the specific sequence amplification, to yield a fluorescently detectable amplification product which is detectable by evanescence when hybridized to the oligonucleotide immobilised on the waveguide surface.
5. The method as claimed in claim 4, wherein the specific sequence amplification primer is a polymerase chain reaction primer.
6. The method as claimed in claim 1 or 2, wherein the fluorescently detectable agent is a fluorescently detectable intercalating dye which is capable of being incorporated into a duplex of the hybridization product and which does not bind to the unhybridized immobilised oligonucleotide.
7. A method for the detection, identification and/or quantification of a material selected from the group consisting of a plant or animal tissue, a microorganism and cell free RNA or DNA, comprising:
(i) providing an oligonucleotide, complementary to only a part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent detector apparatus;
(ii) providing a fluorescently detectable oligonucleotide complementary to all or part of the remainder of the oligonucleotide sequence characteristic of the target RNA or DNA;
(iii) exposing the immobilised oligonucleotide from step (i) to a solution of a sample of the material or DNA or RNA material derived therefrom, under conditions whereby the target DNA or RNA having the characteristic oligonucleotide sequence will hybridize with the immobilised oligonucleotide;
(iv) replacing the solution of the sample used in step (iii) with a solution comprising the fluorescently detectable complementary oligonucleotide from step (ii); and (v) measuring an amount of the fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide, by using the evanescent wave detector apparatus and relating the amount to the presence, identity and/or amount of the material in the sample, wherein a content of the characteristic oligonucleotide sequence is enriched by a specific sequence amplification effected in a solution in contact with the evanescent wave detector apparatus waveguide.
(i) providing an oligonucleotide, complementary to only a part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent detector apparatus;
(ii) providing a fluorescently detectable oligonucleotide complementary to all or part of the remainder of the oligonucleotide sequence characteristic of the target RNA or DNA;
(iii) exposing the immobilised oligonucleotide from step (i) to a solution of a sample of the material or DNA or RNA material derived therefrom, under conditions whereby the target DNA or RNA having the characteristic oligonucleotide sequence will hybridize with the immobilised oligonucleotide;
(iv) replacing the solution of the sample used in step (iii) with a solution comprising the fluorescently detectable complementary oligonucleotide from step (ii); and (v) measuring an amount of the fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide, by using the evanescent wave detector apparatus and relating the amount to the presence, identity and/or amount of the material in the sample, wherein a content of the characteristic oligonucleotide sequence is enriched by a specific sequence amplification effected in a solution in contact with the evanescent wave detector apparatus waveguide.
8. A method for the detection, identification and/or quantification of a material selected from the group consisting of a plant or animal tissue, a microorganism and cell free RNA or DNA, comprising:
(i) providing an oligonucleotide, complementary to only a part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent wave detector apparatus;
(ii) providing a fluorescently detectable oligonucleotide identical to all or part of the remainder of the oligonucleotide sequence characteristic of the target RNA or DNA;
(iii) performing a specific sequence amplification reaction on a sample of the material using the fluorescently detectable oligonucleotide of step (ii) as one of primers, to amplify the characteristic sequence present, thereby obtaining an amplification product which contains the fluorescently detectable oligonucleotide incorporated therein;
(iv) exposing the immobilised oligonucleotide of step (i) to a reaction mixture from step (iii) under conditions whereby hybridization of the amplification product with the immobilised oligonucleotide will occur; and (v) measuring an amount of the fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide, by using the evanescent wave detector and relating the amount to that of the material amplified initially present in the sample.
(i) providing an oligonucleotide, complementary to only a part of an oligonucleotide sequence characteristic of target RNA or DNA of the material, immobilised on a surface of a waveguide of an evanescent wave detector apparatus;
(ii) providing a fluorescently detectable oligonucleotide identical to all or part of the remainder of the oligonucleotide sequence characteristic of the target RNA or DNA;
(iii) performing a specific sequence amplification reaction on a sample of the material using the fluorescently detectable oligonucleotide of step (ii) as one of primers, to amplify the characteristic sequence present, thereby obtaining an amplification product which contains the fluorescently detectable oligonucleotide incorporated therein;
(iv) exposing the immobilised oligonucleotide of step (i) to a reaction mixture from step (iii) under conditions whereby hybridization of the amplification product with the immobilised oligonucleotide will occur; and (v) measuring an amount of the fluorescently detectable oligonucleotide hybridized with the immobilised oligonucleotide, by using the evanescent wave detector and relating the amount to that of the material amplified initially present in the sample.
9. The method as claimed in any one of claims 1 to 7, wherein the waveguide comprises a prism, slab or fibre.
10. The method as claimed in any one of claims 1 to 7, wherein the waveguide is situated within a temperature controllable environment.
11. The method as claimed in claim 10, wherein the temperature controllable environment is a temperature regulated chamber.
12. The method as claimed in claim 11, wherein the temperature is controllable such that stringency of the hybridization of the complementary sequences to the target RNA or DNA may be controlled, or such that denaturation, hybridization and extension temperature cycles of the polymerase chain reaction may be carried out.
13. The method as claimed in claim 3, wherein the fluorescently detectable oligonucleotide is tagged with a fluorescent label, with a moiety to which a fluorescent species can be bound or with an enzyme or catalyst capable of generating a fluorescent species.
