Photophysical characterization of a FRET system using tailor-made DNA oligonucleotide sequences

Bioconjug Chem. 2010 Dec 15;21(12):2347-54. doi: 10.1021/bc100389k. Epub 2010 Nov 29.

Abstract

We have carried out a detailed photophysical study of the FRET D/A pair consisting of a carbostyril donor and a Ru(II)bathophenanthroline complex acceptor in double-stranded synthetic DNA. Altogether 13 different double-stranded 30 base pair DNAs showing small incremental differences in the distances between donor and acceptor were synthesized. Using the fluorescence of the donor as well as of the acceptor, D/A separations were determined and compared to those derived from a well-established model for DNA distance calculations. The model calculations and anisotropy studies revealed that the donor can nearly be seen as a free rotator allowing the application of the established FRET data evaluation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA / chemical synthesis
  • DNA / metabolism*
  • Fluorescence
  • Fluorescence Resonance Energy Transfer / methods*
  • Fluorescent Dyes
  • Hydroxyquinolines / metabolism*
  • Models, Molecular
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / metabolism*
  • Organometallic Compounds / metabolism*
  • Phenanthrolines / metabolism*
  • Photoelectron Spectroscopy
  • Quinolones / metabolism*
  • Spectrometry, Fluorescence

Substances

  • Fluorescent Dyes
  • Hydroxyquinolines
  • Oligonucleotides
  • Organometallic Compounds
  • Phenanthrolines
  • Quinolones
  • carbostyril
  • DNA
  • tris(4,7-diphenyl-1,10-phenanthroline)ruthenium (II)