CAPTURE PRIMERS AND CAPTURE SEQUENCE LINKED SOLID SUPPORTS FOR MOLECULAR DIAGNOSTIC TESTS

• US 20110028334A1
• Filed: 07/30/2010
• Published: 02/03/2011
• Est. Priority Date: 07/31/2009
• Status: Active Grant

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Hayden, Mark A.
• Granted Patent: US 9,416,409 B2
• Time in Patent Office: Days
• US Class Current: 506/8
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

The present invention provides systems, methods, and compositions for performing molecular tests. In particular, the present invention provides methods, compositions and systems for generating target sequence-linked solid supports (e.g., beads) using a solid support linked to a plurality of capture sequences and capture primers composed of a 3′ target-specific portion and a 5′ capture sequence portion. In certain embodiments, the target sequence linked solid support is used in sequencing methods (e.g., pyrosequencing, zero-mode waveguide type sequencing, nanopore sequencing, etc.) to determine the sequence of the target sequence (e.g., in order to detect the identity of a target nucleic acid in sample).

Claims

1. A method comprising;

a) contacting a sample suspected of containing a target nucleic acid with a capture primer and a reverse primer, wherein said capture primer comprises;

i) a 3′

region configured to hybridize to said target nucleic acid such that it can be extended by a polymerase, and ii) a 5′

region comprising a capture sequence; and

wherein said contacting is under conditions such that;

i) said 3′

region of said capture primer hybridizes to said target nucleic acid and is extended to generate a first amplification product, and

ii) said reverse primer hybridizes to said first amplification product and is extended to generate a second amplification product, wherein said second amplification product comprises a 3′

capture sequence complement capable of hybridizing to said capture sequence; and

b) treating said sample under conditions such that said second amplification product is separated from said first amplification product;

c) contacting said second amplification product with a solid support comprising a plurality of bound capture sequences under conditions such that said 3′

capture sequence complement of said second amplification product hybridizes to one of said bound capture sequences to generate a hybridized solid support; and

d) treating said hybridized solid support under conditions such that one of said bound capture sequences is extended along said second amplification product to generate a target sequence that is linked to said solid support.

2. The method of claim 1, further comprising e) contacting said solid support with a plurality of free capture sequences and a plurality of said reverse primers under conditions such that said plurality of bound capture sequences are extended to generate a clonally amplified solid support comprising a plurality of said target sequences.

3. The method of claim 2, wherein said conditions comprise emulsion PCR conditions or bridge PCR conditions.

4. The method of claim 1, wherein said 5′

region is configured to not hybridize to said target nucleic when said 3′

region of said capture primer is hybridized to said target nucleic acid

5. The method of claim 1, further comprising e) treating said target sequence linked to said solid support under conditions such that at least part of the nucleic acid sequence of said target sequence is determined.

6. The method of claim 5, wherein said nucleic acid sequence of said target sequence is determined by a method selected from:

pyrosequencing, sequencing-by-synthesis, sequencing-by-ligation, nanopore sequencing, single molecule SBS, and real-time sequencing.

7. The method of claim 5, wherein said nucleic acid sequence of said target sequence is determined by a method employing at least one zero-mode waveguide.

8. The method of claim 5, wherein said nucleic acid sequence of said target sequence is determined by a method comprising:

contacting said target sequence with at least one nucleotide incorporating biocatalyst, labeled nucleotides, and at least one primer nucleic acid that is at least partially complementary to at least a subsequence of said target sequence, under conditions whereby said nucleotide incorporating biocatalyst extends said primer nucleic acid to produce an extended primer nucleic acid by incorporating said labeled nucleotides at a terminal end of said extended primer nucleic acid, wherein nucleotides that comprise different nucleobases comprise different labels, wherein the different labels produce detectable signals as or after the labeled nucleotides are incorporated at the terminal end of the extended primer nucleic acid, which detectable signals identify the labeled nucleotides incorporated at the terminal end of the extended primer nucleic acid and/or complementary nucleotides in the template nucleic acid, and wherein the detectable signals are detected as or after the labeled nucleotides are incorporated at the terminal end of the extended primer nucleic acid to thereby determine the nucleic acid sequence of at least a subsequence of the target sequence.

9. The method of claim 8, wherein said labels comprise different fluorescent labels and wherein said detectable signals are detected using a fluorescence microscope.

10. The method of claim 8, wherein said at least one primer nucleic acid is a primer primer pair, wherein said primer pair is configured to hybridize with conserved regions of said two or more different bioagents and flank variable regions of said two or more different bioagents.

11. The method of claim 8, wherein the terminal end of said extended primer nucleic acid is the 3′

terminal end.

12. The method of claim 8, wherein said nucleotide incorporating biocatalyst comprises an enzyme selected from the group consisting of:

a polymerase, a terminal transferase, a reverse transcriptase, a polynucleotide phosphorylase, and a telomerase.

13. The method of claim 8, wherein said nucleotide incorporating biocatalyst comprises one or more modifications.

14. The method of claim 8, wherein said nucleotide incorporating biocatalyst is an enzyme derived from an organism that is selected from the group consisting of:

Thermus antranikianii, Thermus aquaticus, Thermus caldophilus, Thermus chliarophilus, Thermus filiformis, Thermus flavus, Thermus igniterrae, Thermus lacteus, Thermus oshimai, Thermus ruber, Thermus rubens, Thermus scotoductus, Thermus silvanus, Thermus species Z05, Thermus species sps 17, Thermus thermophilus, Thermotoga maritima, Thermotoga neapolitana, Thermosipho africanus, Anaerocellum thermophilum, Bacillus caldotenax, Pfu, KOD1, and Bacillus stearothermophilus.

