Modified Nucleic Acid Polymers and Methods for their Production

• US 20090286285A1
• Filed: 10/26/2007
• Published: 11/19/2009
• Est. Priority Date: 06/24/1998
• Status: Active Grant

• Current Assignee: Enzo Diagnostics, Inc.
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack, Walner, Marleen
• Granted Patent: US 8,288,092 B2
• Time in Patent Office: Days
• US Class Current: 435/91.200
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]

Abstract

The invention is directed to nucleic acid sequences having decreased thermodynamic stability to complementary sequence as well as a method for producing these sequences.

Claims

1. A single-stranded or double-stranded modified nucleic acid polymer selected from the group consisting of a linear nucleic acid, branched nucleic acid, an inverted nucleic acid and a peptide-nucleic acid, or a combination of any of the foregoing, wherein said nucleic acid polymer comprises at least one, modified purine or pyrimidine base, wherein said purine or pyrimidine base is modified with a negatively charged chemical moiety which comprises carboxylic acid and wherein said polymer has decreased thermodynamic stability in binding to complementary sequences as compared to a corresponding unmodified nucleic acid polymer.

2. The nucleic acid polymer according to claim 1, wherein said polymer is single-stranded.

3. The nucleic acid polymer according to claim 1, wherein said polymer is double-stranded.

4. A process for producing the nucleic acid polymer of claim 1 comprising the step of incorporating into the nucleic acid sequences produced at least one modified nucleotide or nucleotide analog having a negatively charged chemical moiety, wherein said modified nucleotide or nucleotide analog comprises a purine or pyrimidine base modified with a negatively charged chemical moiety which comprises carboxylic acid.

5. The process according to claim 4, wherein said nucleic acid sequence produced is a single-stranded or doubled-stranded nucleic acid polymer.

6. The process according to claim 4, wherein said single-stranded or double-stranded nucleic acid polymer is selected from the group consisting of a linear nucleic acid, branched nucleic acid, an inverted nucleic acid and a peptide-nucleic acid, or a combination of any of the foregoing.

7. A process for producing a nucleic acid of claim 1, comprising the step of incorporating into the nucleic acid sequences produced at least one modified nucleotide or nucleotide analog having a negatively charged chemical moiety, wherein said negatively charged chemical moiety comprises carboxylic acid, wherein said nucleic acid is produced under thermocycling conditions where an annealing step and denaturation step are undertaken at temperatures that are no more than 12°

C. apart.

8. The process according to claim 7, wherein said nucleic acid sequence produced is a single-stranded or doubled-stranded nucleic acid polymer.

10. The process according to claim 7, wherein said single-stranded or double-stranded nucleic acid polymer is selected from the group consisting of a linear nucleic acid, branched nucleic acid, an inverted nucleic acid and a peptide-nucleic acid, or a combination of any of the foregoing.

11. A process for producing a nucleic acid polymer of claim 1 comprising the step of incorporating into the nucleic acid sequences produced at least one modified nucleotide or nucleotide analog having a negatively charged chemical moiety, wherein said nucleic acid is produced under thermocycling conditions where an extension step and denaturation step are undertaken at temperatures that are no more than 8°

C. apart.

12. The process according to claim 11, wherein said negatively charged chemical moiety comprises carboxylic acid.

13. The process according to claim 11, wherein said single-stranded or double-stranded nucleic acid polymer is selected from the group consisting of a linear nucleic acid, branched nucleic acid, an inverted nucleic acid and a peptide-nucleic acid, or a combination of any of the foregoing.