Artificial mismatch hybridization

• US 5,780,233 A
• Filed: 06/06/1996
• Issued: 07/14/1998
• Est. Priority Date: 06/06/1996
• Status: Expired due to Term

• Current Assignee: US Department of Energy (Government of the United States of America)
• Original Assignee: Wisconsin Alumni Research Foundation (University of Wisconsin System)
• Inventors: Guo, Zhen, Smith, Lloyd M.
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): SHOEMAKER, DEBRA GUNNERSEN
• Application Number:
  US08/659,605
• Time in Patent Office: 768 Days
• Field of Search: 435/6, 435/91.2, 435/91.5, 935/77, 935/78, 536/23.1, 536/24.3, 536/24.33
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine

Abstract

An improved nucleic acid hybridization process is provided which employs a modified oligonucleotide and improves the ability to discriminate a control nucleic acid target from a variant nucleic acid target containing a sequence variation. The modified probe contains at least one artificial mismatch relative to the control nucleic acid target in addition to any mismatch(es) arising from the sequence variation. The invention has direct and advantageous application to numerous existing hybridization methods, including, applications that employ, for example, the Polymerase Chain Reaction, allele-specific nucleic acid sequencing methods, and diagnostic hybridization methods.

Claims

1. A process for hybridizing an oligonucleotide to a first nucleic acid target, the method comprising the steps of:

providing an oligonucleotide having a nucleic acid sequence complementary in part to the first target, but comprising at least one artificial mismatch relative to the first target and having a nucleic acid sequence complementary in part to a second target, but comprising at least one artificial mismatch and a true mismatch relative to the second target; and

combining the oligonucleotide and the first target under selected hybridization conditions to form a first duplex, wherein the first duplex has a melting temperature 1 to 25 C.°

higher than that of a second duplex that would form under the same hybridization conditions between the oligonucleotide and a second nucleic acid target, where the oligonucleotide also comprises a true mismatch relative to the second target and where the true mismatch and the artificial mismatch are separated from one another by three or four nucleotide positions and where the artificial mismatch has base stacking properties of a natural nucleoside.

2. A process as claimed in claim 1 wherein the oligonucleotide comprises two artificial mismatches relative to the first and second targets, the artificial mismatches being separated from one another by eight to twelve nucleotides.

3. A process as claimed in claim 1 wherein the oligonucleotide comprises two artificial mismatches separated by ten nucleotides.

4. A process as claimed in claim 1 wherein the artificial mismatch nucleoside is 1-(2'"'"'-Deoxy-β

-D-ribofuranosyl)-3-nitropyrrole.

5. A process for discriminating between a first nucleic acid target and a second nucleic acid target in a test sample wherein the second nucleic acid target has a sequence variation relative to the first target, the process comprising the steps of:

providing an oligonucleotide having a nucleic acid sequence complementary in part to the first target, including at the position of the sequence variation, but comprising an artificial mismatch relative to the targets at a position other than that of the sequence variation, the artificial mismatch and the sequence variation positions being separated from one another on the oligonucleotide by three or four nucleotide positions, the artificial mismatch having base stacking properties of a natural nucleoside;

combining the oligonucleotide and the test sample under selected hybridization conditions to form a product, the product being selected from the group consisting of (a) a first duplex comprising the oligonucleotide and the first target, (b) a second duplex comprising the oligonucleotide and the second target and being less stable than the first duplex, and (c) a mixture comprising both the first duplex and the second duplex, wherein the first duplex has a melting temperature 1 to 25 C.°

higher than that of the second duplex;

selectively detecting the first duplex comprising the oligonucleotide and the first target or the second duplex comprising the oligonucleotide and the second target.