Thermodynamic and conformational characterization of 5-methylcytosine- versus cytosine-substituted oligomers in DNA triple helices: AB initio quantum mechanical and free energy perturbation studies

Frederick H. Hausheer, U. Chandra Singh, Jeffrey D. Saxe, John P. Flory, Kris B. Tufto

Research output: Contribution to journalArticlepeer-review

Abstract

Substitution of 5-methylcytosine for cytosine in DNA oligomers increases the stability of the Hoogsteen-paired third strand hybridizing to complementary double strand DNA under physiological pH conditions. The physicochemical mechanism(s) underlying the increased stability of DNA triplex formation which accompanies 5-rnethylcytosine substitution in the third DNA, strand is poorly understood. To address these objectives, we performed ab initio quantum mechanical and statistical mechanical studies on the equilibrium geometries and solution proton affinities of 5-methylcytosine and cytosine and incorporated these into large-scale numerical simulation models of a DNA triple helical system d[CT]10-d[GA]10-d[5mC+T]10. The purpose of these molecular simulations was to develop accurate models of cytosine and 5-methylcytosine nuclcosides and to incorporate these structural and proton affinity models in thermodynamic and structural studies of DNA oligomer hybridization. We find that the models correctly represent the net proton affinities of cytosine and 5-methylcytosine in water and that the calculated hybridization free energy difference (ΔΔGhybrid = 13.5 kcal/mol) between 5-methylcytosine and cytosine-substituted triple helices is qualitatively accurate. Using experimental entropy data (ΔS°). we predict that 5-methylcytosine substitution into DNA oligomers stabilizes the net transition enthalpy (ΔH°) of the triple helix by 73.2 kcal/mol, and a net ΔH°MEC 7.3 kcal/mol per base triplet relative to the cytosine-substituted oligomer in the DNA triple helix. We observe no major conformational differences in 5-methylcytosine versus cytosine-substituted triple helices during molecular dynamics. These studies provide a greater understanding of key physicochemical mechanism(s) and properties of DNA oligomers incorporated into DNA triple helices containing 5-methylcytosine versus cytosine involved in modulating the stability of hybridization.

Original languageEnglish (US)
Pages (from-to)5356-5362
Number of pages7
JournalJournal of the American Chemical Society
Volume114
Issue number13
StatePublished - 1992
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)

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