WO2004063728A1

WO2004063728A1 - Strong-absorber-mediated array ellipsometer

Info

Publication number: WO2004063728A1
Application number: PCT/US2003/041601
Authority: WO
Inventors: William M. D. Rassman; David Ralin
Original assignee: Maven Technologies, Llc
Priority date: 2003-01-08
Filing date: 2003-12-30
Publication date: 2004-07-29
Also published as: AU2003300433A1

Abstract

A substrate bearing an array of probes; target molecules attached to the probes, an optically absorbent molecule being attached to each target, each absorbent molecule being responsive to light of a characteristic wavelength and generating a signal indicative of the presence of a probe-target pair in the array; optics for directing light of said characteristic wavelength at the array; optics and instrument for sensing each generated signal.

Description

PCT INTERNATIONAL APPLICATION FOR PATENT:

STRONG-ABSORBER-MEDIATED ARRAY ELLIPSOMETER

INVENTORS :

WILLIAM RASSMAN, M.D.; DAVID RALIN

SPECIFICATION ( DESCRIPTION )

This application is a continuation-in-part of, and incorporates by reference, the following U.S. Patent Applications:

09/614,503, filed July 11, 2000;

10/046,620, filed November 12, 2001; 10/ 158,995, filed May 31, 2002.

BACKGROUND OF THE INVENTION

Field of the Invention

The present invention relates to biomolecule microarrays, more particularly to making observations of microarrays by way of total internal reflection ellipsometry or ellipsometry, and especially to the use of optically absorbent tags for increasing the signal in an ellipsometric measurement of a microarray. Description of the Related Art

DNA-DNA hybridization interactions can be detected and measured using a microarray (see , Shoemaker Nat Gen 1996 14 450, Cheung Nat Gen 1998 18 155). Other microarray formats utilizing proteins (MacBeath G & Schreiber SL (2000). Printing proteins as microarrays for high throughput function determination. Science 289(5485): 1760- 1763. MacBeath G, Koehler AN, & Schreiber SL (1999). Printing small molecules as microarrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 121: 7967-7968) and carbohydrates (http://genome4.cpmc.columbia.edu/researcher/wang_d.html) are developing.

Though label-free imaging ellipsometry, as in the prior applications, is a useful technique, it would be helpful to provide greater sensitivity, wider dynamic range, and allow parallel testing of multiple sample groups. The absorbtive spectra of the molecules under study, or absorbtive dyes and labels, may be utilized to this end. Realtime monitoring may be used to determine the kinetics of such interactions and to detect "near miss" events that may hold clues to further developments.

