Mechanism of DNA triplex formation and its specificity as studied by filter binding assay
Shindo, H.; Kamiya, M.; Torigoe, H.; Sarai, A.
Nucleic Acids Symposium Series 29: 17-18
1993
ISSN/ISBN: 0261-3166 PMID: 8247755 Document Number: 408289
The filter binding method was found to be a very useful method for triple-helical formation of oligo DNA duplexes with homoprymidine single-strands. Using this method, we have obtained dissociation constants of triplexes and association rates of triple-helical formation of a variety of combinations of double-strands (23-mer) and pyrimidine single-strands as functions of pH and temperature. pH dependences of dissociation constants and association rates are theoretically discussed in terms of acid-base equilibrium of pyrimidine strands. Temperature-dependence of dissociation constants and association rates were considerably different between acidic and neutral pH range, suggesting that mechanism of triple-helical formation differs between two pH ranges. The results were best interpreted in terms of a three-state model for the triple-helical formation. Furthermore, the effect of mismatched sequences on the stability of the triplexes were also discussed.