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| | {{STRUCTURE_213d| PDB=213d | SCENE= }} | | {{STRUCTURE_213d| PDB=213d | SCENE= }} |
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| - | '''CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCIGGCCM5CGG) AT 1.6 ANGSTROMS SHOWING THE UNEXPECTED WOBBLE I.M5C BASE PAIR'''
| + | ===CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCIGGCCM5CGG) AT 1.6 ANGSTROMS SHOWING THE UNEXPECTED WOBBLE I.M5C BASE PAIR=== |
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| - | ==Overview==
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| - | The crystal structure of the self-complementary decamer d(CCIGGCCm5CGG), where I and m5C replace A and T, respectively, in the Watson-Crick B-DNA decamer d(CCAGGCCTGG) is in the A-DNA conformation. Furthermore, the A-DNA duplex exhibits the unexpected wobble I.m5C+ base pairs with N3 of 5-methylcytosine protonated. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with a = 25.02, b = 44.95 and c = 47.62 A with one DNA duplex in the asymmetric unit. Intensity data were collected on our Siemens area detector to 1.6 A resolution. The structure was solved by the molecular placement method starting with a model from an isomorphous structure. The refinement gave a final R value of 16.3% for 404 DNA atoms and 104 water molecules using 5119 reflections. The hydration of the I.m5C+ wobble base pairs in the major groove stabilizes them as in the G.T/G.U wobbles. A comparison with the Watson-Crick base pairs of another isomorphous structure d(GCGGGCCCGC) reveals that the wobble base pairs are better described by a rotation of the individual nucleotide units around their centers of gravity. This is in contrast to the earlier description of translation of the bases into the grooves. The exposed N4 amino group of 5-methylcytosine in the wobble base pair provides a rationale for its deamination to thymine. | + | The line below this paragraph, {{ABSTRACT_PUBMED_8527669}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 8527669 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_8527669}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Double helix]] | | [[Category: Double helix]] |
| | [[Category: Modified]] | | [[Category: Modified]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:18:44 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 15:10:01 2008'' |
Revision as of 12:10, 27 July 2008
Template:STRUCTURE 213d
CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCIGGCCM5CGG) AT 1.6 ANGSTROMS SHOWING THE UNEXPECTED WOBBLE I.M5C BASE PAIR
Template:ABSTRACT PUBMED 8527669
About this Structure
Full crystallographic information is available from OCA.
Reference
Crystal structure of the A-DNA decamer d(CCIGGCCm5CGG) at 1.6 A showing the unexpected wobble I.m5C base pair., Ramakrishnan B, Sundaralingam M, Biophys J. 1995 Aug;69(2):553-8. PMID:8527669
Page seeded by OCA on Sun Jul 27 15:10:01 2008
