1fkz - Revision history

OCA at 18:35, 29 November 2023

2023-11-29T18:35:49Z

←Older revision		Revision as of 18:35, 29 November 2023
Line 1:		Line 1:

	==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==		==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==
-	<StructureSection load='1fkz' size='340' side='right'caption='[[1fkz~~]], [[NMR_Ensembles_of_Models \| 2 NMR models~~]]' scene=''>	+	<StructureSection load='1fkz' size='340' side='right'caption='[[1fkz]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[1fky\|1fky]]</div~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [https://pdbe.org/1fkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [https://www.ebi.ac.uk/pdbsum/1fkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkz ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [https://pdbe.org/1fkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [https://www.ebi.ac.uk/pdbsum/1fkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkz ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boulard, Y]]	+	[[Category: Boulard Y]]
-	[[Category: Cognet~~, J A.H~~]]	+	[[Category: Cognet JAH]]
-	[[Category: Fazakerley~~, G V]]~~	+	[[Category: Fazakerley GV]]
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Deoxyribonucleic acid]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: K-ra~~]]	+

OCA at 07:05, 24 March 2021

2021-03-24T07:05:46Z

←Older revision		Revision as of 07:05, 24 March 2021
Line 3:		Line 3:
	<StructureSection load='1fkz' size='340' side='right'caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>		<StructureSection load='1fkz' size='340' side='right'caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fky\|1fky]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [~~http~~://pdbe.org/1fkz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1fkz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [https://pdbe.org/1fkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [https://www.ebi.ac.uk/pdbsum/1fkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:04, 19 June 2019

2019-06-19T07:04:23Z

←Older revision		Revision as of 07:04, 19 June 2019
Line 1:		Line 1:

	==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==		==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==
-	<StructureSection load='1fkz' size='340' side='right' caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>	+	<StructureSection load='1fkz' size='340' side='right'caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Boulard, Y]]		[[Category: Boulard, Y]]
	[[Category: Cognet, J A.H]]		[[Category: Cognet, J A.H]]

OCA at 10:54, 13 September 2017

2017-09-13T10:54:59Z

←Older revision		Revision as of 10:54, 13 September 2017
Line 1:		Line 1:
		+
	==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==		==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==
	<StructureSection load='1fkz' size='340' side='right' caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>		<StructureSection load='1fkz' size='340' side='right' caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://pdbe.org/1fkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://pdbe.org/1fkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fkz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:53, 10 September 2015

2015-09-10T20:53:24Z

←Older revision		Revision as of 20:53, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://pdbe.org/1fkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1fkz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:36, 22 December 2014

2014-12-22T23:36:08Z

←Older revision		Revision as of 23:36, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Boulard, Y.]]	+	[[Category: Boulard, Y]]
-	[[Category: Cognet, J A.H.]]	+	[[Category: Cognet, J A.H]]
-	[[Category: Fazakerley, G V.]]	+	[[Category: Fazakerley, G V]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: K-ra]]		[[Category: K-ra]]

OCA at 13:18, 28 September 2014

2014-09-28T13:18:35Z

←Older revision		Revision as of 13:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1fkz.~~png~~\|~~left~~\|~~200px~~]]	+	==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==
		+	<StructureSection load='1fkz' size='340' side='right' caption='[[1fkz]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FKZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fky\|1fky]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fkz RCSB], [http://www.ebi.ac.uk/pdbsum/1fkz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1fkz\| PDB=1fkz \| SCENE= }}~~	+	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<ref>PMID:9159474</ref>

-	~~===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===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9159474}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1fkz]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1FKZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009159474<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
	[[Category: Cognet, J A.H.]]		[[Category: Cognet, J A.H.]]

OCA: Protected "1fkz" [edit=sysop:move=sysop]

2012-11-21T10:14:03Z

Protected "1fkz" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:14, 21 November 2012

OCA at 10:13, 21 November 2012

2012-11-21T10:13:58Z

←Older revision		Revision as of 10:13, 21 November 2012
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-	{{Seed}}
	[[Image:1fkz.png\|left\|200px]]		[[Image:1fkz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1fkz", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1fkz\| PDB=1fkz \| SCENE= }}		{{STRUCTURE_1fkz\| PDB=1fkz \| SCENE= }}

	===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===		===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===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9159474}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9159474 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9159474}}		{{ABSTRACT_PUBMED_9159474}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA].	+	[[1fkz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA].

	==Reference==		==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:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~9159474 9159474]~~	+	<ref group="xtra">PMID:009159474</ref><references group="xtra"/>
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
	[[Category: Cognet, J A.H.]]		[[Category: Cognet, J A.H.]]
Line 29:		Line 17:
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
		+	[[Category: Dna]]
	[[Category: K-ra]]		[[Category: K-ra]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 03:25:21 2008''

OCA at 00:25, 1 July 2008

2008-07-01T00:25:23Z

←Older revision		Revision as of 00:25, 1 July 2008
Line 1:		Line 1:
-	[[Image:1fkz.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1fkz.png\|left\|200px]]

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	{{STRUCTURE_1fkz\| PDB=1fkz \| SCENE= }}		{{STRUCTURE_1fkz\| PDB=1fkz \| SCENE= }}

-	~~'''~~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~~'''~~	+	===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===


-	~~==Overview==~~	+	<!--
-	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.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9159474}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9159474 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9159474}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKZ OCA].

	==Reference==		==Reference==
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	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: K-ra]]		[[Category: K-ra]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ ~~2 16~~:26:59 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 03:25:21 2008''