Spatially-addressable immobilization of anti-ligands on surfaces

• US 5,482,867 A
• Filed: 04/23/1993
• Issued: 01/09/1996
• Est. Priority Date: 11/13/1989
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymax Incorporated
• Inventors: Barrett, Ronald W., Pirrung, Michael C., Holmes, Christopher P., Sundberg, Steven A., Stryer, Lubert
• Primary Examiner(s): Scheiner, Toni R.
• Assistant Examiner(s): Green, Lora M.
• Application Number:
  US08/054,121
• Time in Patent Office: 991 Days
• Field of Search: 427/338, 427/2.13, 430/270, 430/343, 430/371, 435/7.1, 435/7.5, 435/7.93, 436/501, 436/518, 436/527
• US Class Current: 436/518
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C07D 233/38 with acyl radicals or hetero atoms directly attached to ring nitrogen atoms
• CPC Class Codes: C07D 495/04 Ortho-condensed systems
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: G01N 33/552 Glass or silica
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Methods and compositions are described for immobilizing anti-ligands, such as antibodies or antigens, hormones or hormone receptors, oligonucleotides, and polysaccharides on surfaces of solid substrates for various uses. The methods provide surfaces covered with caged binding members which comprise protecting groups capable of being removed upon application of a suitable energy source. Spatially addressed irradiation of predefined regions on the surface permits immobilization of anti-ligands at the activated regions on the surface. Cycles of irradiation on different regions of the surface and immobilization of different anti-ligands allows formation of an immobilized matrix of anti-ligands at defined sites on the surface. The immobilized matrix of anti-ligands permits simultaneous screenings of a liquid sample for ligands having high affinities for certain anti-ligands of the matrix. A preferred embodiment of the invention involves attaching photoactivatable biotin derivatives to a surface. Photolytic activation of the biotin derivatives forms biotin analogs having strong binding affinity for avidin. Biotinylated anti-ligands can be immobilized on activated regions of the surface previously treated with avidin.

Claims

1. A method for forming predefined regions on a surface of a solid support, the predefined regions capable of selectively immobilizing an anti-ligand, the method comprising:

a) attaching to the surface a caged biotin analog having a low affinity for (i) the anti-ligand or (ii) a specific binding substance capable of binding an anti-ligand, said caged biotin analog comprising a photolabile chemical protecting group, which chemical protecting group is removable by irradiation to convert said caged biotin analog to a biotin analog capable of non-covalently immobilizing (i) the anti-ligand or (ii) the specific binding substance by an interaction having an affinity constant of 107 or stronger; and

b) selectively irradiating a predefined region of the surface to convert the caged biotin analogs in the predefined region to the biotin analog capable of non-covalently immobilizing (i) the anti-liqand or (ii) the specific binding substance.

2. The method of claim 1 wherein the caged biotin analog comprises the formula:

##STR32## wherein X and Z are selected from the group consisting of a) hydrogen,

b) oxycarbonyls of lower alkyl aryl and benzyl groups,

c) a nitroveratryloxycarbonyl group,

d) a nitropiperonyloxycarbonyl group where Z is hydrogen and R is p-nitrophenol formate,

e) ##STR33## wherein R₁ and R₂ are hydrogen, lower alkyl, aryl, benzyl, halogen, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, sulfonate, formamido or phosphido groups,

f) ##STR34## wherein R₁ and R₂ are hydrogen, lower alkyl, aryl, benzyl, pyrenyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino nitro, carboxyl, formate, formamido, or phosphido groups and R₃ and R₄ are hydrogen, lower alkyl, aryl, benzyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formamido or phosphido groups;

g) ##STR35## wherein R₁ and R₂ are hydrogen, lower alkyl, aryl benzyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formamido or phosphido groups, and

h) ##STR36## wherein R₁, R₂, R₃ and R₄ are hydrogen, lower alky, aryl, benzyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formamido or phosphido groups;

provided that when X is hydrogen, Z is not hydrogen or methyloxycarbonyl and provided that when Z is hydrogen, X is not hydrogen or methyloxycarbonyl;

R is selected from the group consisting of hydrogen, lower alkyl, aryl, lower alkyl formate, aryl formate, methyl formate, p-nitrophenol formate, formamide, N-alkylformamide, N-succinimidyl, hydroxyl, alkoxyl, thiol, thioether, disulfide, hydrazide and amine groups and provided that when X or Z is methyloxycarbonyl, R is not methyl formate;

U is O, S or NH;

Y is selected from the group consisting of sulfur, oxygen, methylene, carbonyl, sulfinyl and sulfonyl groups, or Y represents two hydrogen atoms attached to the respective carbons;

n=0-7;

or acid salts of the compound.

3. A method as in claim 1 wherein the binding member is attached to the surface by a crosslinking group.

4. A method as in claim 1 wherein the surface is silica or glass.

5. A method for attaching an anti-ligand to a surface comprising the steps of:

a) linking to the surface caged biotin analogs having a relatively low affinity for avidin;

b) irradiating caged biotin analogs on predefined regions of the surface to form biotin analogs having high binding affinities for avidin;

c) reacting the biotin analogs with either an avidin analog and a biotinylated anti-ligand or an anti-ligand attached to an avidin analog.

