Footprinting of DNA secondary structure by high-intensity (laser) ultraviolet irradiation.

The action of high-intensity ultraviolet pulse laser radiation on a 161 bp fragment of pBR 322 DNA (EcoRI-MspI fragment) was studied. At doses up to 5 X 10(18) photons/cm2 the N-glycosidic bond splitting is negligible. The action of hot piperidine on irradiated DNA leads to chain splitting at the residues, modified via biphotonic processes. The modification and, hence, splitting efficiencies depend on the type of base (G greater than T greater than A greater than C) and on its position in the sequence. Preferentially modified bases in the opposite strands of double-stranded DNA belong, mainly, to the same or adjacent base pairs. Residues in the Pribnow box are modified considerably less, than in the sequences, immediately upstream and downstream. This approach seems to be useful in footprinting of DNA secondary structure peculiarities and alterations, conjugated with the functional role and state of the respective fragment.