Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines

Bioorg Med Chem Lett. 2012 Jun 15;22(12):4103-5. doi: 10.1016/j.bmcl.2012.04.067. Epub 2012 Apr 21.

Abstract

5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Deoxyuridine / analogs & derivatives*
  • Deoxyuridine / chemistry*
  • Fluorescence
  • Naphthalenes / chemistry*
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / chemical synthesis*
  • Spectrometry, Fluorescence

Substances

  • Naphthalenes
  • Oligodeoxyribonucleotides
  • DNA
  • Deoxyuridine