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2LG0

structure of the duplex containing (5'S)-8,5'-cyclo-2'-deoxyadenosine

Summary for 2LG0
Entry DOI10.2210/pdb2lg0/pdb
NMR InformationBMRB: 17789
DescriptorDNA (5'-D(*GP*TP*GP*CP*(02I)P*TP*GP*TP*TP*TP*GP*T)-3'), DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*TP*GP*CP*AP*C)-3') (2 entities in total)
Functional Keywords(5's)-8, 5'-cyclo-2'-deoxyadenosine, cyclopurine, cyclo-da, dna
Total number of polymer chains2
Total formula weight7321.80
Authors
Huang, H.,Das, R.S.,Basu, A.,Stone, M.P. (deposition date: 2011-07-18, release date: 2012-06-27, Last modification date: 2024-05-15)
Primary citationHuang, H.,Das, R.S.,Basu, A.K.,Stone, M.P.
Structure of (5'S)-8,5'-cyclo-2'-deoxyguanosine in DNA.
J.Am.Chem.Soc., 133:20357-20368, 2011
Cited by
PubMed Abstract: Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the β, γ, and χ torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG·dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC·dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG·dC and 3'- neighbor dT·dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.
PubMed: 22103478
DOI: 10.1021/ja207407n
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

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数据于2025-07-09公开中

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