DNA diagnostic based on mass spectrometry

• US 5,605,798 A
• Filed: 03/17/1995
• Issued: 02/25/1997
• Est. Priority Date: 01/07/1993
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Koster, Hubert
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): TRAN, PAUL
• Application Number:
  US08/406,199
• Time in Patent Office: 711 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 935/77, 935/78, 536/25.3, 536/25.4
• US Class Current: 435/5
• 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

The invention provides fast and highly accurate mass spectrometer based processes for detecting a particular nucleic acid sequence in a biological sample. Depending on the sequence to be detected, the processes can be used, for example, to diagnose (e.g. prenatally or postnatally) a genetic disease or chromosomal abnormality; a predisposition to a disease or condition (e.g. obesity, artherosclerosis, cancer), or infection by a pathogenic organism (e.g. virus, bacteria, parasite or fungus).

Claims

1. A process for detecting a target nucleic acid sequence present in a biological sample, comprising the steps of:

a) obtaining a nucleic acid molecule containing a target nucleic acid sequence from a biological sample;

b) hybridizing a detector oligonucleotide with the target nucleic acid sequence, wherein at least one of the detector oligonucleotide or the target nucleic acid sequence has been conditioned;

c) removing unhybridized detector oligonucleotide;

d) ionizing and volatizing the product of step c); and

e) detecting the detector oligonucleotide by mass spectrometry, wherein detection of the detector oligonucleotide indicates the presence of the target nucleic acid sequence in the biological sample.

2. A process of claim 1 wherein prior to step b), the target nucleic acid sequence is immobilized onto a solid support to produce an immobilized target nucleic acid sequence.

3. A process of claim 2, wherein immobilization is accomplished by hybridization between a complementary capture nucleic acid molecule, which has been previously immobilized to a solid support, and a portion of the nucleic acid molecule, which is distinct from the target nucleic acid sequence.

4. A process of claim 2, wherein immobilization is accomplished via direct bonding between the solid support and a portion of the nucleic acid molecule, which is distinct from the target nucleic acid sequence.

5. A process of claim 2, wherein the solid support is selected from the group consisting of:

beads, flat surfaces, pins and combs.

6. A process of claim 5, wherein immobilization is accomplished by hybridization between an array of complementary capture nucleic acid molecules, which have been previously immobilized to a solid support, and a portion of the nucleic acid molecule, which is distinct from the target nucleic acid sequence.

7. A process of claim 6, wherein the complementary capture nucleic acid molecules are oligonucleotides or oligonucleotide mimetics.

8. A process of claim 2, wherein the immobilization is reversible.

9. A process of claim 1, wherein prior to step c), the target nucleic acid sequence is amplified.

10. A process of claim 9, wherein the target nucleic acid sequence is amplified by an amplification procedure selected from the group consisting of:

cloning, transcription, the polymerase chain reaction (PCR), the ligase chain reaction (LCR), and strand displacement amplification (SDA).

11. A process of claim 1 wherein the mass spectrometer is selected from the group consisting of:

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF), Electrospray (ES), Ion Cyclotron Resonance (ICR), and Fourier Transform.

12. A process of claim 1, wherein the sample is conditioned by mass differentiating at least two detector oligonucleotides or oligonucleotide mimetics to detect and distinguish at least two target nucleic acid sequences simultaneously.

13. A process of claim 12, wherein the mass differentiation is achieved by differences in the length or sequence of the at least two oligonucleotides.

14. A process of claim 13, wherein the mass differentiation is acheived by the introduction of mass modifying functionalities in the base, sugar or phosphate moiety of the detector oligonucleotides.

15. A process of claim 12, wherein the mass differentiation is achieved by exchange of cations at the phosphodiester bond.

16. A process of claim 1, wherein the nucleic acid molecule obtained from a biological sample is amplified into DNA using mass modified dideoxynucleoside triphosphates and DNA dependent DNA polymerase prior to mass spectrometric detection.

17. A process of claim 1, wherein the nucleic acid molecule obtained from a biological sample is amplified into RNA using mass modified ribonucleoside triphosphates and DNA dependent RNA polymerase prior to mass spectrometric detection.

18. A process of claim 1 wherein the target nucleic acid sequence is indicative of 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 and a bacterial infection.

