Methods and compositions for sequence-specific purification and multiplex analysis of nucleic acids

• US 9,689,047 B2
• Filed: 01/28/2011
• Issued: 06/27/2017
• Est. Priority Date: 01/29/2010
• Status: Expired due to Fees

• Current Assignee: QIAGEN Gaithersburg, Inc. (Qiagen NV)
• Original Assignee: QIAGEN Gaithersburg, Inc. (Qiagen NV)
• Inventors: Nazarenko, Irina, Shukla, Mridula, Virmani, Arvind, O'Neil, Dominic, Basham, Holly, Agarwal, Shiuli
• Primary Examiner(s): Dauner, Joseph G
• Application Number:
  US13/015,915
• Publication Number:
  US 20110217705A1
• Time in Patent Office: 2,342 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• 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 1/708 for papilloma
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2565/531 characterised by the capture moiety being a protein for target oligonucleotides

Abstract

Methods and materials for determining the presence of at least one nucleic acid in a sample are provided, said methods comprising (1) a purification step using sequence specific hybrid capture; (2) an amplification step; and (3) a detection step using two separate sequence-specific polynucleotide probes. Also provided are nucleic acids comprising SEQ ID NO: 1 to SEQ ID NO: 727 and nucleic acid probes and probe sets comprising the same.

Claims

1. A nucleic acid probe set consisting of:

a) a first nucleic acid probe consisting of one of the nucleotide sequences selected from the group consisting of SEQ ID NO;

102 to SEQ ID NO;

113, and complements thereof and a detectable label, wherein said first nucleic acid probe is capable of hybridizing under selective stringency conditions to a portion of a gene selected from the group consisting of E6 and E7; and

b) a second nucleic acid probe consisting of one of the nucleotide sequences selected from the group consisting of SEQ ID NO;

577 to SEQ ID NO;

580, wherein said second nucleic acid probe is capable of hybridizing under selective stringency conditions to a portion of an L1 gene;

wherein the first nucleic acid probe and second nucleic acid probe are capable of hybridizing under stringent conditions to the same HPV genome, and

wherein the nucleic acid probe set is capable of isolating HPV nucleic acids from non-HPV nucleic acids in a sample.

2. The nucleic acid probe set of claim 1, wherein the first nucleic acid probe further comprises a ligand.

3. The nucleic acid probe set of claim 1, wherein said nucleic acid probe set further comprises:

(a) a purification probe set, wherein the probes of the purification probe set comprise at least one consensus probe capable of hybridizing to a plurality of target nucleic acids from different HPV types.

4. The nucleic acid probe set of claim 3, wherein the probe set further comprises:

(b) an immobilization probe set comprising at least one polynucleotide probe specific for one of the plurality of target nucleic acids.

5. The nucleic acid probe set of claim 4, wherein the immobilization probe set comprises at least one probe specific for each of the plurality of target nucleic acids.

6. The nucleic acid probe set of claim 4, wherein the probe set further comprises:

(c) a detection probe set comprising at least one polynucleotide probe specific for one of the plurality of target nucleic acids.

7. A kit for genotyping a Human Papillomavirus nucleic acid, said kit comprising:

(a) the nucleic acid probe set according to claim 1;

(b) a nucleic acid polymerase;

(c) a primer;

(d) a first solid support;

(e) an anti-DNA;

RNA hybrid antibody bound to or adapted to be bound to the first solid support; and

(f) a detectably labeled second solid support.