Buffer composition and method for hybridization of microarrays on adsorbed polymer siliceous surfaces

• US 6,753,145 B2
• Filed: 07/05/2001
• Issued: 06/22/2004
• Est. Priority Date: 07/05/2001
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Shannon, Karen W., Collins, Patrick J., Lefkowitz, Steven M., Holcomb, Nelson R.
• Primary Examiner(s): HORLICK, KENNETH R
• Assistant Examiner(s): HORLICK, KENNETH R
• Application Number:
  US09/900,084
• Publication Number:
  US 20030013092A1
• Time in Patent Office: 1,083 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/287.2, 435/287.3, 435/7.1, 536/24.3, 536/23.1, 536/24.1, 935/6, 436/518, 436/501, 436/514, 436/807
• US Class Current: 435/6.16
• CPC Class Codes: C12Q 1/689 for bacteria

Abstract

A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving theintactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.

Claims

1. A method of hybridizing a microarray of oligonucleotides bound to a polymer adsorbed on a surface of a siliceous substrate with a nucleic acid material comprising the step of

incubating the nucleic acid material with the microarray of oligonucleotides on the adsorbed polymer surface in a hybridization solution at a hybridization temperature ranging from about 55°

C. to about 70°

C. so as to hybridize the nucleic acid material,

wherein the hybridization solution comprises a buffer composition that comprises a pH within a range of pH 6.4 to 7.5, a non-chelating buffering agent that maintains the pH within the pH range, and a monovalent cation in a monovalent cation concentration ranging from about 0.01 M to about 2.0 M.

2. The method of claim 1, wherein in the step of incubating, the non chelating buffering agent is selected from a group consisting of 2-[N-morpholino]ethanesulfonic acid (MES), 3-(N-Morpholine)propanesulfonic acid (MOPS), Piperazine-N,N′

-bis(2-ethansulfonic acid (PIPES), Tris(hydroxymethyl)aminomethane hydrochloride (TRIS-HCl), Hydroxyethylpiperazine-N′

-2-ethanesulfonic acid (HEPES), and N-Tris(hydroxymethyl)methylglycine (TRICINE).

3. The method of claim 1, wherein in the step of incubating, the monovalent cation is selected from a salt consisting of one or more of LiCl, NaCl and KCl and the monovalent cation concentration ranges from about 0.1 M to about 2.0 M.

4. The method of claim 1, wherein the adsorbed polymer surface comprises a polycationic polymer.

5. The method of claim 4, wherein the polycationic polymer is selected from a group consisting of one or more of polyethylenediamine, poly-acrylamide, poly-L-arginine, poly-L-histidine, and poly-L-lysine.

6. The method of claim 1, wherein in the step of incubating, the buffer composition further comprises a chelating agent selected from a group consisting of one or more of ethylenediaminetetraacetic acid (EDTA),trans-1, 2-diaminocyclohexanetetraacetic acid (CDTA) and diethylenetriaminopentaacetic acid (DTPA) that has a chelating agent concentration of less than about 100 μ

M.

7. The method of claim 1, wherein in the step of incubating, the buffer composition further comprises an ionic surfactant selected from a group consisting of one or more of sodium dodecyl sulfate (SDS), lithium lauryl sulfate (LLS), N-lauryl sarcoside, acylated polypeptides, linear alkybenzene sulfonates, lignin sulfonates, paraffin sulfonates, sulfosuccinate esters, alkylnaphthalene sulfonates, isethionates, alkanolamine condensates, and N-alkylpyrrolidones, and wherein the step of incubating comprises using a hybridization chamber, and the ionic surfactant is provided in an amount sufficient to wet surfaces of the hybridization chamber and loosen bubbles impinged on the surfaces of the hybridization chamber.

8. The method of claim 7, wherein the amount of ionic surfactant is a surfactant concentration ranging from about 0.01% to about 0.2% (w/v).

9. The method of claim 1, wherein the buffer composition has a total cation concentration of about 0.02 M to about 2.0 M.

