Polymer sequencing using selectively labeled monomers and data integration

• US 20050186576A1
• Filed: 02/19/2004
• Published: 08/25/2005
• Est. Priority Date: 02/19/2004
• Status: Abandoned Application

• Current Assignee: Intel Corporation
• Original Assignee: Intel Corporation
• Inventors: Su, Xing, Berlin, Andrew A., Koo, Tae-Woong, Chan, Selena
• Application Number:
  US10/782,014
• Publication Number:
  US 20050186576A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2527/113 Time
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore

Abstract

Methods and apparatuses for sequencing single polymer molecules, such as a nucleic acid strand, are discussed. A discussed method comprises dividing a polymer sample into a number of polymer subsamples equal to the number of different monomer types and partially labeling only one of the monomer types in each polymer subsample. The method may further comprise placing a subsample into a reaction chamber, sequentially separating each monomer from the polymer subsample, and detecting the labels of each separated labeled monomer as a function of time. The time between each labeled monomer may be used to construct a monomer-time map for each polymer sub-sample using overlapping data analysis and frequency analysis. Time maps may then be assembled/aligned into a polymer sequence from the monomer-time maps of each of the polymer subsamples using non-overlapping data analysis.

Claims

1. A method of sequencing a polymer comprising:

a) dividing a polymer sample into a number of polymer subsamples equal to a number of different monomer types comprising the polymer sample, wherein only one of the monomer types in each polymer subsample is partially labeled such that an average time between two adjacent labeled monomers is significantly larger than an average time between two adjacent monomers of the same type in the polymer subsample before labelling;

b) sequentially separating each monomer from the polymer subsample;

c) detecting the labels of each separated labeled monomer as a function of time;

d) constructing a time map for each monomer type in each polymer subsample; and

e) assembling the time maps into a polymer sequence.

2. The method of claim 1 wherein the polymer is a nucleic acid, the monomer is a nucleotide, and the number of polymer subsamples and different monomer types is four.

3. The method of claim 2, wherein each subsample comprises from about 1000 to about 100,000 copies of the nucleic acid.

4. The method of claim 2, wherein the labels are bulky groups.

5. The method of claim 4, wherein the bulky groups are selected from the group consisting of organic groups, quantum dots, antibodies, metallic groups and complex organic-inorganic nanoparticles.

6. The method of claim 2, further comprising attaching the labeled nucleic acid strand to a surface.

7. The method of claim 2 wherein sequentially separating each monomer is done by an enzyme and complex organic-inorganic nanoparticles.

8. The method of claim 7 wherein polymer is a nucleic acid and said enzyme has exonuclease activity.

9. The method of claim 1 wherein detecting the time between labels is accomplished/measured with a time-gated detection device.

10. The method of claim 9, wherein the detection device is an optical device, a nanopore device, or an electrical device.

11. The method of claim 1, wherein constructing monomer time maps of each of the polymer subsamples comprises analyzing the measured time by overlapping data analysis and frequency analysis to construct the time maps.

12. The method of claim 1, wherein assembling monomer time maps into a polymer sequence comprises minimum non-overlapping data analysis.

13. A method of sequencing a polymer comprising:

a) dividing a polymer sample into a number of polymer subsamples equal to a number of different monomer types comprising the polymer sample, wherein only one of the monomer types in each polymer subsample is partially labeled such that an average time between two adjacent labeled monomers is significantly larger than an average time between two adjacent monomers of the same type in the polymer subsample before labelling;

b) moving the intact partially labeled polymer across a detector;

c) measuring a time between the partially labeled monomers;

d) constructing a time map for each detected labeled monomer for each partially labeled polymer strand; and

e) assembling the time maps into a sequence for the polymer.

14. The method of claim 13 wherein the polymer is a nucleic acid, the monomer is a nucleotide, and the number of polymer subsamples and different monomer types is four.

15. The method of claim 14, wherein each subsample comprises from about 1000 to about 100,000 copies of the nucleic acid.

16. The method of claim 14, wherein the labels are bulky groups.

17. The method of claim 16, wherein the bulky groups are selected from the group consisting of organic groups, quantum dots, antibodies, metallic groups and complex organic-inorganic nanoparticles.

18. The method of claim 14, further comprising attaching the labeled nucleic acid strand to a surface.

19. The method of claim 13 wherein detecting the time between labels is accomplished/measured with a time-gated detection device.

20. The method of claim 19, wherein the detection device is an optical device, a nanopore device, or an electrical device.

21. The method of claim 20, wherein the detector is -selected from the group consisting of an ion-channel-lipid bilayer sensor, a photodetector, an electrical detector and a mass detector.

22. The method of claim 13, wherein constructing monomer time maps of each of the polymer subsamples comprises analyzing the measured time by overlapping data analysis and frequency analysis to construct the time maps.

23. The method of claim 13, wherein assembling monomer time maps into a polymer sequence comprises minimum non-overlapping data analysis.

24. The method of claim 13, wherein at least one end of each nucleic acid strand is attached to a distinguishable label.

25. An apparatus comprising:

a) a chamber for cleaving a partially-labeled polymer sample into individual monomers;

b) a means for transporting the individual monomers across a detector.

26. The apparatus of claim 25, further comprising:

(i) an information processing system; and

(ii) a database.

27. The apparatus of claim 25, wherein said detector are capable of detecting labels attached to individual monomers.

28. The apparatus of claim 25, wherein the means for transporting the individual monomers across a detector is a microfluidic chip.

29. The apparatus of claim 25, wherein the detector is selected from the group consisting of an ion-channel-lipid bilayer sensor, a photodetector, an electrical detector and a mass detector.