Surface chemistry and deposition techniques

• US 9,944,982 B2
• Filed: 11/27/2013
• Issued: 04/17/2018
• Est. Priority Date: 02/02/2007
• Status: Active Grant

• Current Assignee: California Institute of Technology, Stanford University, University of Chicago
• Original Assignee: California Institute of Technology, Stanford University, University of Chicago
• Inventors: Schwartz, Jerrod, Quake, Stephen R., Mrksich, Milan
• Primary Examiner(s): Bhat, Narayan
• Application Number:
  US14/092,728
• Publication Number:
  US 20140256561A1
• Time in Patent Office: 1,602 Days
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: G01N 33/54393 Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes.

Claims

1. A method for single molecule visualization, the method comprising:

providing a surface, wherein the surface is a glass surface further comprising a uniform metal film, and wherein the surface is produced by a method comprising depositing a plurality of surface attachment features for specifically immobilizing fluorophore-labeled molecules on said surface by a deposition method that actively forces individual fluorophore-labeled molecules to be spaced apart by a distance equal to at least the diffraction limit for said fluorophore, wherein the deposition method provides at least a 3-fold increase in the maximum number of resolvable fluorophore-labeled molecules, as compared to random deposition;

immobilizing a plurality of fluorophore-labeled molecules via the plurality of surface attachment features; and

performing real time imaging for single fluorophores using surface plasmon resonance (SPR) fluorescence microscopy.

2. The method of claim 1, wherein said performing real time imaging comprises:

producing an evanescent electromagnetic field on said surface; and

visualizing said fluorophore-labeled molecules using surface plasmon resonance-enhanced total internal reflection fluorescence microscopy.

3. The method of claim 1, wherein said plurality of surface attachment features comprises a nucleic acid.

4. The method of claim 3, wherein said nucleic acid is DNA.

5. The method of claim 3, further comprising obtaining a sequence of said nucleic acid.

6. The method of claim 5, wherein said obtaining step comprises conducting a template-dependent sequencing-by-synthesis reaction.

7. The method of claim 1, wherein said surface further comprises a coating selected from a polyelectrolyte multilayer and an epoxide.

8. The method of claim 1, wherein the deposition method provides at least a 7-fold increase in the maximum number of resolvable fluorophore-labeled molecules, as compared to random deposition.

9. The method of claim 1, wherein the deposition method comprises the use of a diffraction limit spacer that produces a diffraction limit spacing by sterically hindering attachment features from depositing within the diffraction limit of a given deposited attachment feature.

10. The method of claim 9, wherein the diffraction limit spacer comprises a bead.

11. The method of claim 9, wherein the diffraction limit spacer comprises a virus or virus capsid.

12. The method of claim 1, wherein the metal film is 1-10 nm thick.

13. The method of claim 1, wherein said depositing a plurality of surface attachment features comprises creating a surface pattern of ordered surface attachment features with diffraction limit spacing, wherein each surface attachment feature comprises a bin, whereby a single fluorophore-labeled molecule immobilized at said bin is optically resolvable from fluorophore-labeled molecules immobilized at other bins.

14. The method of claim 13, wherein said depositing of surface attachment features is carried out by microcontact printing, electron beam lithography, or photolithography.

15. The method of claim 1, wherein said plurality of attachment features is selected from antibodies, ligands, gold particles, beads, wells, surface dimples, amines, and epoxides.

16. The method of claim 1, wherein the method comprises sequencing a nucleic acid, wherein:

said immobilizing a plurality of fluorophore-labeled molecules comprises;

attaching a plurality of nucleic acid primers to the plurality of surface attachment features;

exposing said primers to one or more template nucleic acids that are capable of hybridizing thereto;

introducing a fluorophore-labeled nucleotide and a polymerase under conditions that permit template-dependent incorporation of said nucleotide into said primer;

said performing real time imaging comprises;

detecting said incorporated nucleotides; and

the method additionally comprises;

neutralizing fluorophores associated with said incorporated nucleotides; and

repeating said introducing, detecting, and neutralizing steps at least once, thereby to determine a sequence of said template.