DNA sequencing, mapping, and diagnostic processes using hybridization and stable isotope labels of DNA

• US 5,780,232 A
• Filed: 05/28/1996
• Issued: 07/14/1998
• Est. Priority Date: 05/28/1996
• Status: Expired due to Fees

• Current Assignee: ATOM Sciences Corporation
• Original Assignee: ATOM Sciences Corporation
• Inventors: Arlinghaus, Heinrich F., Jacobson, K. Bruce
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/654,181
• Time in Patent Office: 777 Days
• Field of Search: 435/6, 435/69.1, 435/810, 436/501, 536/22.1, 536/23.1, 536/24.1, 536/24.3-33, 536/25.3, 935/77, 935/78, 935/86, 935/87, 422/68.1, 422/69, 422/78, 422/80, 422/82.05, 422/82.09
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

A DNA sequencing, mapping, and diagnostic process which includes the steps of labeling nucleotide segments or peptide nucleic acids (PNAs) with one or more atoms of specific stable or long-lived radioactive isotopes of a selected element that do not normally occur in DNAs, ODNs or PNAs such that the nucleotide segment or PNA has specific stable or long-lived radioactive isotope of a specified selected element at a terminal or an interior position; hybridizing the labeled nucleotide segment or PNA to complementary nucleic acid segments or PNAs which are fixed on a hybridization surface; and, using mass spectrometric techniques, including RIS, to analyze the presence and position of the labeled hybridized nucleotide segments or PNAs which are bound to the fixed nucleotide segments or PNAs.

Claims

1. A DNA sequencing, mapping, and diagnostic process using known individual isotopes, including stable isotopes and long-lived radioactive isotopes, associated with individual oligodeoxynucleotides (ODNs) or peptide nucleic acids (PNAs), said process comprising the steps of:

labeling nucleotide segments or PNAs with said known isotopes of an element that does not normally occur in DNAs or ODNs;

causing said labeled, complementary, free nucleotide segments or PNAs to hybridize to fixed nucleotide segments or PNAs, said fixed nucleotide segments or PNAs being immobilized in distinct positions on a hybridization surface in an array such that said nucleotide segments or PNAs with known sequences define sequences of nucleotide segments or PNAs that become hybridized;

rinsing non-hybridized labeled nucleotide segments or PNAs from said hybridization array; and

using mass spectrometric methods to analyze the presence and position on said array of said hybridized, labeled complementary nucleotide segments or PNAs and identifying said isotopes.

2. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said labeled nucleotide segments are oligodeoxynucleotides (ODNs) and said fixed nucleotide segments are DNAs.

3. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said labeled nucleotide segments are DNAs and said fixed nucleotide segments are oligodeoxynucleotides (ODNs).

4. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said labeled nucleotide segments or peptide nucleic acids (PNAs) are DNAs and said fixed nucleotide segments or PNAs are PNAs.

5. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said labeled nucleotide segments or peptide nucleic acids (PNAs) are PNAs and said fixed nucleotide segments or PNAs are DNAs.

6. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said hybridization array surface is composed of an appropriate available chemical material, said material including those selected from the group consisting of glass, Pyrex, silicon oxide, nylon membranes, polypropylene, gold surfaces and platinum surfaces.

7. The DNA sequencing, mapping, and diagnostic process of claim 6 wherein a plurality of said known isotopes are used to individually label several nucleotide segments so that data is multiplexed.

8. The DNA sequencing, mapping, and diagnostic process of claim 7 wherein said isotopes used to label said nucleotide segments are enriched several-fold over natural abundance to make them easily detectable and allow many non-isobaric isotopes to be used simultaneously to provide a multiplex type of analysis.

9. The DNA sequencing, mapping, and diagnostic process of claim 8 wherein said hybridization array surface is used to detect mutations in DNA by designing said nucleotide segments to contain sequences that would distinguish normal from abnormal DNA sequences of the gene in question.

10. The DNA sequencing, mapping, and diagnostic process of claim 8 wherein said hybridization surface is designed to provide an error check for raw DNA sequence data obtained by other techniques such as gel electrophoresis.

11. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said mass spectrometric methods used to detect the presence of said labeled, complementary hybridized nucleotide segments on said hybridization array surface include at least one method selected from the group consisting of time-of-flight, quadrupole, magnetic sector and ion trap mass spectrometry.

12. The DNA sequencing, mapping, and diagnostic process of claim 1 wherein said labeled, complementary hybridized nucleotide segments detected on said hybridization array surface are analyzed by surface analysis techniques which require vaporization or those techniques which do not require vaporization.

13. The DNA sequencing, mapping, and diagnostic process of claim 12 wherein said labeled, complementary hybridized nucleotide segments are vaporized and then analyzed by techniques which require ionization or those techniques not requiring ionization.

14. The DNA sequencing, mapping, and diagnostic process of claim 13 wherein said labeled, complementary hybridized nucleotide segments are vaporized and then analyzed using non-ionization techniques selected from the group of methods consisting of resonant and non-resonant Raman spectroscopy, absorption spectroscopy, and optical emission of laser ablated material and ion beam sputtered material.

15. The DNA sequencing, mapping, and diagnostic process of claim 13 wherein said labeled, complementary hybridized nucleotide segments disposed on said hybridization surface are vaporized and analyzed using resonant and non-resonant ionization methods.

16. The DNA sequencing, mapping, and diagnostic process of claim 15 wherein said vaporization of said labeled, complementary hybridized nucleotide segments which are vaporized and then analyzed using resonance ionization method is performed by techniques selected from the group consisting of ion beam sputtering, sputter-initiated resonance ionization spectroscopy (SIRIS), laser ablation, laser-induced desorption, laser atomization resonance ionization spectroscopy (LARIS) and thermal techniques.

17. The DNA sequencing, mapping, and diagnostic process of claim 16 wherein said lasers used in performance of said resonance ionization are wavelength tunable lasers pumped by lasers selected from the group consisting of continuous wave lasers and pulsed lasers.

18. The DNA sequencing, mapping, and diagnostic process of claim 17 wherein said wavelength tunable lasers are selected from the group consisting of dye, solid-state, and optical parametric oscillator lasers.

19. The DNA sequencing, mapping, and diagnostic process of claim 17 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG) Cu-vapor, and sub-nanosecond lasers.

20. The DNA sequencing, mapping, and diagnostic process of claim 15 wherein said vaporization of said labeled, complementary hybridized nucleotide segments which are vaporized and then analyzed using non-resonant ionization is performed by techniques selected from the group consisting of ion beam sputtering, laser ablation, laser-induced desorption, and thermal techniques.

21. The DNA sequencing, mapping, and diagnostic process of claim 20 wherein said non-resonant ionization is performed using a method selected from the group consisting of continuous wave lasers, pulsed lasers and electrons.

22. The DNA sequencing, mapping, and diagnostic process of claim 21 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG), Cu-vapor, and sub-nanosecond lasers.

23. The DNA sequencing, mapping, and diagnostic process of claim 12 wherein said labeled, complementary hybridized nucleotide segments which are analyzed by techniques not requiring vaporization are analyzed by methods requiring ionization or those methods not requiring ionization.

24. The DNA sequencing, mapping, and diagnostic process of claim 23 wherein said labeled, complementary hybridized nucleotide segments which are non-vaporized are analyzed by performance of surface analysis methods not requiring ionization selected from the group consisting of surface-enhanced Raman spectroscopy (SERS), second-harmonic generation (SHG), Auger electron spectroscopy and x-ray photon spectroscopy.

25. The DNA sequencing, mapping, and diagnostic process of claim 12 wherein said labeled, complementary hybridized nucleotide segments are vaporized and then analyzed by performance of methods selected from the group consisting of secondary ion mass spectroscopy (SIMS), laser ionization mass spectroscopy (LIMS), and laser microprobe mass analysis (LAMMA).