6. The method of claim 5 wherein the caged biotin analog has the formula ##STR37## wherein X is selected from the group consisting of a) oxycarbonyls of lower alkyl, aryl and benzyl groups, provided that X is not methyl oxycarbonyl;

b) a nitroveratryloxycarbonyl group,

c) a nitropiperonyloxycarbonyl group, and R is p-nitrophenol

d) ##STR38## wherein R₁ and R₂ are hydrogen, lower alkyl, aryl, benzyl, halogen, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, sulfonate, formamido or phosphido groups,

e) ##STR39## wherein R₁ and R₂ are hydrogen, lower alkyl, aryl, benzyl, pyrenyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formamido, or phosphido groups and R₃ and R₄ are hydrogen, lower alkyl, aryl, benzyl, halogen, hydroxyl, alkoxyl, thiol, thioether, amino, nitro, carboxyl, formate, formamido or phosphido groups;

R is selected from the group consisting of hydrogen, lower alkyl, aryl, benzyl and N-succinimidyl;

or acid addition salts of the compound.

7. A method as in claim 6 wherein the biotin analog has the formula:

##STR40## wherein W is a surface or a crosslinking group attached to a surface.

8. The method of claim 5, wherein the biotin analog and avidin analog have an affinity constant (K_a) of about 10¹⁵ M^-1.

9. The method of claim 5 wherein the anti-ligand is attached to the avidin analog by a bifunctional crosslinking group.

10. A method as in claim 5 wherein the anti-ligand is a monoclonal antibody.

11. A method as in claim 5 wherein the surface is glass or silica.

12. A method for attaching a plurality of anti-ligands having different ligand binding specificities to predefined regions on a surface, said method comprising the steps of:

a) attaching to the surface caged biotin analogs having a low affinity for the anti-ligand or specific binding substances, said caged biotin analogs comprising a photolabile chemical protecting group;

b) irradiating the caged biotin analogs on a first predefined region of the surface, thereby forming biotin analogs on the first predefined region having an affinity constant of 10⁷ or stronger for an anti-ligand or a specific binding substance;

c) reacting the biotin analogs on the first predefined region with either (i)(a) the specific binding substance and a first anti-ligand or (b) a first anti-ligand attached to a specific binding substance, to form a biotin analog-specific binding substance-anti-ligand complex;

or (ii) a first anti-ligand to form a biotin analog-anti-ligand complex;

d) washing the surface to remove unbound specific binding substance or anti-ligand;

e) repeating steps (b-d) on a different region of the surface with a different anti-ligand.

13. The method of claim 12 wherein the anti-ligand is an immunoglobulin.

14. A method of screening a plurality of anti-ligands localized on predefined regions of a surface for affinity for ligands in solution comprising:

a) attaching to the surface caged biotin analogs having a low affinity for the anti-ligand or specific binding substances, said caged biotin analogs comprising a photolabile chemical protecting group;

b) irradiating the caged biotin analogs on a first predefined region of the surface, thereby forming biotin analogs on the first predefined region having an affinity constant of 10⁷ or stronger for an anti-ligand or a specific binding substance;

c) reacting the biotin analogs on the first predefined region with either (i)(a) the specific binding substance and a first anti-ligand or (b) a first anti-ligand attached to a specific binding substance, to form a biotin analog-specific binding substance-anti-ligand complex;

or (ii) a first anti-ligand to form a biotin analog-anti-ligand complex;

d) washing the surface to remove unbound specific binding substance or anti-ligand;

e) repeating steps (b-d) on a different region of the surface with a different anti-ligand to create a surface having a plurality of anti-ligands non-covalently bound on predefined regions of the surface;

f) exposing the surface from step (e) to a solution containing at least one marked ligand;

g) washing the surface free of unbound ligand; and

h) identifying ligands binding to anti-ligands by determining regions on the surface where markers are located.

15. A method of performing a competitive assay of a ligand in solution by measuring the ligand'"'"'s affinity for anti-ligands immobilized on predefined regions of a surface by the steps of:

a) attaching to the surface caged biotin analogs having a low affinity for the anti-ligand or specific binding substances, said caged biotin analogs comprising a photolabile chemical protecting group;

b) irradiating the caged biotin analogs on a first predefined region of the surface, thereby forming biotin analogs on the first predefined region having an affinity constant of 10⁷ or stronger for an anti-ligand or a specific binding substance;

c) reacting the biotin analogs on the first predefined region with either (i)(a) the specific binding substance and a first anti-ligand or (b) a first anti-ligand attached to a specific binding substance, to form a biotin analog-specific binding substance-anti-ligand complex;

or (ii) a first anti-ligand to form a biotin analog-anti-ligand complex;

d) washing the surface to remove unbound specific binding substance or anti-ligand;

e) repeating steps (b-d) on a different region of the surface with a different anti-ligand to create a surface having a plurality of anti-ligands non-covalently bound on predefined regions of the surface;

f) incubating a solution containing at one or more marked ligands and unknown ligands with the surface of step (e);

g) washing the surface free of unbound ligand; and

h) measuring an amount of marked ligand remaining on the predefined regions of the surface.

16. The method of claim 15, wherein step (f) comprises first binding unknown ligands to anti-ligands on the surface and then incubating a solution containing one or more marked ligands with the surface.