15. The method of claim 8, wherein said nucleotide incorporating biocatalyst comprises a Φ

29 DNA polymerase.

16. The method of claim 8, wherein a label is attached to one of a heterocyclic base of a labeled nucleotide, a sugar moiety of a labeled nucleotide, and a phosphate group of a labeled nucleotide.

17. The method of claim 8, wherein a linker attaches a label to a labeled nucleotide.

18. The method of claim 8, wherein said extended primer nucleic acid is complementary to a subsequence of said target sequence.

19. The method of claim 8, wherein said extended primer nucleic acid is complementary to a full-length sequence of said target sequence.

20. The method of claim 8, wherein said primer nucleic acid comprises an intelligent primer.

21. The method of claim 8, wherein said label comprises a fluorescent dye, a non-fluorescent label, a colorimetric label, a chemiluminescent label, a bioluminescent label, a radioisotope, an antibody, an antigen, biotin, a hapten, or an enzyme.

22. The method of claim 21, wherein said label is a fluorescent dye selected from the group consisting of:

a rhodamine dye, a fluorescein dye, a halofluorescein dye, a dichlororhodamine dye, an energy transfer dye, a Lucifer dye, Oregon Green, and a cyanine dye.

23. The method of claim 21, wherein said label is a fluorescent dye selected from the group consisting of:

JOE, VIC, TET, HEX, PAM, R6G, R110, TAMRA, and ROX.

24. The method of claim 21, wherein said label is a radioisotope selected from the group consisting of:

³H, ¹⁴C, ²²Na, ³²P, ³³P, ³⁵S, ⁴²K, ⁴⁵Ca, ¹²⁵I, and ²⁰³Hg.

25. The method of claim 1, wherein said capture primer and said reverse primer are configured to hybridize with conserved regions of two or more different bioagents and flank variable regions of said two or more different bioagents.

26. The method of claim 1, wherein the target nucleic acid comprises a mammalian nucleic acid, a bacterial nucleic acid, a viral nucleic acid, a fungal nucleic acid, or a protozoal nucleic acid.

27. The method of claim 1, comprising obtaining said target nucleic acid from one or more sample sources selected from the group consisting of:

an environmental sample and a sample derived from a subject.

28. The method of claim 5, wherein said nucleic acid sequence of said target sequence is compared to a database in order to determine the organismal source of said target nucleic acid.

29. The method of claim 28, wherein the organismal source is identified at one or more taxonomic rank levels selected from the group consisting of:

a Domain, a Superphylum, a Superdivision, a Superclass, a Superorder, a Superfamily, a Superspecies, a Kingdom, a Phylum, a Division, a Class, a Legion, an Order, a Family, a Tribe, a Genus, a Species, a Subkingdom, a Subphylum, a Subclass, a Cohort, a Suborder, a Subfamily, a Subtribe, a Subgenus, a Subspecies, an Infrakingdom, a Branch, an Infraphylum, an Infraclass, an Infraorder, an Alliance, an Infraspecies, a Microphylum, a Pan/class, and a Parvorder.

30. The method of claim 1, wherein said capture primer comprises a bar-code sequence between said 3′

region and said 5′

region.

31. A system comprising:

a) at least one sequencing device; and

b) a primer pair comprising a capture primer and a reverse primer, wherein said capture primer comprises;

i) a 3′

region configured to hybridize to a target nucleic acid such that it can be extended by a polymerase to form a first amplification product, and ii) a 5′

region comprising a capture sequence, wherein said 5′

region is configured to not hybridize to said target nucleic when said 3′

region of said capture primer is hybridized to said target nucleic acid, and wherein said reverse primer is configured to hybridize to said first extension product and be extended to form a second extension product.

32. A system, comprising:

a) a primer pair comprising a capture primer and a reverse primer, wherein said capture primer comprises;

i) a 3′

region configured to hybridize to a target nucleic acid such that it can be extended by a polymerase to form a first amplification product, and ii) a 5′

region comprising a capture sequence, wherein said 5′

region is configured to not hybridize to said target nucleic when said 3′

region of said capture primer is hybridized to said target nucleic acid, and wherein said reverse primer is configured to hybridize to said first extension product and be extended to form a second extension product;

b) a reaction vessel or substrate; and

c) a detector configured to detect detectable signals produced in or on the reaction vessel or substrate, which detectable signals correspond to at least some nucleobases incorporated into a nucleic acid to generate nucleobase incorporation data.

33. The system of claim 32, wherein the reaction vessel or substrate comprises at least one zero-mode waveguide.

34. The system of claim 32, wherein the detector comprises a fluorescence microscope.

35. A system, comprising:

(a) a sequencing device configured to generate nucleic acid sequence data corresponding to the nucleic acid sequence of one or more amplicons produced using at least one purified oligonucleotide primer pair that comprises a capture primer and a reverse primer, wherein said capture primer comprises;

i) a 3′

region configured to hybridize to a target nucleic acid such that it can be extended by a polymerase to form a first amplification product, and ii) a 5′

region comprising a capture sequence, wherein said 5′

region is configured to not hybridize to said target nucleic when said 3′

region of said capture primer is hybridized to said target nucleic acid, and wherein said reverse primer is configured to hybridize to said first extension product and be extended to form a second extension product; and

(b) a controller operably connected to said sequencing device, said controller configured to query a database with said nucleic acid sequence data to identify said target nucleic acid.