What's old is new: an alternative DNA excision repair pathway. Definitions and nomenclature of nucleic acid structure parameters.Repair of oxidative damage to DNA: enzymology and biology. Solution conformation determined by proton NMR and molecular mechanics calculations. Cuniasse P, Sowers LC, Eritja R, Kaplan B, Goodman MF, Cognet JA, Le Bret M, Guschlbauer W, Fazakerley GV.Cuniasse P, Sowers LC, Eritja R, Kaplan B, Goodman MF, Cognet JA, LeBret M, Guschlbauer W, Fazakerley GV.A nuclear magnetic resonance study of G, C and T opposite a model abasic site. The abasic site as a challenge to DNA polymerase. Cuniasse P, Fazakerley GV, Guschlbauer W, Kaplan BE, Sowers LC.Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC) x d(GCGTGTGTGCG): the unpaired thymine stacks inside the helix. Coppel Y, Berthet N, Coulombeau C, Coulombeau C, Garcia J, Lhomme J.Coding properties of poly(deoxycytidylic acid) templates containing uracil or apyrimidinic sites: in vitro modulation of mutagenesis by deoxyribonucleic acid repair enzymes. Structure and function of apurinic/apyrimidinic endonucleases. Arnott S, Chandrasekaran R, Birdsall DL, Leslie AG, Ratliff RL.This may not be the complete list of references from this article.
#AYADI CALCULATIONS PDF PDF#
The Full Text of this article is available as a PDF (130K). For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA.
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