Ionic microenvironmental effects on triplex DNA stabilization: Cationic counterion effects on poly(dT)·poly(dA)·poly(dT)

Amanda Beck, Veena Vijayanathan, Thresia Thomas, T. J. Thomas

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li+, Na+, K+, Rb+, Cs+ and NH4+) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li+ to 30.6 °C in the presence of 150 mM K+. NH4+ was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg2+ > Ca2+ > Sr2+ > Ba2+. All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M+,2+] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.

Original languageEnglish (US)
Pages (from-to)1310-1318
Number of pages9
Issue number6
StatePublished - Jun 2013


  • Alkyl ammonium ions
  • Ammonium ion
  • Circular dichroism
  • Melting temperature
  • Triplex DNA

ASJC Scopus subject areas

  • Biochemistry


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