SUMMARY OF THE INVENTION

It is an object of the present invention to apply the observation of differential absorbtion and or polarization response of the target materials to the following activities: imaging, parallel biosensing and multi-color label experiments. Total internal reflection (TIR) spectroscopy is a well-established technique for studying the spectral properties of highly absorbing species (refs: Harrick, N.J., "Internal Reflection Spectroscopy," Wiley, NY, 1967. "Internal Reflection Spectroscopy Review and Supplement," Harrick, N.J., Harrick Scientific Corp., Ossining, NY, 1979.) In TIR spectroscopy, a beam traveling in a dense medium encounters a more rarified medium at an angle within the TIR range. The evanescent field associated with TIR penetrates into the more rarefied medium. If the rarefied medium is optically absorbing, then the spectral properties of the TIR light will be different from those of the incident light. The reflection event is no longer total; for this reason, this type of spectroscopy is sometimes called "frustrated" total internal reflection. Typically, TIR spectroscopy data is presented as plots of reflected intensity versus wavelength. It is well known that these plots are polarization-dependent, with the light polarized parallel to the plane of incidence (s-polarized light) being more strongly affected by the presence of the absorbing material than light of perpendicular polarization (p-polarized light). In practical TIR spectroscopy instruments, data is collected at both polarizations, and processed to yield the "native" spectrum of the rarefied medium. At a single wavelength, the presence of a material that absorbs light at that wavelength in the rarefied medium during TIR causes less light of that wavelength to be reflected, with the effect being less pronounced for p- than for s-polarized light. Essentially, this occurs because the p- polarized light has a smaller evanescent-field penetration depth than the s-polarized light, and so encounters more of the absorbing material. The more strongly the material absorbs, the greater the effect. In this way, the presence of an optical absorbing material affects the ratio of s- to p-polarization in TIR-reflected light Another way in which the presence of an absorber affects the s- to p- ratio of TIR reflected light is through "anomalous dispersion" in the refractive index of a material at wavelengths near the absorbance maximum. At wavelengths higher than the absorbance maximum, the evanescent field penetration is greater than it would be in the absence of the absorbing material. In the absence of an absorber, the ratio of s- to p-polarized TIR light intensity can be used to detect refractive index changes associated with changes in surface density of the rarefied medium. The use of this effect to achieve a polarization-based system for imaging changes in the density of biomolecules (or other substances) on the rarefied side of a TIR surface is the subject of one or more of pending patent applications 09/614,503, filed July 11, 2000; 10/046,620, filed November 12, 2001; and 10/ 158,995, filed May 31, 2002. In the current invention, the differential effect of an absorber on p- versus s-polarized TIR reflected light, explained above, is used to greatly enhance the response of polarization-based surface-density imaging systems. For example the surface-binding of target biomolecules tagged with optically absorbing "labels" can induce far greater changes in polarization ratio in a biomolecular nanoarray than the binding of unlabeled, optically clear (non-absorptive) native biomolecules.

In one of its aspects, this invention is based on the principle that certain molecules absorb light at characteristic wavelengths, and this can be used to generate a significant signal indicative of its presence by interrogation by polarized light in an evanescent field at the characteristic wavelength. The unique presence of such a molecule in or attached to a hybridized target in a microarray or nanoarray provides for an easily sensed signal that hybridization has occurred, and that the target is present in the sample. The signal is sensed as a change in light intensity because the tag molecule operates by absorbing, or rotating the plane of polarization, of the "interrogating" polarized light. Sensing of the output can be by an ellipsometer, or an evanescent wave-based device.

The exposure to a nanoarray, at various locations in which different hybridization reactions occur, of a variety of such absorbing molecules can be used to tag different subsets of the array which produce signals at different wavelengths. Thus, large numbers of hybridization subsets of the array can be characterized. If sample materials from different sources carry molecules with different absorbing characteristics, the presence of the different sample materials at each point in the array may be measured and compared by interrogating the array with light at particular wavelengths. Relative abundance of particular target materials in the respective samples may then be determined.

Different classes of absorbent molecules and their wavelengths are listed in sources including certain Alexa Dyes, Cy Dyes and other Fluors; succinimidyl esters, Pharmacia-amersham and Molecular Probes, described in Table 2 appended hereto and referenced in the web page titled: hereto.http:/ /info. med.yale.edu/genetics/ward/tavi/FISHdyes2.html.

In one of its aspects, this invention is based on the recognition that the presence of certain molecules or molecular structures

(markers) in association with or integral to probe/ target/ marker on a

TIR surface, at which interrogating polarized light is directed in a manner to generate an evanescent field encompassing those complexes, is operative to augment the localized rotation of the plane of polarization of the light over what is achieved in the absence of such a marker. The marker typically operates as a light absorber at a characteristic wavelength, but the marker need not be an absorber itself. Instead it may be operative to make the complex absorbing even though none of the constituents of the complex is absorbing in the absence of the other constituents. In some instances the absorber may only become active after washing with an activator.

There are several ways for the "absorber" to attach to form a complex. The absorber may be attached to target molecules prior to hybridization. The absorber may attach to probe/target pairs after hybridization. The absorber may attach to the target after hybridization.

