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Panels A and B of Figure 10 show the base stacking of the adduct region.
Panels C and D of Figure 10 show the base stacking of the adduct region.
At the adducted base pair, the base stacking of the duplex containing cyclic hemiacetal 8 was improved as compared to that of the duplex containing cyclic hemiacetal 10.
However, perturbations of the ε and ζ backbone torsion angles were observed, and the base stacking of the duplex was perturbed, which correlates with the observation that the α anomer of the AFB1 FAPY adduct blocks DNA replication.
This interaction is typically found in nucleic acid RRM domain complexes, along with base stacking of the next nucleotide with the fifth residue of RNP1, which is Phe157 in RRM1.
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Base pairing through hydrogen bonding between the cognate pairs A-T and C-G together within the base stack of the DNA double helix provides the molecular basis for the genetic code.
Plumridge A, Meisburger S.P, Andresen K, Pollack L, "The impact of base stacking on the conformations and electrostatics of single-stranded DNA," Nucleic Acids Research 45 7), 3932-3943 2017.
Plumridge A, Meisburger SP, Andresen K, Pollack L, "The impact of base stacking on the conformations and electrostatics of single-stranded DNA," Nucleic Acids Research 45 7), 3932-3943 (2017).
The poor base stacking of 5-hoC in duplex DNA has also been observed in the structures and pre-steady-state kinetics of dNTP insertion opposite the lesion.
These results, taken together with the lack of correlation between the affinity of MutS for a mismatch and its ability to signal repair, suggest that differences in hydrogen bonding, as well as base stacking, of mismatches may govern, in part, the efficiency of mismatch repair.
The exocyclic N6 group of A83 approaches the side chain carboxyl of E362 (helix α1) and its base stacks on the side chain of F354 (helix α1; Figure 4A).
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