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1fky

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{{STRUCTURE_1fky| PDB=1fky | SCENE= }}
{{STRUCTURE_1fky| PDB=1fky | SCENE= }}
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'''NMR STUDY OF B-DNA CONTAINING A MISMATCHED BASE PAIR IN THE 29-39 K-RAS GENE SEQUENCE: CC CT C+C C+T, 2 STRUCTURES'''
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===NMR STUDY OF B-DNA CONTAINING A MISMATCHED BASE PAIR IN THE 29-39 K-RAS GENE SEQUENCE: CC CT C+C C+T, 2 STRUCTURES===
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==Overview==
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The DNA duplexes 5' d(GCCACCAGCTC) x d(GAGCTXGTGGC), where the base X is either cytosine or thymine, have been studied by one and two-dimensional nuclear magnetic resonance, energy minimization and molecular dynamics. The sequence studied corresponds to the region 29 to 39 of the K-ras gene and is a hot spot for mutations. The results show that both duplexes adopt a globally B-DNA-type structure. For the C x C mismatch, we observe a structural change as a function of pH with an apparent pK of 6.95. The neutral species has only one hydrogen bond between the two bases but shows two families of wobble structures where one base or the other is displaced in the major groove. The protonated species has two hydrogen bonds and two structures but of unequal populations. In both systems, the sugar puckers remain predominantly C2'-endo and no significant changes in the backbone structure are observed. The neutral C . T mismatch is stabilized by two hydrogen bonds but, surprisingly, it can also be protonated, although the apparent pK is much lower, 5.65. In this case, protonation does not result in an additional hydrogen bond but must be due to better base-stacking interactions for C+ x T. The NMR data show that the environment of the T imino proton is very similar for C x T and C+ x T, although the hydrogen bond acceptor would be expected to be a nitrogen atom in the former case and an oxygen atom in the latter. We propose that for both structures there is an intervening water molecule which in addition reduces backbone strain. We have also measured the fluctuations during molecular dynamics runs in these mismatches. All are greater than for Watson-Crick base-pairs and the C x C mismatch shows very pronounced mobility.
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(as it appears on PubMed at http://www.pubmed.gov), where 9159474 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9159474}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKY OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKY OCA].
==Reference==
==Reference==
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[[Category: Deoxyribonucleic acid]]
[[Category: Deoxyribonucleic acid]]
[[Category: K-ra]]
[[Category: K-ra]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 16:27:00 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 03:25:20 2008''

Revision as of 00:25, 1 July 2008

Image:1fky.png

Template:STRUCTURE 1fky

NMR STUDY OF B-DNA CONTAINING A MISMATCHED BASE PAIR IN THE 29-39 K-RAS GENE SEQUENCE: CC CT C+C C+T, 2 STRUCTURES

Template:ABSTRACT PUBMED 9159474

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure as a function of pH of two central mismatches, C . T and C . C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics., Boulard Y, Cognet JA, Fazakerley GV, J Mol Biol. 1997 May 2;268(2):331-47. PMID:9159474

Page seeded by OCA on Tue Jul 1 03:25:20 2008

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