26. A DNA sequencing, mapping, and diagnostic process using known individual isotopes, including stable isotopes and long-lived radioactive isotopes, associated with individual oligodeoxynucleotides (ODNs), said process comprising the steps of:

labeling nucleotide segments with said known isotopes of an element that does not normally occur in DNAs or ODNs, said labeling nucleotides segments being one of said DNAs and said ODNs;

causing said labeled, complementary, free nucleotide segments to hybridize to fixed nucleotide segments, said fixed nucleotide segment being the other of said DNAs and said ODNs, said fixed nucleotide segments being immobilized in distinct positions on a hybridization surface in an array such that said nucleotide segments of said DNAs and said ODNs with known sequences define sequences of nucleotide segments that become hybridized;

rinsing non-hybridized labeled nucleotide segments from said hybridization array; and

using mass spectrometric methods to analyze the presence and position on said array of said hybridized, labeled complementary nucleotide segments or ODNs and identifying said isotopes.

27. The DNA sequencing, mapping, and diagnostic process of claim 26 wherein said hybridization array surface is composed of an appropriate available chemical material, said material including those selected from the group consisting of glass, Pyrex, silicon oxide, nylon membranes, polypropylene, gold surfaces and platinum surfaces.

28. The DNA sequencing, mapping, and diagnostic process of claim 27 wherein a plurality of said known isotopes are used to individually label several nucleotide segments so that data is multiplexed.

29. The DNA sequencing, mapping, and diagnostic process of claim 28 wherein said isotopes used to label said nucleotide segments are enriched several-fold over natural abundance to make them easily detectable and allow many non-isobaric isotopes to be used simultaneously to provide a multiplex type of analysis.

30. The DNA sequencing, mapping, and diagnostic process of claim 29 wherein said hybridization array surface is used to detect mutations in DNA by designing said nucleotide segments to contain sequences that would distinguish normal from abnormal DNA sequences of the gene in question.

31. The DNA sequencing, mapping, and diagnostic process of claim 29 wherein said hybridization array surface is designed to provide an error check for raw DNA sequence data obtained by other techniques such as gel electrophoresis.

32. The DNA sequencing, mapping, and diagnostic process of claim 26 wherein said mass spectrometric methods used to detect the presence of said labeled, complementary hybridized nucleotide segments on said hybridization array surface include at least one method selected from the group consisting of time-of-flight, quadrupole, magnetic sector and ion trap mass spectrometry.

33. The DNA sequencing, mapping, and diagnostic process of claim 26 wherein said labeled, complementary hybridized nucleotide segments detected on said hybridization array surface are analyzed by surface analysis techniques which require vaporization or those techniques which do not require vaporization.

34. The DNA sequencing, mapping, and diagnostic process of claim 33 wherein said labeled, complementary hybridized nucleotide segments are vaporized and then analyzed by techniques which require ionization or those techniques not requiring ionization.

35. The DNA sequencing, mapping, and diagnostic process of claim 34 wherein said labeled hybridized nucleotide segments which are vaporized are analyzed using non-ionization techniques selected from the group of methods consisting of resonant and non-resonant Raman spectroscopy, absorption spectroscopy, and optical emission of laser ablated or ion beam sputtered material.

36. The DNA sequencing, mapping, and diagnostic process of claim 34 wherein said labeled, complementary hybridized nucleotide segments disposed on said hybridization surface are vaporized and then analyzed using resonant and non-resonant ionization methods.

37. The DNA sequencing, mapping, and diagnostic process of claim 36 wherein said vaporization of said labeled, complementary hybridized nucleotide segments which are vaporized and then analyzed using resonance ionization method is performed by techniques selected from the group consisting of ion beam sputtering, sputter-initiated resonance ionization spectroscopy (SIRIS), laser ablation, laser-induced desorption, laser atomization resonance ionization spectroscopy (LARIS) and thermal techniques.

38. The DNA sequencing, mapping, and diagnostic process of claim 37 wherein said lasers used in performance of said resonance ionization are wavelength tunable lasers pumped by lasers selected from the group consisting of continuous wave lasers and pulsed lasers.

39. The DNA sequencing, mapping, and diagnostic process of claim 38 wherein said wavelength tunable lasers are selected from the group consisting of dye, solid-state and optical parametric oscillator lasers.

