1N5C

Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG

Summary for 1N5C

• Entry DOI: 10.2210/pdb1n5c/pdb
• Descriptor: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3', SODIUM ION (3 entities in total)
• Functional Keywords: b form double helix, 3, n4-etheno-2'-cytidine modification opposite g, dna
• Total number of polymer chains: 1
• Total formula weight: 3710.40

Authors

Freisinger, E.,Fernandes, A.,Grollman, A.P.,Kisker, C.F. (deposition date: 2002-11-05, release date: 2003-06-03, Last modification date: 2024-04-03)

Primary citation

Freisinger, E.,Fernandes, A.,Grollman, A.P.,Kisker, C.F.
Crystallographic Characterization of an Exocyclic DNA Adduct: 3,N4-etheno-2'-deoxycytidine in the Dodecamer 5'-CGCGAATT(ethenoC)GCG-3'
J.Mol.Biol., 329:685-697, 2003

PubMed Abstract: Exocyclic DNA adducts are formed from metabolites of chemical carcinogens and have also been detected as endogenous lesions in human DNA. The exocyclic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilon dC), positioned opposite deoxyguanosine in the B-form duplex of the dodecanucleotide d(CGCGAATTepsilonCGCG), has been crystallographically characterized at 1.8A resolution. This self-complementary oligomer crystallizes in space group P3(2)12, containing a single strand in the asymmetric unit. The crystal structure was solved by isomorphous replacement with the corresponding unmodified dodecamer structure. Exposure of both structures to identical crystal packing forces allows a detailed investigation of the influence of the exocyclic base adduct on the overall helical structure and local geometry. Structural changes are limited to the epsilon C:G and adjacent T:A and G:C base-pairs. The standard Watson-Crick base-pairing scheme, retained in the T:A and G:C base-pairs, is blocked by the etheno bridge in the epsilon C:G pair. In its place, a hydrogen bond involving O2 of epsilon C and N1 of G is present. Comparison with an epsilon dC-containing NMR structure confirms the general conformation reported for epsilon C:G, including the hydrogen bonding features. Superposition with the crystal structure of a DNA duplex containing a T:G wobble pair shows similar structural changes imposed by both mismatches. Evaluation of the hydration shell of the duplex with bond valence calculations reveals two sodium ions in the crystal.

PubMed: 12787670
DOI: 10.1016/S0022-2836(03)00445-5

Experimental method

X-RAY DIFFRACTION (1.79 Å)