Although the structures introduced to form probe/target/marker complexes are not necessarily absorbers themselves, they do operate to impart an absorption effect to the resulting complexes. Accordingly, they are referred to herein as "absorbers". The absorbers are operative to increase locally the rotation of the plane of polarization of the interrogating light and are responsive to interrogating light at characteristic wavelengths. Thus, different "absorber" molecules attach to form different complex patterns which can be interrogated separately at different wavelengths to produce an image of the different patterns of localized variations as light intensity variations.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

With reference to Fig. 1, a schematic representation of the apparatus (position of the filter is non-critical, so long as it is in the illumination arm), equipment included the following:

Imaging ellipsometer, Beaglehole Instruments, Wellington New Zealand;

High-pixel-count camera; Assembly including a prism or grating that allows interrogating light to reach the array at an angle for achieving TIR with respect to the plane of the array (as described in Imaging Device);

Microarray optically mated to a device for attaining TIR;

For real-time studies, a flow cell is employed to deliver the sample to the array, and successive measurements are taken over the time course of the experiment, before introduction of the sample, during hybridization, and after washing. The ellipsometer uses the phase modulation technique to provide data in terms of two parameters x and y: x = Re(r) x 2 /(l + Re(r)2 + lm^'(r)2 y = lm(r) x 2 / (1 + Re(r)2 + lm(r)2 Simulations using the ellipsometer's multilayer modeling software were used to determine the angle of incidence, corresponding to the reflectivity peak of the model system, which should be near the evanescent wave generation peak as well in both s and p incident polarizations. Simulations were constructed of a four layer system, containing the substrate of BK7 glass, n=1.52, a layer composed of the silane, a C6 spacer and 5nm of dsDNA oligonucleotide (n=1.45), a variable layer of dsDNA with and without CY3, and another 5nm layer of dsDNA. The thickness variation of the CY3-tagged oligonucleotide from zero to one nm is intended to approximate the maximum surface coverage that could be achieved with a fluorescent label with an absorbtion coefficient of 150,000 at 550nm.

Fig. 2 illustrates a simulated Ellipsometry response over a lnm film thickness Change.

Over the film thickness change, a swing of +.08, -0.30 in y is observed, which though complex and non-linear, is inarguably a greater signal change than the dsDNA alone provides, which has a linear slope of .0012/nm. In practice, the half-nm high CY3 molecules would likely never cover more than 25% of the surface, and for the purposes of approximation, a discontinuous layer may be treated as a proportionately thinner layer, . Given the sensitivity of the instrument of .0001 in y, and a useful range of .80 to .44 in y, this provides good theoretical dynamic range of 3000 points within an extraordinarly small thickness change. The ellipsometry response from a typical 70mer probe - 70mer synthetic target system, without labels, is seen in Fig. 3. The change in y is only .025, allowing for 250 points of dynamic range, over a large linear change in thickness.

A test was devised to determine whether the labels truly enhance the TIR ellipsometry response. To obviate the need for chip fabrication, Check-It™ Chips from Telechem International, Sunnyvale, CA, were processed and hybridized according to the manufacturer's instructions, with minor necessary modifications for our application. A Check-It™ Chip is a 25x75mm microarray printed with 70-mer oligonucleotides corresponding to human, mouse, and E. coli gene sequences, in 300 micron diameter spots, on a SuperAmine Microarray Substrate, in two identical subarrays. The probe concentration in the spots varies as well. It is provided with 50 :L of See-It Universal Probe Solution, 50:M concentration and labeled with CY3, a fluorescent dye with an absorbtion peak at 550 nm, which will differentially hybridize to the probe spots on the array.

A QC image of the array from the manufacturer is shown in Fig. 4. This QC image is notable for the lack of consistency between the two "identical" subarrays. The bright green spots are CY3 probe spots with maximal affinity for the target sequences, intended as the "saturating maximum response" for setting up confocal scanning / laser excitation microarray readers. The processing and hybridization was performed as follows.

