Composition and method for array hybridization

• US 7,618,777 B2
• Filed: 03/16/2005
• Issued: 11/17/2009
• Est. Priority Date: 03/16/2005
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Barrett, Michael, Myerson, Joel
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US11/082,476
• Publication Number:
  US 20060210997A1
• Time in Patent Office: 1,707 Days
• Field of Search: 435/6, 536/24.3, 536/24.33
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer

Abstract

The present disclosure relates to a system, composition, and method for hybridizing a microarray. The composition includes a superwetting agent. The method includes contacting the microarray with an aqueous mixture including the superwetting agent.

Claims

1. A method of hybridizing comprising:

contacting a first oligonucleotide bound to a silaceous surface with a second unbound oligonucleotide in the presence of an aqueous mixture comprising a superwetting agent,

wherein said contacting is done under conditions that provide for hybridization of the first oligonucleotide with the second oligonucleotide, and

wherein the contacting is done in the presence of a moving gas bubble that dispels the aqueous mixture across said silaceous surface.

2. The method according to claim 1 wherein the superwetting agent comprises an organosilicone wetting agent, an organofluorine wetting agent, a hydrocarbyl wetting agent, or mixtures thereof.

3. The method according to claim 2 wherein the superwetting agent is a polyether siloxane copolymer.

4. The method according to claim 2 wherein the superwetting agent is an organofluorine compound selected from the group consisting of compounds of the formulas:

{(C_nF_2n+1—

C_n′

H_2n′

)_p—

SO_m—

R}_x 

 

a)

wherein m is from 1 to 3;

n is from about 3 to about 20;

n′

is from about 0 to about 20;

p is from 1 to 2;

x is from about 1 to about 100;

R is hydrogen, (C_1-10) saturated alkyl, or (C_2-10) unsaturated alkyl;

or salts thereof;

(C_nF_2n+1—

C_n′

H_2n′

)_p—

R¹ 

 

b)

wherein

R¹ is monovalent or divalent radical selected from

—

H,

halo,

—

OH,

(C_1-10) alkyl,

(C_2-10) unsaturated alkyl,

—

CH₂—

O—

C(═

O)—

(C_1-20) alkyl

—

CH₂—

O—

C(═

O)—

(C_2-20) unsaturated alkyl

—

O—

P(═

O)(OH)₂,

—

O—

P(═

O)(—

OH)—

,

—

O—

P(═

O)(OH)(—

O—

CH₂—

CH₂—

)_o—

OH,

—

CO₂H,

—

⁽⁺⁾N(R²)²—

O<sup>(−

)</sup>,

—

⁽⁺⁾N(R²)²—

CH ₂—

CO₂H,

—

O—

C(═

O)—

CH₂—

CH(SO₃H)—

C(═

O)—

O—

,

—

O(CH₂—

CH₂—

O)y—

H,

—

S—

CH₂—

CH₂—

C(═

O)—

OH, and

(C_1-10)alkyl-C(═

O)—

O—

CH—

CH₂—

⁽⁺⁾N(R²)₂—

(—

CH₂)_1-4—

CO₂H,

each R² is independently hydrogen, or (C_1-10) alkyl,

m is from 1 to 2;

n is from about 1 to about 20;

n′

is from about 1 to about 20;

o is from about 1 to about 10;

p is from 1 to 2; and

y is from 0 to about 20;

or salts thereof;

5. The method according to claim 2 wherein the hydrocarbyl wetting agent is an alkoxylated hydrocarbyl compound of the formula:

6. The method according to claim 1 wherein the buffer capacity and the pH of the aqueous mixture is at from about 5 to about 9.

7. The method according to claim 1 wherein contacting is accomplished at a temperature of from about 30°

C. to about 70°

C.

8. The method according to claim 1 wherein the aqueous mixture further comprises at least one of:

an organosulfonic acid;

an organosulfate surfactant;

an organopolyalkoxylate;

a source of a monovalent cation;

a chelator;

or

mixtures thereof.

9. The method according to claim 1 wherein the aqueous mixture further comprises a second oligonucleotide material.

10. The method according to claim 1 further comprising a second contacting of the surface with an aqueous mixture comprising a superwetting agent and a second oligonucleotide material.

11. The method according to claim 1 wherein the surface is a silane surface-modified siliceous microarray.

12. The method of claim 1, wherein the aqueous mixture is a buffer comprising an organic compound, an inorganic compound, or mixtures thereof.

13. The method of claim 12, wherein the buffer comprises one or more of

a source of a monovalent cation;

a water soluble organosulfonic acid or salt thereof;

a chelator or salt thereof;

an organosulfonic surfactant or salt thereof;

an organopolyalkoxylate; and

an aqueous carrier.

14. The method of claim 13, wherein

the source of a monovalent cation is an alkali metal halide salt;

the organosulfonic acid is a morpholino-substituted alkyl sulfonic acid;

the chelator is a divalent cation chelating agent;

the organosulfate surfactant is a (C₈-C₁₆)alkyl sulfate;

the organopolyalkoxylate is an alkoxylated alkylphenol;

the superwetting agent is a polyether siloxane copolymer; and

the aqueous carrier is water.

15. The method of claim 13, wherein

the superwetting agent is present in the buffer from about 0.05 to about 50 weight percent of the total buffer;

the water soluble organosulfonic acid is present in the buffer from about 0.01 to about 10 weight percent of the total buffer;

the organosulfate surfactant is present in the buffer from about 0.1 to about 50 weight percent of the total buffer;

the organopolyalkoxylate is present in the buffer from about 0.1 to about 50 weight of the total buffer;

the chelator is present in the buffer from about 0.01 to about 10 weight percent of the total buffer; and

the source of a monovalent cation is present in the buffer from about 0.01 to about 50 weight percent of the total buffer.

16. The method of claim 2, wherein the superwetting agent is selected from the group consisting of:

an organosilicone compound of the formula