ELECTRON BEAM NUCLEIC ACID SEQUENCING

• US 20100331196A1
• Filed: 06/21/2010
• Published: 12/30/2010
• Est. Priority Date: 03/16/2007
• Status: Abandoned Application

• Current Assignee: Cornell University
• Original Assignee: Cornell University
• Inventors: Bellan, Leon M., Craighead, Harold G.
• Application Number:
  US12/819,766
• Publication Number:
  US 20100331196A1
• Time in Patent Office: Days
• US Class Current: 506/7
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00666 One-dimensional arrays within three-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C07H 1/00 Processes for the preparation of sugar derivatives
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 1/14 Extraction; Separation; Purification
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: D01D 5/0007 Electro-spinning non-woven fabrics produced by electro-spinning D04H1/728
• CPC Class Codes: G01N 2021/6432 Quenching
• CPC Class Codes: G01N 2021/7723 Swelling part, also for adsorption sensor, i.e. without chemical reaction
• CPC Class Codes: G01N 2021/773 Porous polymer jacket; Polymer matrix with indicator
• CPC Class Codes: G01N 2021/7786 Fluorescence
• CPC Class Codes: H01J 47/00 Tubes for determining the presence, intensity, density or energy of radiation or particles discharge tubes using igniting by associated radioactive materials or fillings, e.g. current stabilising tubes H01J17/32 ; photoelectric discharge tubes not involving the ionisation of a gas H01J40/00 ; discharge tubes for measuring the pressure, partial pressure of introduced gas or for detecting presence of gas H01J41/02; ionisation chambers using a solid dielectric G01T3/008
• CPC Class Codes: Y10T 428/298 : Physical dimension

Abstract

The present invention relates to compositions, methods, and uses for obtaining sequence information from nucleic acid molecules.

Claims

1. A method for obtaining sequence information from nucleic acid molecules, comprising:

scanning with an electron beam a population of labeled nucleic acid molecules on a substrate, wherein the nucleic acid molecules are deposited from a tip onto said substrate that is moving in a direction such that the nucleic acid molecules are elongated on the substrate and aligned along the direction of the movement, wherein said scanning detects said labels and thereby obtaining sequence information of said nucleic acid molecules.

2. The method of claim 1, wherein the nucleic acid molecules are labeled prior to the molecules are deposited onto the substrate.

3. The method of claim 1, wherein the nucleic acid molecules are labeled after the molecules are deposited onto the substrate.

4. The method of claim 1, wherein the deposition is caused by the application of an electrical potential on the tip relative to the substrate.

5. The method of claim 1, wherein the substrate is rotating.

6. The method of claim 1, wherein the nucleic acid molecules comprise DNA.

7. The method of claim 1, wherein 1, 2, 3, or 4 of the types of bases of said nucleic acid molecules are labeled.

8. The method of claim 1, wherein said labels comprise one or more heavy metal atoms.

9. The method of claim 8, wherein the one or more heavy metal atoms comprise gold, iron, lead, iridium, cobalt, mercury, osmium, silver;

mercury, uranium, platinum, rhodium, ruthenium, palladium, copper, or selenium.

10. The method of claim 1, wherein the detection of the labels comprises using electron energy loss spectroscopy to determine the identity of the labels.

11. The method of claim 1, wherein said nucleic acid molecules are held within a fiber material.

12. The method of claim 11, wherein the fiber material comprises a polymer.

13. The method of claim 11, wherein the fiber material comprises a water soluble polymer.

14. A method for obtaining sequence information from a nucleic acid molecule deposited on a substrate surface, wherein said molecule is elongated, comprising:

scanning said nucleic acid molecule with an electron beam, wherein one or more types of nucleotide bases of said nucleic acid molecule is labeled, said scanning yields a signal that is resolved via electron energy loss spectroscopy (EELS), and wherein said signal is indicative of the identity and order of said labeled nucleotide base within said nucleic acid molecule, thereby obtaining sequence information from said nucleic acid molecule.

15. The method of claim 14, wherein a plurality of elongated nucleic acid molecules are deposited onto said substrate surface.

16. The method of claim 14, comprising scanning a plurality of elongated nucleic acid molecules deposited onto said substrate surface.

17. The method of claim 14, wherein one or more of the labels comprise one or more heavy metal atoms.

18. The method of claim 17 wherein the one or more heavy atoms comprise gold, iron, lead, iridium, cobalt, mercury, osmium, silver;

mercury, uranium, platinum, rhodium, ruthenium, palladium, copper, or selenium.

19. The method of claim 14, wherein the nucleic acid molecule comprises DNA.

20. The method of claim 14, wherein the types of bases comprise A, G, T and C.

21. The method of claim 14, wherein 1, 2, 3, or 4 of the types of bases are labeled.

22. The method of claim 14, wherein the nucleic acid molecule is held within a fiber material.

23. The method of claim 22, wherein the fiber material comprises a polymer.

24. The method of claim 22, wherein the fiber material comprises a water soluble polymer.