The procedure included the following steps:

1. Mark the position of the array by scoring the edges of the slides, so as not to interfere with the reading field.

2. Wash for 2 minutes at 25° in 2X SSC + 0.1% SSC.

3. Wash for 2 minutes at 25° in 2X SSC.

4. Treat for 2 minutes in dH₂O at 100°C

5. Cool to room temperature. 6. Fix for 2 minutes in 0° C absolute ethanol

7. Dry by nitrogen stream. At this point, slides were removed to serve as an unhybridized control.

8. Dilute an aliquot of the See-It probe to provide lOuL of lOuM " solution.

9. Place the probe solution on a microscope slide cover slip that has been cleaned with ethanol.

10. Invert the cover slip, and gently lower the droplet onto the microarray slide, taking care to spread the probe solution over the array surface without trapping any bubbles.

11. Incubate the slide in a hybridization chamber for 30 minutes at 25oC, with dH20 in the chamber to prevent dessication.

12. Cool the hybridization chamber to room temperature by immersing in dH2O. 13. Remove the microarray slide from the chamber and drop into 2X SSC + 0.1% sarkosyl, with the cover slip side down so that it drops off without scratching the array. Leave it in this solution 1.5 minutes with moderate agitation.

14. Wash the array with strong agitation for 10 seconds in 0.5X SSC 15. Wash the array in dH20 for 10 seconds with strong agitation

16. Dry by nitrogen stream.

17. Mate the slide to the TIR assembly with immersion oil.

18. Image all slides at the chosen angle of incidence with the imaging ellipsometer, using each of the four filters (lOnm bandpass, 550, 600, 650, and 700 nm, Coherent Inc) using the least-exciting wavelengths first so as not to photobleach the CY3.

Results and Discussion: With reference to Fig. 5 (y image at 51.6 degrees, inverted relative to QC image, at 550nm), Fig. 8 (direct image at 51.6 degrees, 550 nm), and Fig. 9 (unpolarized image at 51.6 degrees, 550nm), images of the x, y, direct polarized, and unpolarized signals were taken.

With reference to Table 1, row 1, column 1 through 10 was analyzed, as was the "Max Spot" at row 10 column 1. Local background level was determined by taking averaged measurements at the four corners of the array and interpolating. Signals within the presumptive spots (a 300 micron diameter circle) were averaged, and the difference between local background and each spot was calculated.

Table 1

The slides are not compared to themselves before hybridizing and after, because the composition of the amine substrate surface changes substantially in response to the hybridization buffer itself, making comparisons difficult. Also, the procedure of un-mounting the array

ID from the TIR elements so that further processing can occur ensures that the array will be contaminated with index matching fluids.

Signal response is clearly stronger at 550nm, before and after hybridization, though not of the magnitude expected from the simulations. The response of the unhybridized slide to both wavelengths, with a wide variation among spots, though they are presumably all nearly the same fraction of a 70mer monolayer, is interesting, and hints that there is a substantial amount of material in the spot besides the probe, which complicates claims of specificity in the label-free measurements. The pre-made array, buffers, and probes were formulated for use with fluorescent emission detectors, and other surface changes, chemical or otherwise, are not relevant in their formulation or intended use. In our measurements, any material left on the surface may be detected. In other model systems, where we have complete knowledge of the components of the substrate, the spotting buffers, and the hybridization buffers, this will not be an issue.

This experiment does not demonstrate simple absorbtion of the penetrating light or the evanescent field, as the direct and unpolarized images above show. Were the labels simply absorbing, the array pattern would be evident in both pictures, and it is clearly not. Polarization changes are occurring, through the mechanisms explained in Chapter 7 of de Fornel, Evanescent Waves, Springer. This experiment was perfomed with a single dye, but it is envisioned that multiple color assays may be performed by coupling each respective sample group with a different dye, modulating the interrogating wavelength, and analyzing the responses accordingly.

