DNA sequencing using fluorescence background electroblotting membrane

• US 5,112,736 A
• Filed: 06/14/1989
• Issued: 05/12/1992
• Est. Priority Date: 06/14/1989
• Status: Expired due to Fees

• Current Assignee: Brigham Young University A Not-For-Profit Corporation of UT, University of Utah A Nonprofit Corporation of UT
• Original Assignee: University of Utah (State of Utah), Brigham Young University (The Church of Jesus Christ of Latter-Day Saints)
• Inventors: Chu, Tun-Jen, Pitt, William G., Caldwell, Karin D.
• Primary Examiner(s): Yarbrough, Amelia Burgess
• Assistant Examiner(s): Marsche, Ardin H.
• Application Number:
  US07/365,693
• Time in Patent Office: 1,063 Days
• Field of Search: 435/6, 435/91, 435/129, 435/291, 435/313, 435/805, 436/501, 436/113, 436/172, 436/800, 436/807, 536/27, 935/17, 935/19, 935/77, 935/86, 935/88
• US Class Current: 435/6.12
• CPC Class Codes: B01D 2323/30 Cross-linking
• CPC Class Codes: B01D 67/0093 Chemical modification
• CPC Class Codes: B01D 67/00931 by introduction of specific groups after membrane formation, e.g. by grafting
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: Y10S 435/805 Test papers
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10S 436/807 Apparatus included in process claim, e.g. physical support structures
• CPC Class Codes: Y10T 436/175383 Ammonia

Abstract

A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

Claims

1. A method for the multiplex sequencing of DNA comprising:

(a) providing a target DNA sample to be sequenced wherein the DNA fragments have been chain terminated and separated according to a specific adenine, guanine, cytosine or thymine base groupings;

(b) subjecting base separated groupings of target DNA fragments to gel electrophoresis to resolve the DNA fragments in each base grouping by chain length;

(c) electroblotting said resolved target DNA fragments from said gel onto the surface of a non-aromatic polymeric microporous membrane said membrane being selected from the group consisting of hydrocarbons, fluorocarbons, chlorofluorocarbons, vinyl alcohols and vinyl chlorides and copolymers and blends thereof and exhibiting low background fluorescence said membrane having been surface modified by subjecting said membrane to an aminating agent in the presence of radio frequency plasma discharge or microwave frequency plasma discharge to contain amino groups in order to physically adsorb said DNA fragments on said membrane surface and washing said membrane to remove unadsorbed DNA fragments;

(d) treating said membrane containing said physically adsorbed DNA fragments with crosslinking means to chemically bind said DNA fragments to said membrane through said amino groups contained on the surface thereof;

(e) subjecting said chemically bound DNA fragments on said membrane to hybridization probing with a tagged probe specific to the sequence of the DNA fragments and washing said membranes to remove probe which has not been hybridized; and

(f) detecting and reading said tagged probes hybridized to said target DNA fragments.

2. A method according to claim 1 wherein said probes are tagged with radiosotopes or fluorophores.

3. A method according to claim 2 wherein said surface modified membrane is a member selected from the group consisting of polypropylene, polyethylene, polytetrafluoroethylene, polyvinylidenefluoride, polyvinylchloride, polyfluoroethylene-propylene, ethylenevinylalcohol, and polyethylene-chlorotrifluoroethylene and blends and copolymers thereof.

4. A method according to claim 3 wherein said aminating group is a member selected from the group consisting of ammonia gas and C₁ -C₁₀ aliphatic or cyclic amines and mixtures thereof.

5. A method according to claim 4 wherein said aminating group is a member selected from the group consisting of ammonia gas, methyl amine, allyl amine, ethylenediamine and diaminocyclohexane and mixtures thereof.

6. A method according to claim 5 wherein the aminating agent is ammonia gas.

7. A method according to claim 6 wherein the membrane has been aminated using radio frequency plasma discharge in the presence of ammonia gas.

8. A method according to claim 7 wherein the membrane is a member selected from the group consisting of polypropylene, polyethylene and polytetrafluoroethylene.

9. A method according to claim 8 wherein the membrane is polypropylene.

10. A method according to claim 9 wherein said crosslinking means comprises irradiating the membrane with ultraviolet light or subjecting the membrane to a chemical cross linking agent.

11. A method according to claim 10 wherein said membrane is subjected to a non-aromatic bifunctional chemical crosslinking agent having an affinity for amino-groups on said DNA fragments and on said membrane to chemically crosslink said DNA to said membrane.

12. A method according to claim 11 wherein said chemical crosslinking agent is a member selected from the group consisting of glutaraldehyde, bisoxiranes, divinylsulfone and dimethylsuberimidate.

13. A method according to claim 12 wherein said chemical crosslinking agent is glutaraldehyde.

14. A method according to claim 13 wherein said membrane is subjected to treatment with ethanolamine to passivate any aldehyde groups which have not reacted with an amine.

15. A method according to claim 14 wherein said probe has been tagged with a fluorophore and is read by means of fluorescent detection.

16. A method according to claim 15 wherein, after said reading, said fluorophore tagged probe is removed from said target DNA fragments bound to said membrane by stripping and said target DNA fragments are reprobed with additional fluorophore tagged probe.

17. A method according to claim 14 wherein said probe has been tagged with a radioisotope and is read by means of an autoradiogram.

18. A method of aminating the surface of a non-aromatic polymeric microporous membrane exhibiting low background fluoroescence, wherein said membrane is selected from the group consisting of hydrocarbons, fluorocarbons, chlorofluorocarbons, vinyl alcohols and vinyl chlorides and copolymers and blends thereof, which comprises subjecting said membrane to an aminating agent in the presence of radio frequency plasma discharge or microwave frequency plasma discharge.

19. A method according to claim 18 wherein said membrane is a member selected from the group consisting of polypropylene, polyethylene, polytetrafluoroethylene, polyvinylidenefluoride, polyvinylchloride, polyfluoroethylene-propylene, ethylenevinylalcohol, and polyethylene-chlorotrifluoroethylene and blends and copolymers thereof.

20. A method according to claim 19 wherein said amination of said surface is accomplished by subjecting said membrane to an aminating agent selected from the group consisting of ammonia gas and C₁ -C₁₀ aliphatic or cyclic amines and mixtures thereof.

21. A method according to claim 20 wherein said aminating agent is a member selected from the group consisting of ammonia gas, methyl amine, allyl amine, ethylenediamine and diaminocyclohexane and mixtures thereof.

22. A method according to claim 21 wherein the aminating agent is ammonia gas.

23. A method according to claim 22 wherein the membrane has been aminated using radio frequency plasma discharge in the presence of ammonia gas.

24. A method according to claim 23 wherein the membrane is a member selected from the group consisting of polypropylene, polyethylene and polytetrafluoroethylene.

25. A method according to claim 24 wherein the membrane is polypropylene.

26. An aminated polypropylene membrane according to claim 25.