Sequence dependence of energy transfer in DNA oligonucleotides

Academic Article

Abstract

  • The sequence, temperature, concentration, and solvent dependence of singlet energy transfer from normal DNA bases to the 2-aminopurine base in synthesized DNA oligomers were investigated by optical spectroscopy Transfer was shown directly by a variable fluorescence excitation band at 260-280 nm. Adenine (A) is the most efficient energy donor by an order of magnitude. Stacks of A adjacent to 2AP act as an antenna for 2AP excitation. An interposed G, C, or T base between A and 2AP effectively blocks transfer from A to 2AP. Base stacking facilitates transfer, while base pairing reduces energy transfer slightly. The efficiency is differentially temperature dependent in single- and double-stranded oligomers and is highest below 0°C in samples measured. An efficiency transition occurs well below the melting transition of a doublestranded decamer. The transfer efficiency in the duplex decamer d(CTGA[2AP]TTCAG)2 is moderately dependent on the sample and salt concentration and is solvent dependent. Transfer at physiological temperature over more than a few bases is improbable, except along consecutive A's, indicating that singlet energy transfer is not a major factor in the localization of UV damage in DNA. These results have features in common with recently observed electron transfer from 2AP to G in oligonucleotides.
  • Authors

    Published In

    Digital Object Identifier (doi)

    Author List

  • Xu DG; Nordlund TM
  • Start Page

  • 1042
  • End Page

  • 1058
  • Volume

  • 78
  • Issue

  • 2