Dyes usable in carrying out the present invention include those listed in Table 2 (this table occupies several pages).

Table 2 Alexa Dyes, Cy Dyes and other Fluors: succinimidyl esters (from Pharmacia-Amersham and Molecular Probes)

1Ξ * = Approximate absorption (Abs) and fluorescence emission (Em) maxima for conjugates, in nm.

T[ = Human vision is insensitive to light beyond -650 nm, and therefore it is not possible to view the far- red&endash;fluorescent dyes by looking through the eyepiece of a conventional fluorescence microscope. e = Extinction coefficient at I max in cm -1 M -1 . y = Correction factor for absorbance readings (Abs280) at 280 nm; e.g. Abs280,actual = Abs280,observed - (CF280 •

Absmax).

§ = Correction factor for absorbance readings (Abs260) at 260 nm; e.g. Abs260,actual = Abs260,observed - (CF260 •

Absmax).

AF = Alexa Fluor ND = not determined. NA= not applicable.

Calculations:

DNA

A = e (extinction) * I (path cm) * c (M concentration) {Beer-Lambert law}

A_base = A_260 - (A_dye*CF) base:dye = (A_base*e_dye)/(A_dye*e_base) cone (mg/ml) = [(A_base*MW)/(e_base*path length in cm)]*dil

Proteins

A_protein = A_280 - (A_dye*CF) prot cone (M) = (A_prot*dilution)/(e_280*path cm) mole dye/mole prot = (A_dye*dilution)/(e_280*M prot cone) cone (mg/ml) = [(A_prot*MWprot)/(e_280*path cm)]*dil

Source: http://info.med.yale.edu/genetics/ward/tavi/FISHdyes.html

Note: T e CY dyes and Alexa fluors are the most common in nucleic acid microarray analysis, being relatively easily to incorporate.

Common fluorophores

(from Zeiss Corporation website)*

m

lb

lδ

π

ΞD

El

ΞΞ

E3

54

55

Source: http://info.med.yale.edu/genetics/ward/tavi/FISHdyes2.html * The primary information source can not be located.

While the foregoing detailed description includes several embodiments of the present invention, it is to be understood that the above description is illustrative only and not limiting of the disclosed invention. Indeed, it will be appreciated that the embodiments discussed above and the virtually infinite embodiments that are not mentioned could easily be within the scope and spirit of the present

10 invention. Thus, the present invention is to be limited only by the claims appended hereto.

EL

Claims

CLAIMS:

1. Apparatus including a first surface, said apparatus including an array of probes immobilized on said surface and target molecules attached to a subset of said array of probes to form a pattern of probe /target pairs, each of said probe /target pairs having a marker attached thereto for forming a pattern of probe/target/marker complexes, said apparatus including means for directing at said surface polarized light at an angle to said surface to impose total internal reflection and to create an evanescent field encompassing said complexes.

2. Apparatus as in claim 1 wherein said marker is absorbent of light at a first wavelength and said means for directing polarized light at an angle to said surface comprises light at said first wavelength.

3. Apparatus as in claim 1 also including means for acquiring an image of said pattern.

4. Apparatus as in claim 3 wherein first and second target molecules attach to said probes in a manner to form first and second patterns of probe/target pairs, first and second markers attached to the probe /target pairs of said first and second patterns for forming first and second probe/target/market complexes respectively, said first and second markers being operative to make said first and second patterns of complexes responsive to polarized light of first and second wavelengths respectively, and said means for directing light at said surface comprises means for directing light selectively at said first and at said second wavelength.

5. Apparatus as in claim 4 also including means for acquiring an image of each of said first and second patterns.

6. Apparatus comprising a substrate having a first surface, an array of probes immobilized on said surface, target molecules attached to at least a subset of said probes in said array forming probe /target pairs there, an absorber attached to each of said probe/ target pairs for forming probe/target/absorber complexes, each of said absorbers absorbing light at a first wavelength, means for directing at said surface polarized light at said first wavelength and at an angle to achieve total internal reflection, and means for sensing the image of localized polarization changes produced by said complexes, said apparatus being operative to capture said image after only a single reflection of said light.

