Nucleic acid directed immobilization arrays and methods of assembly

• US 7,569,341 B2
• Filed: 11/07/1997
• Issued: 08/04/2009
• Est. Priority Date: 01/31/1994
• Status: Expired due to Fees

• Current Assignee: Trustees of Boston University
• Original Assignee: Trustees of Boston University
• Inventors: Sano, Takeshi, Cantor, Charles R., Niemeyer, Christof M., Smith, Cassandra L.
• Primary Examiner(s): Lin; Jerry
• Application Number:
  US08/967,269
• Publication Number:
  US 20030118595A1
• Time in Patent Office: 4,288 Days
• Field of Search: 435/6, 435/7.1, 435/7.2, 435/810, 435/9, 436/501, 536/22.1, 536/23.1, 536/24.1, 536 243- 2433, 536/25.3, 935/77, 935/78
• US Class Current: 435/6.19
• CPC Class Codes: A61K 47/54 the modifying agent being an organic compound
• CPC Class Codes: A61K 47/55 the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds
• CPC Class Codes: A61K 47/557 the modifying agent being biotin
• CPC Class Codes: A61K 47/6949 inclusion complexes, e.g. clathrates, cavitates or fullerenes
• CPC Class Codes: A61K 51/1268 host-guest, closed hollow molecules, inclusion complexes, e.g. with cyclodextrins, clathrates, cavitates, fullerenes
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C03C 17/30 with silicon-containing compounds
• CPC Class Codes: C03C 17/3405 with at least two coatings of organic materials C03C17/36, C03C17/42 take precedence
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/682 Signal amplification

Abstract

The invention relates to supramolecular bioconjugates and to methods for assembling and utilizing supramolecular bioconjugates. Supramolecular bioconjugates comprise a plurality of first nucleic acids and a plurality of mediators wherein each mediator comprises a second nucleic acid complementary to a sequence within said plurality of first nucleic acids. To assemble a supramolecular bioconjugate, one or more sets of bioreactive agents are coupled to the plurality of mediators, forming a plurality of bioreactive complexes The plurality of bioreactive complexes are hybridized to the plurality of first nucleic acids to form the supramolecular bioconjugate. Bioconjugates can be used to detect and isolate targets, to screen samples for targets such as antigens, to treat patients with multiple agents or to diagnose disorders in the form of a kit.

Claims

1. A method for forming a nucleic acid-directed immobilization array of supramolecular bioconjugates comprising the steps of:

a) attaching a first nucleic acid to a support in a regiospecific manner;

b) providing at least a second nucleic acid complementary to a sequence within said first nucleic acid, wherein said second nucleic acid is coupled to a bioreactive agent, wherein said second bioreactive agent is a non-nucleic acid bioreactive agent and contains a separate binding moiety that is selected to further react with a specific target;

c) providing at least a third nucleic acid complementary to a sequence within said first or second nucleic acid, wherein said third nucleic acid is coupled to a bioreactive agent, wherein said third bioreactive agent is a non-nucleic acid bioreactive agent and contains a separate binding moiety that is selected to further react with a specific target;

(d) hybridizing in one step said first nucleic acid to said second nucleic acid and said third nucleic acid to said first or second nucleic acid to form a supramolecular bioconjugate; and

d) repeating steps (a)-(d) to form a plurality of immobilized supramolecular bioconjugates, wherein the separate binding moiety of each of said bioreactive agent is selected to further react with a specific target.

2. The method of claim 1, wherein the second and the third bioreactive agent in steps b) and c) further comprises a binding agent.

3. The method of claim 2, wherein the binding agent is selected from the group consisting of avidin, streptavidin, and biotin.

4. The method of claim 1, wherein the support is a ceramic, a glass, a plastic, a metal, a resin, a gel, an elastic, a wood or a combination thereof.

5. A method for assembling a supramolecular bioconjugate comprising the steps of:

a) providing a first bioreactive complex said bioreactive complex comprising a first nucleic acid, said first nucleic acid attached to a first bioreactive agent, said first bioreactive agent comprising a first binding agent selected from the group consisting of protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule, wherein said first bioreactive agent is coupled to a molecule binding to said first bioreactive agent;

b) providing at least a second bioreactive complex comprising at least two second nucleic acids, wherein one of the at least second nucleic acids serves as a first mediator nucleic acid that comprises a nucleic acid sequence that is complementary to a sequence within said first nucleic acid, said at least two second nucleic acids attached to a second bioreactive agent, said second bioreactive agent comprising a second binding agent selected from the group consisting of protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule, and wherein one of the at least second nucleic acids serves as a second mediator nucleic acid;

c) providing at least a third bioreactive complex comprising at least one nucleic acid, wherein the at least one nucleic acid comprises a nucleic acid sequence that is complementary to at least portion of the second mediator nucleic acid attached to the second bioreactive complex; and

d) hybridizing in one step said complementary nucleic acids of said second and third bioreactive complex to said first and second nucleic acid of said first and second bioreactive complex to form a supramolecular bioconjugate, wherein at least one of the second or the third bioreactive agent, is selected to further react with a bioreactive target, while part of the supramolecular bioconjugate.