40. The DNA sequencing, mapping, and diagnostic process of claim 38 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG), Cu-vapor, and sub-nanosecond lasers.

41. The DNA sequencing, mapping, and diagnostic process of claim 36 wherein said vaporization of said labeled, complementary hybridized nucleotide segments which are vaporized and then analyzed using non-resonant ionization is performed by techniques selected from the group consisting of ion beam sputtering, laser ablation, laser-induced desorption, and thermal techniques.

42. The DNA sequencing, mapping, and diagnostic process of claim 41 wherein said lasers used in performance of said non-resonant ionization are selected from the group consisting of continuous wave and pulsed lasers.

43. The DNA sequencing, mapping, and diagnostic process of claim 42 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG), Cu-vapor, and sub-nanosecond lasers.

44. The DNA sequencing, mapping, and diagnostic process of claim 33 wherein said labeled, complementary hybridized nucleotide segments which are analyzed by techniques not requiring vaporization are analyzed by methods requiring ionization or those methods not requiring ionization.

45. The DNA sequencing, mapping, and diagnostic process of claim 44 wherein said labeled, complementary hybridized nucleotide segments which are non-vaporized are analyzed by performance of surface analysis methods not requiring ionization selected from the group consisting of surface-enhanced Raman spectroscopy (SERS), second-harmonic generation (SHG), Auger electron spectroscopy and x-ray photon spectroscopy.

46. The DNA sequencing, mapping, and diagnostic process of claim 33 wherein said labeled, complementary hybridized nucleotide segments are vaporized and than analyzed by performance of methods selected from the group consisting of secondary ion mass spectroscopy (SIMS), laser ionization mass spectroscopy (LIMS), and laser microprobe mass analysis (LAMMA).

47. A DNA sequencing, mapping, and diagnostic process using known individual isotopes, including stable isotopes and long-lived radioactive isotopes, associated with individual oligodeoxynucleotides (ODNs) or peptide nucleic acids (PNAs), said process comprising the steps of:

labeling nucleotide segments of PNAs with said known isotopes of an element that does not normally occur in DNAs or PNAs, said labeling nucleotide segments or PNAs being one of said PNAs and said DNAs;

causing said labeled, complementary, free nucleotide segments or PNAs to hybridize to fixed nucleotide segments or PNAs, one of said fixed or free nucleotide segments or PNAs being PNAs, said fixed nucleotide segments or PNAs being immobilized in distinct positions on a hybridization surface in an array such that said PNAs with known sequences define sequences of nucleotide segments that become hybridized;

rinsing non-hybridized labeled nucleotide segments or PNAs from said hybridization array; and

using mass spectrometric methods to analyze the presence and position on said array of said hybridized, labeled complementary nucleotide segments or PNAs and identifying said isotopes.

48. The DNA sequencing, mapping, and diagnostic process of claim 47 wherein said hybridization array surface is composed of an appropriate available chemical material, said material including those selected from the group consisting of glass, Pyrex, silicon oxide, nylon membranes, polypropylene, gold surfaces and platinum surfaces.

49. The DNA sequencing, mapping, and diagnostic process of claim 48 wherein a plurality of said known isotopes are used to individually label several nucleotide segments or PNAs so that data is multiplexed.

50. The DNA sequencing, mapping, and diagnostic process of claim 49 wherein said isotopes used to label said nucleotide segments or PNAs are enriched several-fold over natural abundance to make them easily detectable and allow many non-isobaric isotopes to be used simultaneously to provide a multiplex type of analysis.

51. The DNA sequencing, mapping, and diagnostic process of claim 50 wherein said hybridization array surface is used to detect mutations in DNA by designing said nucleotide segments or PNAs to contain sequences that would distinguish normal from abnormal DNA sequences of the gene in question.

52. The DNA sequencing, mapping, and diagnostic process of claim 50 wherein said hybridization surface is designed to provide an error check for raw DNA sequence data obtained by other techniques such as gel electrophoresis.

