Method for imaging informational biological molecules on a semiconductor substrate

• US 5,314,829 A
• Filed: 12/18/1992
• Issued: 05/24/1994
• Est. Priority Date: 12/18/1992
• Status: Expired due to Fees

• Current Assignee: California Institute of Technology
• Original Assignee: California Institute of Technology
• Inventors: Coles, L. Stephen
• Primary Examiner(s): Alexander, Lyle A.
• Assistant Examiner(s): WALLENHORST, MAUREEN
• Application Number:
  US07/992,601
• Time in Patent Office: 522 Days
• Field of Search: 436/56, 436/63, 436/89, 436/94, 436/164, 436/165, 436/527, 436/422, 422/55, 422/58, 422/82.05, 422/104, 422/88, 422/92, 422/102, 250/306, 250/307, 250/311, 250/440.11, 435/6, 435/91, 204/129.3, 935/77
• US Class Current: 436/165
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00549 2-dimensional
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 2300/0803 Disc shape
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/0893 having a very large number of wells, microfabricated wells
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0472 Diffusion
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/508 rigid containers not provided for above
• CPC Class Codes: B01L 9/56 Means for indicating position of a recipient or sample in an array
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: Y10S 977/853 : Biological sample
• CPC Class Codes: Y10T 436/13 : Tracers or tags
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

Imaging biological molecules such as DNA at rates several times faster than conventional imaging techniques is carried out using a patterned silicon wafer having nano-machined grooves which hold individual molecular strands and periodically spaced unique bar codes permitting repeatably locating all images. The strands are coaxed into the grooves preferably using gravity and pulsed electric fields which induce electric charge attraction to the molecular strands in the bottom surfaces of the grooves. Differential imaging removes substrate artifacts.

Claims

1. A method of imaging molecular strands using a substrate having a plurality of straight grooves in a top surface of said substrate, each of said grooves being of a size capable of holding only a single individual one of said molecular strands along any one section of a length of the groove, and being capable of forcing single individual molecular strands into a straight position when positioned in one of said plurality of grooves, said method comprising:

preparing a specimen of said molecular strands and depositing said specimen onto said top surface;

aligning and depositing individual ones of said molecular strands into individual ones of said plurality of grooves whereby the shape and size of each groove forces the molecular strands into a straight position; and

recording a first image of a selected section of said top surface of said substrate having at least one of said molecular strands in one of said grooves using an atomic imaging device.

2. The method of claim 1 wherein:

said aligning and depositing of said specimen onto said top surface of said substrate is preceded by recording a preliminary image of said selected section of said substrate in the absence of any molecular strand specimen thereon using said atomic imaging device; and

said recording of said first image is followed by substrating said preliminary image from said first image to produce a second image of a molecular strand by itself substantially free of image artifacts of said substrate.

3. The method of claim 2 wherein said aligning and depositing individual ones of said molecular strands into individual ones of said plurality of grooves comprises using gravity to draw said individual ones of said molecular strands into individual ones of said plurality of grooves.

4. The method of claim 2 wherein said molecular strands are of the type which are attracted by one of (i) a positive electrical field, and (ii) a negative electrical field and wherein said aligning and depositing individual ones of said molecular strands into individual ones of said plurality of grooves comprises placing an electric field of a type which attracts said molecular strands perpendicular to said top surface of said substrate so as to draw said individual ones of said molecular strands into individual ones of said plurality of grooves.

5. The method of claim 4 wherein:

said substrate comprises a crystalline semiconductor.

6. The method of claim 4 wherein said placing an electric field perpendicular to said top surface is preceded by aligning said molecular strands in a direction parallel to at least some of said grooves.

7. The method of claim 6 wherein said aligning of said molecular strands parallel to at least some of said grooves comprises placing an electric field across said top surface of said substrate in a direction parallel to at least some of said grooves.

8. The method of claim 7 wherein said electric field parallel to at least some of said grooves is a pulsed electric field.

9. The method of claim 6 wherein said electric field perpendicular to said top surface is a pulsed electric field.

10. The method of claim 1 wherein said preparing said specimen comprises preparing a specimen of denatured DNA molecular strands.

11. The method of claim 10 wherein said preparing includes marking each of the different bases of said DNA molecular strands with a particular and unique heavy metal atom.

12. The method of claim 1 wherein said substrate further comprises address markers located at periodic locations associated with said plurality of grooves across said top surface of said substrate and wherein a different address marker uniquely identifies each of said periodic locations in said top surface of said substrate, and wherein said method of recording a first image includes recording an image of said address markers associated with said periodic locations within said selected section, whereby the location and orientation of each recorded image of a molecular strand is deducible from the address markers visible in said first image.

13. The method of claim 12 wherein each of said address markers comprises a different computer-readable bar code.