19. A process for detecting a target nucleic acid sequence present in a biological sample, comprising the steps of:

a) obtaining a nucleic acid molecule containing a target nucleic acid sequence from a biological sample;

b) amplifying the target nucleic acid sequence, thereby obtaining an amplified target nucleic acid sequence;

c) hybridizing a detector oligonucleotide with the amplified target nucleic acid sequence, wherein at least one of the detector oligonucleotide or the amplified target nucleic acid sequence has been conditioned;

d) removing unhybridized detector oligonucleotide;

e) ionizing and volatizing the product of step c); and

f) detecting the detector oligonucleotide by mass spectrometry, wherein detection of the detector oligonucleotide indicates the presence of the target nucleic acid sequence in the biological sample.

20. A process of claim 19, wherein the target nucleic acid is amplified by an amplification procedure selected from the group consisting of:

cloning, transcription, the polymerase chain reaction (PCR), the ligase chain reaction (LCR), and strand displacement amplification (SDA).

21. A process of claim 20, wherein the mass spectrometer is selected from the group consisting of:

Matrix-Assisted Laser Desorption/Ionization, Time-of-Flight (MALDI-TOF), Electrospray (ES), Ion Cyclotron Resonance (ICR), and Fourier Transform.

22. A process of claim 19, wherein the sample is conditioned by mass differentiation.

23. A process of claim 22, wherein the mass differentiation is achieved by mass modifying functionalities attached to primers used for amplifications.

24. A process of claim 22, wherein the mass differentiation is achieved by exchange of cations at the phosphodiester bond.

25. A process of claim 22, wherein the mass differentiation is achieved by introduction of a mass modifying functionality into a base, sugar or phosphate moiety of an amplified nucleic acid molecule.

26. A process of claim 19, wherein the nucleic acid molecule is DNA.

27. A process of claim 19, wherein the nucleic acid molecule is RNA.

28. A process of claim 19, wherein prior to step c) amplified target nucleic acid sequences are immobilized onto a solid support to produce immobilized target nucleic acid sequences.

29. A process of claim 28, wherein immobilization is accomplished by hybridization between a complementary capture nucleic acid molecule, which has been previously immobilized to a solid support, and the target nucleic acid sequence.

30. A process of claim 28, wherein the solid support is selected from the group consisting of:

beads, flat surfaces, pins and combs.

31. A process of claim 28, wherein the immobilization is reversible.

32. A process of claim 19 wherein the target nucleic acid sequence is indicative of 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 and a bacterial infection.

33. A process for detecting a target nucleic acid sequence present in a biological sample, comprising the steps of:

a) obtaining a target nucleic acid sequence from a biological sample;

b) amplifying and conditioning the target nucleic acid sequence, thereby producing amplified and conditioned nucleic acid molecules;

c) digesting the amplified and conditioned nucleic acid molecules using at least one appropriate nucleases, thereby producing conditioned fragments;

d) ionizing and volatizing the conditioned fragments; and

e) detecting the conditioned fragments to determine the presence of the target nucleic acid sequence.

34. A process of claim 33, wherein prior to step d), amplified target nucleic acid sequences are immobilized onto a solid support to produce immobilized target nucleic acid sequences.

35. A process of claim 34, wherein immobilization is accomplished by hybridization between an array of complementary capture nucleic acid molecules, which have been previously immobilized to a solid support, and a portion of the nucleic acid molecule, which is distinct from the target nucleic acid sequence.

36. A process of claim 34, wherein the solid support is selected from the group consisting of:

beads, flat surfaces, pins and combs.

37. A process of claim 34, wherein the complementary capture nucleic acid sequences are oligonucleotides or oligonucleotide mimetics.

38. A process of claim 34, wherein the immobilization is reversible.

39. A process of claim 33 wherein the mass spectrometer is selected from the group consisting of:

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF), Electrospray (ES), Ion Cyclotron Resonance (ICR), and Fourier Transform.

40. A process of claim 33, wherein the amplified nucleic acid molecules are conditioned by mass differentiation.

41. A process of claim 40, wherein the mass differentiation is achieved by exchange of cations at the phosphodiester bond.

42. A process of claim 33, wherein the mass differentiation is achieved by the introduction of mass modifying functionalities in the base, sugar or phosphate moiety of an amplified nucleic acid molecules.

43. A process of claim 33, wherein step a), the target nucleic acid sequence is amplified into DNA using mass modified dideoxynucleoside triphosphates and DNA dependent DNA polymerase.

44. A process of claim 33, wherein step a), the target nucleic acid sequence is amplified into RNA using mass modified ribonucleoside triphosphates and DNA dependent RNA polymerase.

45. A process of claim 33 wherein the target nucleic acid sequence is indicative of 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 and a bacterial infection.