Helical periodicity of GA-alternating triple-stranded DNA

Homopurine · homopyrimidine tracts (18 or 28 bp) containing predominantly GA-alternating sequences were inserted between two bent DNA loci composed of six (dA)₆ · (dT)₆ repeats. For each homopurine tract, the DNA length between the bent DNA loci was varied by one base pair over a full helical turn. The two series of bent DNA fragments were electrophoresed in 5% polyacrylamide gel to measure the gel mobilities, which reflected the overall extent of DNA bending of each DNA fragment. By comparing the gel mobilities between the two series of bent DNA fragments, the helical periodicity of the GA-alternating duplex was determined to be 10.4 bp/turn. The two series of bent DNA fragments were also electrophoresed upon formation of the intermolecular triplex at the homopurine · homopyrimidine tracts. Comparison of the gel mobilities between the two series of DNA fragments showed that the helical periodicity of triplexed DNA of GA-alternating sequence was 11.2 bp/turn. Triplexed DNA with homopurine and homopyrimidine oligodeoxyribonucleotides had the same helical periodicity, while hybrid triplex DNA associated with homopyrimidine oligoribonucleotide had a slightly more wound structure with 11.1 bp/turn.