title: Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on poly(dT)·poly(dA)·poly(dT).
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 [Formula: see text] ) 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(+). [Formula: see text] 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: Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). 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.
authors: Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 125 Paterson St, New Brunswick, NJ 08903, USA.
authors: Amanda
authors: A
authors: Beck
authors: Veena
authors: V
authors: Vijayanathan
authors: Thresia
authors: T
authors: Thomas
authors: T J
authors: TJ
authors: Thomas
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D008672:Metals, Alkali / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011061:Poly A / Q000737:chemistry*; D011071:Poly T / Q000737:chemistry*; D000644:Quaternary Ammonium Compounds / Q000737:chemistry
chemical_list: D008672:Metals, Alkali; D000644:Quaternary Ammonium Compounds; C051802:triplex DNA; D011061:Poly A; D011071:Poly T; C015465:poly(dA); D004247:DNA