Hybridization-dependent fluorescence of oligodeoxynucleotides incorporating new pyrene-modified adenosine residues

Bioorg Med Chem. 2008 Sep 1;16(17):8287-93. doi: 10.1016/j.bmc.2008.05.042. Epub 2008 May 22.

Abstract

We report the synthesis and properties of oligonucleotides incorporating N(6)-[N-(pyren-1-ylmethyl)carbamoyl]-deoxyadenosine (dA(pymcm)). We designed the ODN which incorporated two consecutive dA(pymcm) residues. It was revealed that on hybridization with the target DNA and RNA oligomers, the fluorescence spectra of ODNs having two consecutive dA(pymcm) molecules near the 5'-terminal position can change from the pyrene monomer emission to the excimer, depending on the chain length of the target DNA and RNA. These results indicated that dA(pymcm)-modified ODNs can be used as interesting hybridization sensors that are sensitive to the size of the target strand.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Biosensing Techniques
  • DNA / chemistry
  • Deoxyadenosines / chemistry*
  • Electrochemistry / methods
  • Electrodes
  • Fluorescence
  • Magnetic Resonance Spectroscopy / methods
  • Models, Molecular
  • Molecular Structure
  • Nucleic Acid Hybridization*
  • Oligodeoxyribonucleotides / chemical synthesis*
  • Oligodeoxyribonucleotides / chemistry*
  • Pyrenes / chemistry*
  • RNA / chemistry
  • Sensitivity and Specificity
  • Spectrometry, Fluorescence / methods

Substances

  • Deoxyadenosines
  • Oligodeoxyribonucleotides
  • Pyrenes
  • RNA
  • DNA