Sunday, February 6, 2011

A G-T mismatch with perfect Watson-Crick geometry

In the February 1, 2011 issue of PNAS [108(5)], there is an interesting article "Replication infidelity via a mismatch with Watson–Crick geometry" by Bebenek et al. They solved the Pol λ DL ternary complex (PDB id: 3PML) which has a G-T nascent mispair in "perfect" Watson-Crick geometry (see their Fig 4, linked below).

From an H-bonding (energitic) point of view, the G-T mispair (with three "H-bonds") can only be possible if G or T is in the rare enol tautomeric state, or is ionized. The pH dependence of single nucleotide disincorporation seems to be consistent with an ionized base pair. Note the G-T mispair is different from a Wobble pair in which G and T have a relative sheared motion (see also Fig. 4C above).

I am glad to find that 3DNA was used in deriving the parameters. By design, 3DNA should be able to identify such "unusual" mispair as easily as for a normal Watson-Crick pair. As noted in our 2008 3DNA Nature Protocols paper,
By taking advantage of the standard base reference frame and selected geometric features, the find_pair program within 3DNA can identify all possible nucleic-acid base pairs, whether they are canonical Watson–Crick or noncanonical pairs and are made up of normal or modified bases, in any tautomeric form or protonation state. (p1217)
Moreover, 3DNA does notice and signify (wit a * instead of the normal -) the atypical H-bonding feature of the G-T mispair to draw further attentions.
5 T-*---g  [3]  O2 - N2  3.06  N3 * N1  2.97  O4 * O6  2.66
Hopefully, this example helps illustrate some of 3DNA's unique features that would hopefully be more widely recognized and applied.