Nucleic acid-binding polymers

• US 7,223,851 B2
• Filed: 02/06/2003
• Issued: 05/29/2007
• Est. Priority Date: 02/06/2003
• Status: Expired due to Fees

• Current Assignee: Veridian Systems Divisions, Inc.
• Original Assignee: General Dynamics Advanced Information Systems Incorporated (General Dynamics Corporation)
• Inventors: Terlesky, Kathy, Earle, Chris
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US10/359,084
• Publication Number:
  US 20040157217A1
• Time in Patent Office: 1,573 Days
• Field of Search: 536/23.1, 536/24.3, 536/26.6, 435/6
• US Class Current: 536/23.1
• CPC Class Codes: C08F 220/60 containing nitrogen in addition to the carbonamido nitrogen

Abstract

The present invention relates to a nucleic acid binding polymer which has affinity for nucleic acid molecules such as DNA, RNA, or hybrids thereof. The polymer is comprised of a nucleic acid binding backbone linked to a nucleic acid binding agent, preferably by a linking moiety. The polymer can be used to isolate and purify nucleic acid molecules from a variety of sample types including but not limited to clinical and environmental.

Claims

1. A water soluble nucleic acid binding polymer comprising a backbone polymer and a nucleic acid binding agent, wherein the backbone polymer is not a polynucleotide, and wherein said nucleic acid binding agent is an intercalating agent or a minor groove binder.

2. The nucleic acid binding polymer of claim 1, comprising a bifunctional linker.

3. The nucleic acid binding polymer of claim 2, wherein said nucleic acid binding polymer binds in aqueous solution to a nucleic acid by hydrogen, electrostatic or cationic binding.

4. The nucleic acid binding polymer of claim 3, wherein said nucleic acid is DNA, RNA, or a hybrid thereof.

5. The nucleic acid binding polymer of claim 3, wherein said nucleic acid binding polymer remains soluble after binding to a nucleic acid.

7. The nucleic acid binding polymer of claim 1, wherein said nucleic acid binding agent is both an intercalating agent and a minor groove binder.

8. The nucleic acid binding polymer of claim 1, wherein said intercalating agent is ethidium, ethidium bromide, methidium acridine, aminoacridine, acridine orange and derivatives thereof, psoralen, proflavin, ellipticine, actinomycin D, daunomycin, malachite green, phenyl neutral red, mitomycin C, HOECHST 33342, HOECHST 33258, aclarubicin, DAPI, SYBR, Adriamycin, pirarubicin, actinomycin, tris (phenanthroline) zinc salt, tris (phenanthroline) ruthenium salt, tris (phenantroline) cobalt salt, di (phenanthroline) zinc salt, di (phenanthroline) ruthenium salt, di (phenanthroline) cobalt salt, bipyridine platinum salt, terpyridine platinum salt, phenanthroline platinum salt, tris (bipyridyl) zinc salt, tris (bipyridyl) ruthenium salt, tris (bipyridyl) cobalt salt, di (bipyridyl) zinc salt, di (bipyridyl) ruthenium salt or di (bipyridyl) cobalt salt.

9. The nucleic acid binding polymer of claim 1, wherein said intercalating agent is psoralen.

10. The nucleic acid binding polymer of claim 1, wherein said minor groove binder is Hoechst 33258, CDPI_1-3, netropsin, distamycin A, lexitropsin, mithramycin, chromomycin A₃, olivomycin, anthramycin, sibriomycin, bisquaternary ammonium heterocyclic compound, pentamidine, berenil, phthalanilide, stilbamidine, or DAPI.

11. The nucleic acid binding polymer of claim 2, wherein said bifunctional linker is N-Boc-1,3-diaminopropane, N-Boc-1,4-diaminobutane, N-Boc-1,5-diaminopentane, N-Boc- 1,6-diaminohexane, 3-(Boc-amino)-1-propanol, 4-(Boc-amino)-1-butanol, 5-(Boc-amino)-1-pentanol, 6-(Boc-amino)-1-hexanol, Na-Boc-L-lysine, NE-Boc-L-lysine, or Na-Boc-L-serine methyl ester.

12. The nucleic acid binding polymer of claim 2, wherein said bifunctional linker is linked to the nucleic acid binding agent by an amide, ester, thioether, carbamate, urea or amine bond.

13. The nucleic acid binding polymer of claim 1, wherein said backbone polymer comprises pendant OH, NH₂, COOH, or quaternary ammonium groups having at least one H atom.

16. The nucleic acid binding polymer of claim 2, wherein said bifunctional linker is in about a 1:

1 mole ratio with the nucleic acid binding agent.

6. A water soluble nucleic acid binding polymer comprising a backbone polymer and a nucleic acid binding agent, wherein said backbone polymer is linear polyacrylamide, and wherein said nucleic acid binding agent is an intercalating agent or a minor groove binder.

14. A water soluble nucleic acid binding polymer comprising a backbone polymer and a nucleic acid binding agent, wherein said backbone polymer comprises monomers which include acrylic acid, acrylamide, an acrylate, a glycol, an amino acid, or a substituted styrene, and wherein said nucleic acid binding agent is an intercalating agent or a minor groove binder.

15. The nucleic acid binding polymer of claim 14, wherein said polymer is a derivatized acrylamide.

17. A nucleic acid binding polymer comprising:

a backbone polymer comprising polyacrylamide; and

a nucleic acid binding agent linked to the backbone polymer, wherein the nucleic acid binding agent binds a double-stranded segment of a nucleic acid preferentially to a single-stranded segment of a nucleic acid, and wherein said nucleic acid binding agent is an intercalating agent or a minor groove binder.

18. The nucleic acid binding polymer of claim 17, wherein the nucleic acid binding agent is linked to the backbone polymer by a bifunctional linker.

19. The nucleic acid binding polymer of claim 18, wherein the bifunctional linker comprises a moiety selected from the group consisting of:

—

NH—

(CH₂)₃—

NH—

, —

NH—

(CH₂)₄—

NH—

, —

NH—

(CH₂)₅—

NH—

, —

NH—

(CH₂)₆—

NH—

, —

O—

(CH₂)₃—

NH—

, —

O—

(CH₂)₃—

NH—

, —

O—

(CH₂)₅—

NH−

, —

O—

(CH₂)₃—

NH—

, —

NH—

CH(CO₂H)—

(CH₂)₄NH—

, and —

O—

CH₂—

CH(CO₂H)—

NH—

.

20. The nucleic acid binding polymer of claim 17, wherein the polymer includes a moiety having the formula: