Mass spectrometric methods for detecting mutations in a target nucleic acid

• US 20060223105A1
• Filed: 05/11/2006
• Published: 10/05/2006
• Est. Priority Date: 03/17/1995
• Status: Active Grant

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Koster, Hubert
• Granted Patent: US 7,419,787 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/706 for hepatitis
• CPC Class Codes: C12Q 2521/325 Single stranded exonuclease
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2537/113 Heteroduplex formation
• CPC Class Codes: C12Q 2565/625 being a nucleic acid test strip device, e.g. dipsticks, strips, tapes, CD plates
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: G01N 35/1067 for transfer to or from containers having different spacing
• CPC Class Codes: H01J 49/00 : Particle spectrometers or separator tubes
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/24 : Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided.

Claims

1. A process for detecting one or more target nucleotide sequences in a biological sample, comprising:

a) amplifying a target nucleic acid molecule, wherein the amplification product is a natural deoxyribonucleic acid;

b) ionizing and volatilizing the product of step (a); and

c) analyzing the product of step (b) by mass spectrometry, wherein detection of the target nucleotide sequence by mass spectrometry indicates the presence of the target nucleotide sequence in the biological sample.

2. The process of claim 1, wherein the target nucleotide sequence is a mutation.

3. The process of claim 1, wherein a plurality of nucleic acids are arranged on a solid support in an array and each spot on the array is subject to mass spectrometry.

4. The process of claim 1, wherein the mass spectrometry format is matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

5. The process of claim 1, wherein the mass spectrometry format is electrospray (ES) mass spectrometry.

6. The process of claim 1, wherein the target nucleotide sequence is a DNA fingerprint or is implicated in a disease or condition selected from the group consisting of a genetic disease, a chromosomal abnormality, a genetic predisposition, a viral infection, a fungal infection, a bacterial infection and a protest infection.

7. The process of claim 6, whereby a genetic disease, chromosomal abnormality, genetic predisposition to a disease or condition or infection by a pathogen can be detected or identity determined.

8. The process of claim 1, which further comprises exchanging cations bound to the product of step (a).

9. The process of claim 1, wherein the product of step (a) and step (b) are natural oligoribo nucleic acids or natural oligodeoxyribo nucleic acids.

10. The process of claim 1, wherein the backbone of the product of step (a) and step (b) is a phospodiester backbone.

11. The process of claim 1, wherein each sugar-sugar linkage in the target nucleic acid comprises a negative charge.

12. The process of claim 1, wherein each sugar-sugar linkage in the amplification product comprises a negative charge.

13. The process of claim 1, wherein each sugar-sugar linkage in the target nucleic acid comprises a phosphate.

14. The process of claim 1, wherein each sugar-sugar linkage in the amplification product comprises a phosphate.

15. The process of claim 1, wherein the product of step (a) is contacted with a capture oligonucleotide linked to a solid support.

16. The process of claim 1, wherein the target nucleic acid is contacted with a capture oligonucleotide linked to a solid support.