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 journalArticle

7 Citations (Scopus)

Abstract

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
JournalBiochimie
Volume95
Issue number6
DOIs
StatePublished - Jun 2013
Externally publishedYes

Fingerprint

Poly T
Stabilization
Ions
Metal ions
Cations
Metals
Monovalent Cations
Nucleic Acid Denaturation
Single-Stranded DNA
Polyamines
Ammonium Compounds
Melting point
DNA
Melting
Freezing
Temperature
Alkali Metals
Nucleic Acid Conformation
Oligonucleotides
Nucleic Acids

Keywords

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

ASJC Scopus subject areas

  • Biochemistry

Cite this

Ionic microenvironmental effects on triplex DNA stabilization : Cationic counterion effects on poly(dT)·poly(dA)·poly(dT). / Beck, Amanda; Vijayanathan, Veena; Thomas, Thresia; Thomas, T. J.

In: Biochimie, Vol. 95, No. 6, 06.2013, p. 1310-1318.

Research output: Contribution to journalArticle

Beck, Amanda ; Vijayanathan, Veena ; Thomas, Thresia ; Thomas, T. J. / Ionic microenvironmental effects on triplex DNA stabilization : Cationic counterion effects on poly(dT)·poly(dA)·poly(dT). In: Biochimie. 2013 ; Vol. 95, No. 6. pp. 1310-1318.
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AB - 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.

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