Helical periodicity of (dT)_n·(dA)_n·(dT)_n triple-stranded DNA

The helical periodicity of the triple-stranded (dT)_n·(dA)_n·(dT)_n sequence was determined by measuring gel-mobilities of bent DNA fragments containing the sequence. In the bent DNA fragments, a GA₂₂G-CT₂₂C sequence was located between two bent DNA loci composed of six A₆·T₆ repeats, and the DNA length between the bent DNA loci was varied by 1 base pair over a full helical turn. The gel mobility of each bent DNA fragment reflected the overall extent of DNA bending and varied with the DNA length between the two bent loci. Mobilities of the bent DNA fragments in 5% polyacrylamide gel were measured after preincubating the DNA fragments both in the presence and absence of CT₂₂C oligonucleotide. By comparing the bent DNA fragments containing an intermolecular triplex structure with those of a genuine duplex structure in the gel mobilities, the helical periodicity of the T_n·A_n·T_n triplex DNA was determined to be 11.5 (±0.3) bp/turn.