14. The method as claimed in claim 13, wherein the fluorescent label is fluorescein.
15. The method as claimed in claim 2, wherein the fluorescently detectable oligonucleotide is tagged with an enzyme or catalyst capable of generating a fluorescent species and, prior to reading fluorescence with the evanescent wave detector apparatus waveguide, a substrate for the enzyme or catalyst is added.
16. The method as claimed in any one of claims 1 to 15, wherein the material is pretreated with restriction endonucleases to cleave its RNA or DNA.
17. The method as claimed in any one of claims 1 to 16, wherein the complementary oligonucleotide has a base length of 5 to 30 bases.
18. The method as claimed in claim 17, wherein the base length is from 10 to 25 bases.
19. The method as claimed in claim 17, wherein the base length is 15 to 20 bases.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB9119735.0 | 1991-09-16 | ||
| GB919119735A GB9119735D0 (en) | 1991-09-16 | 1991-09-16 | Gene probe biosensor method |
| PCT/GB1992/001698 WO1993006241A1 (en) | 1991-09-16 | 1992-09-16 | Gene probe biosensor method |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2116239A1 CA2116239A1 (en) | 1993-04-01 |
| CA2116239C true CA2116239C (en) | 2008-11-18 |
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|---|---|---|---|
| CA002116239A Expired - Fee Related CA2116239C (en) | 1991-09-16 | 1992-09-16 | Gene probe biosensor method |
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| US (1) | US5750337A (en) |
| EP (1) | EP0604506B1 (en) |
| JP (1) | JP3324607B2 (en) |
| KR (1) | KR100249288B1 (en) |
| AT (1) | ATE174968T1 (en) |
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| HU (1) | HU218596B (en) |
| NO (1) | NO315380B1 (en) |
| RU (1) | RU2116349C1 (en) |
| SK (1) | SK280713B6 (en) |
| WO (1) | WO1993006241A1 (en) |
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| SE9502608D0 (en) * | 1995-07-14 | 1995-07-14 | Pharmacia Biosensor Ab | Method for nucleic acid sequencing |
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| CN1152140C (en) * | 1997-07-28 | 2004-06-02 | 医疗生物系统有限公司 | Nucleic acid sequence analysis |
| GB2335035B (en) * | 1998-03-03 | 2003-05-28 | Brax Genomics Ltd | Screening for functional antisense agents |
| GB9805935D0 (en) * | 1998-03-19 | 1998-05-13 | Ciba Geigy Ag | Organic compounds |
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| US6429023B1 (en) | 1998-07-20 | 2002-08-06 | Shayda Technologies, Inc. | Biosensors with polymeric optical waveguides |
| CA2304260C (en) * | 1999-04-20 | 2009-03-24 | Japan Bioindustry Association | Method for determining a concentration of target nucleic acid molecules, nucleic acid probes for the method and method for analyzing data obtained by the method |
| AU2002213362A1 (en) * | 2000-10-19 | 2002-04-29 | Trans Photonics, L.L.C. | Novel substituted-polyaryl chromophoric compounds |
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| JP5429962B2 (en) * | 2006-03-16 | 2014-02-26 | 国立大学法人秋田大学 | Nucleic acid detection method and nucleic acid detection kit |
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| EP1935496A1 (en) | 2006-12-22 | 2008-06-25 | Eppendorf Array Technologies SA | Device and/or method for the detection of amplified nucleotides sequences on micro-arrays |
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1991
- 1991-09-16 GB GB919119735A patent/GB9119735D0/en active Pending
-
1992
- 1992-09-16 KR KR1019940700843A patent/KR100249288B1/en not_active IP Right Cessation
- 1992-09-16 HU HU9400770A patent/HU218596B/en not_active IP Right Cessation
- 1992-09-16 AT AT92919549T patent/ATE174968T1/en not_active IP Right Cessation
- 1992-09-16 CZ CZ1994521A patent/CZ286927B6/en not_active IP Right Cessation
- 1992-09-16 DK DK92919549T patent/DK0604506T3/en active
- 1992-09-16 JP JP50589793A patent/JP3324607B2/en not_active Expired - Fee Related
- 1992-09-16 RU RU94019336A patent/RU2116349C1/en not_active IP Right Cessation
- 1992-09-16 GB GB9402823A patent/GB2274710B/en not_active Revoked
- 1992-09-16 ES ES92919549T patent/ES2125272T3/en not_active Expired - Lifetime
- 1992-09-16 EP EP92919549A patent/EP0604506B1/en not_active Expired - Lifetime
- 1992-09-16 SK SK306-94A patent/SK280713B6/en not_active IP Right Cessation
- 1992-09-16 CA CA002116239A patent/CA2116239C/en not_active Expired - Fee Related
- 1992-09-16 DE DE69227997T patent/DE69227997T2/en not_active Expired - Lifetime
- 1992-09-16 WO PCT/GB1992/001698 patent/WO1993006241A1/en active IP Right Grant
- 1992-09-16 AU AU25641/92A patent/AU665369B2/en not_active Ceased
- 1992-09-16 US US08/196,185 patent/US5750337A/en not_active Expired - Lifetime
-
1994
- 1994-03-14 NO NO19940901A patent/NO315380B1/en not_active IP Right Cessation
- 1994-03-15 FI FI941220A patent/FI108463B/en active
- 1994-03-15 BG BG98660A patent/BG62337B1/en unknown
-
1999
- 1999-03-18 GR GR990400807T patent/GR3029722T3/en unknown
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