Parallel-Stranded Linear Homoduplexes of d(A + -G) /n > 10 and d(A-G) n > 10 Manifesting the Contrasting Ionic Strength Sensitivities of Poly(A + ·A + ) and DNA

Author： Dolinnaya Nina G. Ulku Aylin Fresco Jacques R.

Publisher： Oxford University Press

ISSN： 1362-4962

Source： Nucleic Acids Research, Vol.25, Iss.6, 1997-01, pp. : 1100-1107

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Abstract

In contrast to shorter homologs which only form a single-stranded nucleic acid α-helix in acid solution at [Na⁺] ≤ 0.02 M Na⁺, d(A-G)_20,30 form in addition a parallel-stranded duplex with (A⁺·A⁺) and (G·G) base pairs and interstrand dA^+…PO₂⁻ ionic and dA⁺NH₂^…O=P H-bonds. Under conditions where duplex prevails over α-helix, the contribution of the base-backbone interactions to stability varies directly with [H⁺] and inversely with [Na⁺], just as in poly(A⁺·A⁺). These duplexes are characterized by intense circular dichroism and a large cooperative thermally-induced hyperchromic transition that is dependent on oligomer concentration. Dimethylsulfate reactivity of the dG residues indicates G·G and therefore dA⁺·dA⁺ rather than dA⁺·G base pairs. At much higher ionic strength (Na⁺ ≥ 0.2 M) the protonated base-backbone interactions are so weakened that duplex stability becomes increasingly dependent upon H-bonded base pairing and stacking and almost independent of pH. Between pH 6 and 8 this duplex structure is devoid of protonated dA residues and shows positive dependence of T _m on ionic strength similar to that of DNA.