7. Apparatus as in claim 6 wherein said surface includes at least first and second patterns of different probes and different target molecules attached to said different probes forming first and second patterns of probe/target pairs, first and second absorbers attached to said first and second patterns of probe /target pairs and selected to absorb light at first and second wavelengths respectively, means for directing at said surface polarized light selectively at said first and second wavelengths, and means for sensing the images of localized variations in polarization produced at said first and at said second wavelengths.

8. A method for imposing relatively strong localized changes in polarization on a beam of polarized light directed at a surface at an angle to obtain total internal reflection, said method comprising the steps of immobilizing an array of probes on said surface, exposing said probes to a solution of target molecules to produce a pattern of probe/target pairs on said surface, exposing said surface to a solution of absorber molecules selected from a group of molecules which bond selectively to said probe/target pairs and positioning a sensor of the image of said pattern of probe/target pairs such that the sensor captures said image after only a single reflection from said surface.

9. A method as in claim 8 wherein said polarized beam is at a first wavelength and said absorber molecules absorbs light at said first wavelength.

10. A method as in claim 9 including the steps of immobilizing patterns of different probes on said surface, exposing said probes to different target molecules for producing at least first and second patterns of probe/ target pairs, exposing said surface to a solution including at least first and second absorber molecules for binding to said first and second probe/ target pairs respectively, directing at said surface light of a first wavelength at which said first absorber molecule absorbs, directing at said surface light of a second wavelength at which said second absorber molecules absorbs, and activating said sensor in a manner to capture first and second images produced in response to said light of said first and second wave lengths respectively.

11. An apparatus including a total internal reflection surface and a means for directing polarized light at said surface in a manner to create an evanescent field there, the steps of immobilizing an array of probes on said surface and adding to said surface target and marker molecules for forming patterns of probe/target/marker complexes, and directing polarized light at said surface for providing in said field a pattern of localized intensity variations indicative of the positions of said complexes in said array.

12. An apparatus as in claim 11 wherein said step of adding target and marker molecules comprises the steps of exposing said probes to target molecules for forming a pattern of probe /target pairs in said array, and introducing to said surface said marker molecules for forming said pattern of probe/ target pairs into a pattern of probe/target/marker complexes.

13. Apparatus comprising a substrate having a first surface, an array of probes affixed to said surface, target molecules attached to said 0/9 probes of said array, an absorbent molecule attached to each target of said subset, each of said absorbent molecules being responsive to light of a characteristic wavelength for generating a signal indicative of the presence of a probe-target pair in said array, means for directing at said surface light of said characteristic wavelength, and means for sensing each signal so generated.

14. Apparatus as in claim 13 wherein said array comprises a plurality of sets of different probes, the probes of each of said sets being capable of hybridizing with targets to form probe-target pairs, different absorbent molecules attached to different sample target subsets, said different absorbent molecules being responsive to light of different characteristic wavelengths for generating signals indicative of the presence of hybridized probe-target pairs, said apparatus including means for directing at said surface light at different ones of said characteristic wavelengths, and means for sensing the signals generated at each of said wavelengths.

15. Apparatus as in claim 14 also including means for recording the locations in said array of said signals generated at each of said wavelengths.

16. Apparatus as in claim 13, also including means for storing a record of each signal so generated.

17. Apparatus as in claim 14, also including means for simultaneously sensing and recording a plurality of said signals.

18. Apparatus as in claim 1, comprising means for directing at said surface polarized light of individual wavelengths.

19. Apparatus as in claim 6, said absorbers absorbing light at a plurality of individual wavelengths; said apparatus comprising means for directing at said surface polarized light at a plurality of individual wavelengths.