Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation

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Abstract
The binding of a 19-mer guanosine-rich oligodeoxyribonucleotide, TG 3 TG 4 TG 4 TG 3 T (ODN 1), to a complementary polypurine DNA target was investigated by DNase I footprinting and restriction endonuclease protection assays. Monovalent cations inhibited intermolecular purine - purine - pyrimidine triple-helical DNA formation, with K * and Rb * being most effective, followed by NH 4* and Na * . Li * and Cs * had little to no effect. Similar results were observed with the G/Arich oligonucleotide AG3AG4AG4AG3AGCT. Kinetic studies indicated that monovalent cations interfered with oligonucleotide - duplex DNA association but did not significantly promote triplex dissociation. The observed order of monovalent cation inhibition of triplex formation is reminiscent of their effect on tetraplex formation with G/T-rich oligonucleotides. However, using electrophoretic mobility shift assays we found that the oligonucleotide ODN 1 did not appear to form a four-stranded species under conditions promoting tetraplex formation. Taken together, our data suggest that processes other than the selfassociation of oligonucleotides into tetraplexes might be involved in the inhibitory effect of monovalent cations on purine - pyrimidine - purine triplex formation.