SINGLE MOLECULE NUCLEIC ACID SEQUENCE ANALYSIS PROCESSES AND COMPOSITIONS

• US 20160040231A1
• Filed: 04/15/2015
• Published: 02/11/2016
• Est. Priority Date: 01/17/2008
• Status: Active Grant

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: CANTOR, Charles R.
• Granted Patent: US 10,144,966 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2531/101 Linear amplification, i.e. non exponential
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Claims

1. (canceled)

2. A solid support comprising single-stranded solid phase nucleic acid species, wherein:

(a) each solid phase nucleic acid species of the solid support comprises an identifier sequence and a probe sequence;

(b) the probe sequence is complementary to a nucleotide sequence in a sample nucleic acid;

(c) the solid phase nucleic acid species of the solid support share a common probe sequence or do not share a common probe sequence; and

(d) the solid phase nucleic acid species of the solid support share a common identifier sequence.

3. The solid support of claim 2, wherein:

(a) the solid support is in a collection of solid supports;

(b) at least one molecule of the solid phase nucleic acid species of each of the solid supports in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other solid supports; and

(c) the solid phase nucleic acid species of each of the solid supports in the collection share a unique identifier sequence different than the identifier sequences of the solid phase nucleic acid species of the other solid supports in the collection.

4. The solid support of claim 2, wherein each solid phase nucleic acid species of the solid support further comprises a primer sequence, wherein the primer sequence, the identifier sequence and the probe sequence are oriented 5′

-(primer sequence)-(identifier sequence)-(probe sequence)-3′

, wherein the 5′

terminal nucleotide of the solid phase nucleic acid is linked to the solid support.

5. The solid support of claim 3, wherein each solid phase nucleic acid species of each of the solid supports in the collection further comprises a primer sequence, wherein the primer sequence, the identifier sequence and the probe sequence are oriented 5′

-(primer sequence)-(identifier sequence)-(probe sequence)-3′

, wherein the 5′

terminal nucleotide of the solid phase nucleic acid is linked to the solid support.

6. The solid support of claim 4, wherein the solid phase nucleic acid species share a common primer sequence.

7. The solid support of claim 6, wherein the primer sequence is a universal primer sequence.

8. The solid support of claim 5, wherein the solid phase nucleic acid species of all the solid supports in the collection share a common primer sequence.

9. The solid support of claim 8, wherein the primer sequence is a universal primer sequence.

10. The solid support of claim 2, wherein the solid phase nucleic acid species share a common probe sequence.

11. The solid support of claim 2, wherein the solid phase nucleic acid species do not share a common probe sequence.

12. The solid support of claim 2, wherein the solid support is a bead or particle.

13. The solid support of claim 12, wherein the solid support is a microbead, a nanobead, a microparticle or a nanoparticle.

14. The solid support of claim 12, wherein the bead or particle is a gel.

15. A substrate comprising a collection of the beads of claim 12, wherein the beads are oriented in an array and wherein:

(a) at least one solid phase nucleic acid species of each of the beads in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other beads in the collection; and

(b) the solid phase nucleic acid species of each bead in the collection share a unique identifier sequence different than the identifier sequences of the solid phase nucleic acid species of the other beads of the collection.

16. A method of manufacturing the solid support of claim 2, which comprises

(a) sequentially linking nucleotides to a nucleotide covalently linked to the solid support, whereby each of the single-stranded solid phase nucleic acid species is prepared and is in association with the solid support;

or

(b) linking each single-stranded nucleic acid species in solution phase to the solid support, whereby the single-stranded solid phase nucleic acid species are in association with the solid support;

wherein;

(i) each single-stranded solid phase nucleic acid species comprises n identifier sequence and a probe sequence;

(ii) the solid phase nucleic acid species share a common probe sequence or the solid phase nucleic acid do not share a common probe sequence; and

(iii) the solid phase nucleic acid species share a common identifier sequence.

17. The method of claim 16, wherein:

(a) the solid support is in a collection of solid supports;

(b) at least one molecule of the solid phase nucleic acid species of each of the solid supports in the collection has a unique probe sequence different than a probe sequence of the solid phase nucleic acid species of the other solid supports; and

(c) the solid phase nucleic acid species of each of the solid supports in the collection share a unique identifier sequence different than the identifier sequences of the solid phase nucleic acid species of the other solid supports in the collection.