Formation of a triple-stranded DNA between d(GGA:TCC) repeats and d(GGA) repeat oligonucleotides.

Incubation of the 162-bp duplex containing d(GGA:TCC)11 repeats with d(GGA)11 and d(GGT)11 oligonucleotides, but not with d(TCC)11, gave a mobility-shifted band in polyacrylamide gel electrophoresis, suggestive of the triplex formation. The two conformers, however, showed difference in binding affinity and structure. The complex formed with d(GGT)11 exhibited patterns protected from DNase I digestion and from modifications with osmium tetroxide and dimethyl sulfate. The patterns were conformed to a proposed triplex model. In contrast, the complex with d(GGA)11 was sensitive to DNase I and to osmium tetroxide, which is reactive to pyrimidine bases of single-stranded DNA. These results suggest that the d(GGA:TCC)11 and d(GGA)11 triple-stranded complex forms a D-loop-like structure. By considering the ability of d(GGA)11 oligonucleotides to form a parallel homoduplex, the structure may be one in which the GGA-strand of the duplex pairs with d(GGA)11 in parallel, with the TCC-strand being looped out.