10. The method of claim 1, wherein in the step of incubating, the non chelating buffering agent is 2-[N-morpholino]ethanesulfonic acid (MES), the monovalent cation is LiCl, the monovalent cation concentration is greater than or equal to 300 mM, the pH is within the range of pH 6.6 to 6.8.

11. The method of claim 10, wherein in the step of incubating, the buffer composition further comprises one or both of a chelating agent ethylenediaminetetraacetic acid EDTA having a chelating agent concentration of about 50 μ

M, and an ionic surfactant selected from sodium dodecyl sulfate (SDS), lithium lauryl sulfate (LLS) having a surfactant concentration that ranges from about 0.02% to about 0.1% (w/v), and the buffer composition has a total cation concentration of about 750 mM.

12. The method of claim 1, before the step of incubating, further comprising the step of combining the nucleic acid material with the buffer composition.

13. The method of claim 1, after the step of incubating, further comprising the step of interrogating the hybridized microarray at a first location, the first location being a physical location either where the incubation of the microarray is performed or another location separate from the microarray incubation location.

14. The method of claim 13, further comprising the step of transmitting data representing a result of the interrogation.

15. The method of claim 14, further comprising the step of receiving the transmitted data at a second location, the second location being a physical location that is different from one or both of the first location where the microarray interrogation is performed and the microarray incubation location.

16. The method of claim 15, wherein the first location is remote from the second location, the remote first location being physically separated from the second location.

17. A method of performing a high temperature hybridization assay comprising the step of:

incubating a nucleic acid material with a microarray of oligonucleotides in a hybridization solution at a hybridization temperature ranging from about 55°

C. to about 70°

C. so as to hybridize the nucleic acid material,

wherein the microarray comprises a siliceous substrate with an adsorbed polymer surface and oligonucleotides bound to the adsorbed polymer surface, and

wherein the hybridization solution comprises a pH within a range of pH 6.4 and 7.5 and a buffer composition, the buffer composition comprising a non-chelating buffering agent that maintains the pH within the range and a monovalent cation having a monovalent cation concentration ranging from 0.01 M and 2.0 M.

18. A method of hybridizing a microarray of oligonucleotides with a nucleic acid material comprising the step of:

incubating the nucleic acid material with the microarray of oligonucleotides in a hybridization solution at a hybridization temperature ranging from about 55°

C. to about 70°

C. so as to hybridize the nucleic acid material, the oligonucleotides being bound to a polymer coating adsorbed on a surface of a siliceous substrate, the adsorbed polymer coating being non-covalently bound to the siliceous substrate surface,

wherein the hybridization solution comprises a buffer composition that comprises a pH within a range of pH 6.4 to 7.5, a non-chelating buffering agent that maintains the pH within the pH range, and a monovalent cation in a monovalent cation concentration ranging from about 0.01 M to about 2.0 M.

19. The method of claim 18, wherein the non chelating buffering agent is 2-[N-morpholino]ethanesulfonic acid (MES), the monovalent cation being LiCl, the monovalent cation concentration being greater than or equal to about 300 mM, the pH being within the range of about pH 6.6 to about 6.8, and wherein the adsorbed polymer coating is a polycationic polymer.

20. A method of reducing surface degradation to a microarray of oligonucleotides during a high temperature hybridization assay comprising:

incubating a nucleic acid material with the microarray of oligonucleotides in a hybridization solution at a hybridization temperature ranging from about 55°

C. to about 70°

C. so as to hybridize the nucleic acid material, the oligonucleotides being bound to a polycationic polymer that is adsorbed to a surface of a siliceous substrate, the adsorbed polycationic polymer being non-covalently bound to the siliceous substrate surface,

wherein the hybridization solution comprises a buffer composition that comprises a pH within a range of pH 6.4 to 7.5, a non-chelating buffering agent that maintains the pH within the pH range, and a monovalent cation in a monovalent cation concentration ranging from about 0.01 M to about 2.0 M.