Sequence dependence of energy transfer in DNA oligonucleotides

The sequence, temperature, concentration, and solvent dependence of singlet energy transfer from normal DNA bases to the e-aminopurine base in synthes ized DNA oligomers were investigated by optical spectroscopy. Transfer was shown directly by a variable fluorescence excitation band at 260-280 nm. Ad enine (A) is the most efficient energy donor by an order of magnitude. Stac ks 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 2A P. Base stacking facilitates transfer, while base pairing reduces energy tr ansfer slightly. The efficiency is differentially temperature dependent in single- and double-stranded oligomers and is highest below 0 degrees C in s amples measured. An efficiency transition occurs well below the melting tra nsition of a double-stranded decamer. The transfer efficiency in the duplex decamer d(CTGA[2AP]TTCAG)(2) is moderately dependent on the sample and sal t concentration and is solvent dependent. Transfer at physiological tempera ture 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 loca lization of UV damage in DNA. These results have features in common with re cently observed electron transfer from 2AP to G in oligonucleotides.