The Effect of a G:T Mispair on the Dynamics of DNA

Abstract

Distortions in the DNA sequence such as damages or mispairs are specifically recognized and processed by DNA repair enzymes. A particular challenge for the enzymatic specificity is the recognition of a wrongly-placed native nucleotide such as thymine in T:G mispairs. An important step of substrate binding which is observed in many repair proteins is the flipping of the target base out of the DNA helix into the enzyme’s active site. In this work we investigate how much the intrinsic dynamics of mispaired DNA is changed compared to canonical DNA. Our molecular dynamics simulations of DNA with and without T:G mispairs show significant differences in the conformation of paired and mispaired DNA. The wobble pair T:G shows local distortions such as twist, shear and stretch which deviate from canonical B form values. Moreover, the T:G mispair is found to be kinetically less stable, exhibiting two states with respect to base opening: a closed state comparable to the canonical base pairs, and a more open state, indicating a proneness for base flip. In addition, we observe that the thymine base in a T:G mispair is significantly more probable to be flipped than thymine in a T:A pair or cytosine in a C:G pair. Such local deformations and in particular the existence of a second, more-open state can be speculated to help the target-site recognition by repair enzymes.

DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip

“…Extrahelical conformations form local minima separated from the principal minimum by activation barriers. Similar results have been reported in the literature for a subset of the base pairs considered in this study (30,46,47).…”

“…al. (30) observed a notable (∼10 • ) shift of the minimum from unbiased to biased simulation of the TG mismatched system. They hypothesize that the long timescale of flipping and re-stacking causes the free energy to converge slowly.…”

“…With our 2D potential we identify configurations we would otherwise not observe biasing only one base; this explains why our results disagree with previous studies: they each bias one base where we bias two. (10,13,30,46,48) For most configurations studied, a lower-energy "plus" shape is apparent in the 2D FES, with low-energy states extending both vertically and horizontally from the global minimum. We display representative free energies in Fig.…”

Dynamics of spontaneous flipping of a mismatched base in DNA duplex

“…Because, as discussed above, the base flipping is a slow process that is beyond the capability of normal molecular dynamics simulations, enhanced sampling techniques are needed. In most previous studies, the umbrella sampling method, for which a predefined reaction coordinate has to be taken, was applied to calculate the free-energy profile for base flipping and has yielded much important information (18,21,47,48). However, Song et al showed (48) that slightly different preselected reaction coordinates can lead to very different results.…”

Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

“…The reaction coordinate for the base flip has been defined as a pseudo-dihedral angle between the flipping base, the sugar moiety of the same nucleotide, the sugar of the next nucleotide and the base of the next nucleotide, plus the base and sugar of the opposing nucleotide downstream (see Figure 8). This definition of the flipping coordinate is the same as we had used in an earlier study [14] and is similar to the one proposed and applied in [21,40,41]. The potential of mean force (free energy profile) was obtained by discretizing the reaction coordinate between 10° and 180° into windows of a 2° width, and in each window, 2000 samples were collected before the bias was applied.…”