Effect of cations on the melting behavior of a triplex DNA

Three-stranded (triplex) DNA is a unique DNA structure formed when a DNA or RNA oligonucleotide specifically binds to a homopurine region of DNA via Hoogsteen hydrogen bonds in the major groove (Figure on the right). After first observed in 1957 by Felsenfeld et al.,1 the formation of triplex DNA has been recognized as a novel strategy for genetic manipulation. It is used to inhibit DNA transcription and replication, generate sitespecific mutations, cleave DNA, and induce homologous recombination.2 However, triplex DNA is not as stable as its duplex counterpart under physiological conditions. Short DNA triplexes often melt below room temperature, making it difficult to study their corresponding properties under normal conditions. In the present work, we studied the thermal denaturation of a 22 TAT DNA triplex at various salt conditions. The melting curves reveal a clear phase transition and the melting temperatures (Tm) increase as a function of increasing cation (Na+, K+ and Mg2+) concentrations. Our results show that Tm values above room temperature can be obtained at high cation concentrations. The binding of neomycin to this triplex DNA was also investigated at suitable salt conditions determined by our experiments. References: 1. Felsenfeld, G.; Davies, D. R.; Rich, A. J. Am. Chem. Soc.,1957, 79, 2023-2024. 2. Chan, P. P.; Glazer, M. P. J. Mol. Med.,1997, 75, 267-282