Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes

J Org Chem. 2016 Apr 15;81(8):3335-46. doi: 10.1021/acs.joc.6b00369. Epub 2016 Mar 30.

Abstract

The development of molecular strategies that enable recognition of specific double-stranded DNA (dsDNA) regions has been a longstanding goal as evidenced by the emergence of triplex-forming oligonucleotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and--more recently--engineered proteins such as CRISPR/Cas9. Despite this progress, an unmet need remains for simple hybridization-based probes that recognize specific mixed-sequence dsDNA regions under physiological conditions. Herein, we introduce pseudocomplementary Invader probes as a step in this direction. These double-stranded probes are chimeras between pseudocomplementary DNA (pcDNA) and Invader probes, which are activated for mixed-sequence dsDNA-recognition through the introduction of pseudocomplementary base pairs comprised of 2-thiothymine and 2,6-diaminopurine, and +1 interstrand zipper arrangements of intercalator-functionalized nucleotides, respectively. We demonstrate that certain pseudocomplementary Invader probe designs result in very efficient and specific recognition of model dsDNA targets in buffers of high ionic strength. These chimeric probes, therefore, present themselves as a promising strategy for mixed-sequence recognition of dsDNA targets for applications in molecular biology and nucleic acid diagnostics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 2-Aminopurine / analogs & derivatives*
  • 2-Aminopurine / chemistry
  • Base Pairing
  • DNA / chemical synthesis*
  • DNA / chemistry
  • Molecular Biology
  • Nucleic Acids / chemistry*
  • Oligonucleotides / chemical synthesis*
  • Oligonucleotides / chemistry
  • Peptide Nucleic Acids / chemical synthesis*
  • Peptide Nucleic Acids / chemistry
  • Thermodynamics
  • Thymine / analogs & derivatives*
  • Thymine / chemistry

Substances

  • Nucleic Acids
  • Oligonucleotides
  • Peptide Nucleic Acids
  • 2-Aminopurine
  • 2,6-diaminopurine
  • 2-thiothymine
  • DNA
  • Thymine