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| | {{STRUCTURE_1n5c| PDB=1n5c | SCENE= }} | | {{STRUCTURE_1n5c| PDB=1n5c | SCENE= }} |
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| - | '''Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG'''
| + | ===Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG=== |
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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_12787670}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 12787670 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_12787670}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: 3,n4-etheno-2'-cytidine modification opposite g]] | | [[Category: 3,n4-etheno-2'-cytidine modification opposite g]] |
| | [[Category: B form double helix]] | | [[Category: B form double helix]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:06:55 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 13 15:17:08 2008'' |
Revision as of 12:17, 13 July 2008
Template:STRUCTURE 1n5c
Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATT(ethenoC)GCG
Template:ABSTRACT PUBMED 12787670
About this Structure
Full crystallographic information is available from OCA.
Reference
Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2'-deoxycytidine in the dodecamer 5'-CGCGAATTepsilonCGCG-3'., Freisinger E, Fernandes A, Grollman AP, Kisker C, J Mol Biol. 2003 Jun 13;329(4):685-97. PMID:12787670
Page seeded by OCA on Sun Jul 13 15:17:08 2008
