title: Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation.
abstract: The binding of a 19-mer guanosine-rich oligodeoxyribonucleotide, TG3TG4TG4TG3T (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 NH4+ and Na+. Li+ and Cs+ had little to no effect. Similar results were observed with the G/A-rich 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 self-association of oligonucleotides into tetraplexes might be involved in the inhibitory effect of monovalent cations on purine-pyrimidine-purine triplex formation.
authors.affiliation: Department of Tumor Biology, University of Texas M.D. Anderson Cancer Center, Houston 77030.
authors.forename: A J
authors.initials: AJ
authors.lastname: Cheng
authors.forename: M W
authors.initials: MW
authors.lastname: Van Dyke
mesh_terms: D001483:Base Sequence; D002412:Cations; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011188:Potassium / Q000737:chemistry; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D002412:Cations; D009838:Oligodeoxyribonucleotides; D011687:Purines; D011743:Pyrimidines; D008274:Magnesium; D011188:Potassium