6. The method of claim 5 wherein said first nucleic acid is between about 10 to about 1000 nucleotides in length.

7. The method of claim 5 wherein said second nucleic acid is between about 10 to about 1000 nucleotides in length.

8. A supramolecular bioconjugate assembled by the method of claim 5.

9. A plurality of supramolecular bioconjugates formed by the method of claim 5.

10. The method of claim 5, wherein said first nucleic acid and said second nucleic acid are DNA, RNA or PNA.

11. The method of claim 5, wherein the second nucleic acid is between 10 to 600 nucleotides in length.

12. A method for forming a plurality of immobilized supramolecular bioconjugates comprising the steps of:

a) attaching to a support in a regiospecific manner a first bioreactive complex wherein said first bioreactive complex comprises a first nucleic acid wherein said first nucleic acid is attached to a first bioreactive agent, said first bioreactive agent comprising a first binding agent selected from the group consisting of avidin, streptavidin, biotin, protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule and coupling said first bioreactive agent to a molecule capable of binding to said first binding agent;

b) providing at least a second bioreactive complex said second bioreactive complex comprising a second nucleic acid complementary to a sequence within said first nucleic acid, said second nucleic acid attached to a second bioreactive agent, said second bioreactive agent comprising a second binding agent selected from the group consisting of avidin, streptavidin, biotin, protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule, and further comprising a third nucleic acid;

c) providing at least a third bioreactive complex said third bioreactive complex comprising a fourth nucleic acid complementary to a sequence within said third nucleic acid, said fourth nucleic acid attached to a third bioreactive agent, said third bioreactive agent comprising a third binding agent selected from the group consisting of avidin, streptavidin, biotin, protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule;

d) hybridizing, in one step said first nucleic acid to said second nucleic acid and said third nucleic acid to said fourth nucleic acid to form a supramolecular bioconjugate; and

e) repeating steps (a)-(d) to form a plurality of immobilized supramolecular bioconjugates, wherein the second bioreactive agent is selected to react further with a specific bioreactive target while part of the supramolecular bioconjugates.

14. The method of claim 12 or 13, wherein the plurality of immobilized supramolecular bioconjugates comprises at least 10 immobilized supramolecular bioconjugates.

15. The method of claim 12 or 13, wherein the plurality of immobilized supramolecular bioconjugates comprises at least 1,000 immobilized supramolecular bioconjugates.

16. The method of claim 12 or 13, wherein the plurality of immobilized supramolecular bioconjugates comprises at least 100,000 immobilized supramolecular bioconjugates.

17. The method of claim 12 or 13, wherein the plurality of immobilized supramolecular bioconjugates comprises at least 1,000,000 immobilized supramolecular bioconjugates.

18. The method of claim 12 or 13, wherein the first, the second and the third binding agent is selected from the group consisting of avidin, streptavidin, and biotin.

20. The method of claim 12 or 19, wherein the support is a ceramic, a glass, a plastic, a metal, a resin, a gel, an elastic, a wood or a combination thereof.

13. A method for assembling a supramolecular bioconjugate comprising the steps of:

a) providing a first bioreactive complex said bioreactive complex comprising a first nucleic acid, said first nucleic acid attached to a first bioreactive agent, said first bioreactive agent comprising a first binding agent selected from the group consisting of protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule, wherein said first bioreactive agent is coupled to a molecule binding to said first bioreactive agent;

b) providing at least a second bioreactive complex comprising a second nucleic acid, wherein the at least second nucleic acid comprises a nucleic acid sequence that is complementary to a portion of the sequence within said first nucleic acid, said second nucleic acid attached to a second bioreactive agent, said second bioreactive agent comprising a second binding agent selected from the group consisting of protein A, an antibody, an Fc fragment, a Fab fragment, an antigen, a nucleic acid binding protein, and a cell adhesion molecule;

c) providing at least a third bioreactive complex comprising a third nucleic acid, wherein the third nucleic acid comprises a nucleic acid sequence that is complementary to at least portion of the first nucleic acid ; and

d) in one step hybridizing said complementary nucleic acids in said at least the second and the third bioreactive complex to said first nucleic acid of said first bioreactive complex to form a supramolecular bioconjugate, wherein at least one of the second or the third bioreactive agent will further react with an intended bioreactive target, while part of the supramolecular bioconjugate.

19. A method for forming a nucleic acid-directed immobilization array of supramolecular bioconjugates comprising the steps of:

a) attaching a first nucleic acid to a support in a regiospecific manner;

b) providing at least a second nucleic acid complementary to a sequence within said first nucleic acid, wherein said second nucleic acid is coupled to a bioreactive agent, wherein said second bioreactive agent is a non-nucleic acid bioreactive agent and contains a separate binding moiety that is selected to further react with a specific target;

c) providing at least a third nucleic acid complementary to a sequence within said first or second nucleic acid, wherein said third nucleic acid is coupled to a bioreactive agent, wherein said third bioreactive agent is a non-nucleic acid bioreactive agent and contains a separate binding moiety that is selected to further react with a specific target;

(d) hybridizing in one step said first nucleic acid to said second nucleic acid and said third nucleic acid to said first or second nucleic acid to form a supramolecular bioconjugate; and

d) repeating steps (a)-(d) to form a plurality of immobilized supramolecular bioconjugates, wherein the separate binding moiety of each of said bioreactive agent is selected to further react with a specific target.