53. The DNA sequencing, mapping, and diagnostic process of claim 47 wherein said mass spectrometric methods used to detect the presence of said labeled, complementary hybridized nucleotide segments or PNAs on said hybridization array surface include at least one method selected from the group consisting of time-of-flight, quadrupole, magnetic sector and ion trap mass spectrometry.

54. The DNA sequencing, mapping, and diagnostic process of claim 47 wherein said labeled, complementary hybridized nucleotide segments or PNAs detected on said hybridization array surface are analyzed by surface analysis techniques which require vaporization or those techniques which do not require vaporization.

55. The DNA sequencing, mapping, and diagnostic process of claim 54 wherein said labeled, complementary hybridized nucleotide segments or PNAs are vaporized and then analyzed by techniques which require ionization or those techniques not requiring ionization.

56. The DNA sequencing, mapping, and diagnostic process of claim 55 wherein said labeled hybridized nucleotide segments or PNAs which are vaporized are analyzed using non-ionization techniques selected from the group of methods consisting of resonant and nonresonant Raman spectroscopy, absorption spectroscopy, and optical emission of laser ablated or ion beam sputtered material.

57. The DNA sequencing, mapping, and diagnostic process of claim 55 wherein said labeled, complementary hybridized nucleotide segments or PNAs disposed on said hybridization surface are vaporized and then analyzed using resonant and non-resonant ionization methods.

58. The DNA sequencing, mapping, and diagnostic process of claim 57 wherein said vaporization of said labeled, complementary, hybridized nucleotide segments or PNAs which are vaporized and then analyzed using resonance ionization method is performed by techniques selected from the group consisting of ion beam sputtering, sputter-initiated resonance ionization spectroscopy (SIRIS), laser ablation, laser-induced desorption, laser atomization resonance ionization spectroscopy (LARIS) and thermal techniques.

59. The DNA sequencing, mapping, and diagnostic process of claim 58 wherein said lasers used in performance of said resonance ionization are wavelength tunable lasers pumped by lasers selected from the group consisting of continuous wave lasers and pulsed lasers.

60. The DNA sequencing, mapping, and diagnostic process of claim 59 wherein said wavelength tunable lasers are selected from the group consisting of dye, solid-state and optical parametric oscillator lasers.

61. The DNA sequencing, mapping, and diagnostic process of claim 59 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG), Cu-vapor, and sub-nanosecond lasers.

62. The DNA sequencing, mapping, and diagnostic process of claim 57 wherein said vaporization of said labeled, complementary, hybridized nucleotide segments or PNAs which are vaporized and then analyzed using non-resonant ionization is performed by techniques selected from the group consisting of ion beam sputtering, laser ablation, laser-induced desorption and thermal techniques.

63. The DNA sequencing, mapping, and diagnostic process of claim 62 wherein said non-resonant ionization is performed using a method selected from the group consisting of continuous wave lasers, pulsed lasers and electrons.

64. The DNA sequencing, mapping, and diagnostic process of claim 63 wherein said pulsed lasers are selected from the group consisting of excimer, neodymium ion doped yttrium aluminum garnet crystal (Nd:

YAG), Cu-vapor, and sub-nanosecond lasers.

65. The DNA sequencing, mapping, and diagnostic process of claim 54 wherein said labeled, complementary, hybridized nucleotide segments or PNAs which are analyzed by techniques not requiring vaporization are analyzed by methods requiring ionization or those methods not requiring ionization.

66. The DNA sequencing, mapping and diagnostic process of claim 65 wherein said labeled, complementary, hybridized nucleotide segments or PNAs which are non-vaporized are analyzed by performance of surface analysis methods not requiring ionization selected from the group consisting of surface-enhanced Raman spectroscopy (SERS), second-harmonic generation (SHG), Auger electron spectroscopy and x-ray photon spectroscopy.

67. The DNA sequencing, mapping, and diagnostic process of claim 54 wherein said labeled, complementary, hybridized nucleotide segments or PNAs are vaporized and then analyzed by performance of methods selected from the group consisting of secondary ion mass spectroscopy (SIMS), laser ionization mass spectroscopy (LIMS), and laser microprobe mass analysis (LAMMA).