C5-Methylation of Cytosine in B-DNA Thermodynamically and Kinetically Stabilizes BI

Abstract

We have examined the backbone dynamics of two alternating purine-pyrimidine dodecamers. One sequence consists of "pure" GC bases; the other one contains 5-methylcytosines. The effect of the methyl groups on the backbone substates BI/BII was investigated by means of molecular dynamics. The methylation influences, on one hand, the transition barrier between BI and BII and, on the other hand, the state of equilibrium. The kinetic consequences are an increase of the DeltaG of Gp5mC steps by 1.5 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol (compared with the nonmethylated DNA). Thus, the additive group differentiates between the two occurring dinucleotide steps and renders the phosphate of the 5-methylcytosine more rigid, as proposed by experimental studies. The thermodynamic consequences are an increase of the DeltaG of Gp5mC steps by 1.1 kcal/mol and a decrease of the DeltaG of 5mCpG steps by 0.8 kcal/mol. The reason for this shift in equilibrium is still not completely clear on a molecular basis. But we can conclude that the indirect readout of DNA is influenced by methylation.

The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA

“…The simulations for 5mCB-DNA, on the other hand, show a BI population of 92% and, correspondingly, a BII population of 8%. The results of the time evolution of ε−ζ for B- and 5mCB-DNA (Figures S13 and S14) and the cumulative averages of the BI states from the simulations (Figure S15, top panel) support the conclusion that methylation stabilizes the BI state [28]. Using a similar approach to Rauch et al [28], the free energy profiles for the BI/BII transitions were calculated from the B- and 5mCB-DNA simulations.…”

“…With the emergence of improved force fields [23], [24] and increasing computer power, simulations of B-DNA in the microsecond timescales have been conducted [22], [23], [25], [26]. However, despite the large number of simulations available, only 10–15 ns simulations of methylated B-DNA [27], [28] or unmethylated Z-DNA have been reported [23]. Since a detailed understanding of the effects of CpG methylation on the dynamics of both B- and Z-DNA at the molecular level is still lacking, the factors underlying methylation-assisted B-to-Z DNA transition remain largely unknown.…”

Methylation of Cytosine at C5 in a CpG Sequence Context Causes a Conformational Switch of a Benzo[a]pyrene diol epoxide-N2-guanine Adduct in DNA from a Minor Groove Alignment to Intercalation with Base Displacement

“…45 Sowers et al 38 reported that the major effect of the methyl group in meC is an increase in the polarizability of the pyrimidine that results in increased hydrophobic basestacking interactions and, in turn, a thermal stabilization of double-stranded DNA. A recent molecular dynamics study of the effects of cytosine methylation in a CpG sequence context suggests that the thermodynamic equilibrium between the BI and BII phosphate backbone conformational states is influenced by the presence of the methyl group, thus thermodynamically leading to an increased base-stacking energy, 46 as reported earlier. 38 An experimental FTIR study of a different double-stranded CpG oligonucleotide sequence context was interpreted in terms of a different alteration of the BI/BII equilibrium, an enhanced contribution of the C2′-endo sugar conformation, and a change in the glycosidic torsion angle upon methylation.…”

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

“…It was argued that the presence of 5mC rigidifies the backbone of the DNA [50] increases base pair stacking [51,52] and alters the solvation dynamics in the major groove [53]. It was also shown that 5mC changes the net curvature of A-tract containing DNA [54].…”