Base-pairing geometry

FIGURE 25-6 Contribution of base-pair geometry to the fidelity of DNA replication, (a) The standard A=T and G=C base pairs have very similar geometries, and an active site sized to fit one (blue shading) will generally accommodate the other, (b) The geometry of incorrectly paired bases can exclude them from the active site, as occurs on DNA polymerase I. 

Excellent summary of the molecular basis of replication fidelity by a DNA polymerase—base-pair geometry as well as hydrogen bonding. 

Fig. 7-5 Sequence-dependent variations in the base-pairing geometry of DNA.

The Structure of DNA and RNA Double Helices is Determined by Watson-Crick Base-Pair Geometry... 

Table 1 Parameters describing complementary base-pair geometry in high-resolution DNA crystal structures ...

Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu X-J, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung C-S, Westhof E, Wolberger C, Berman HM. A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 2001 313 229-237. 

Where E(XY) is the total energy of the XY base pair in the ground state E(Xxy) and E(Yxy) are the total energies of X (adenine in case of the AT (AU) base pair and guanine in the case of tiie GC base pair) and Y (thymine (uracil) in the case of the AT (AU) base pair and cytosine in the case of the GC base pair) monomeric moieties using the optimized XY base pair geometry and ghost atoms in place of the complementary base. 

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