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New page: left|200px<br /><applet load="2awv" size="350" color="white" frame="true" align="right" spinBox="true" caption="2awv" /> '''NMR Structural Analysis of the dimer of 5MCC...
 
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[[Image:2awv.gif|left|200px]]<br /><applet load="2awv" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2awv" />
'''NMR Structural Analysis of the dimer of 5MCCTCATCC'''<br />


==Overview==
==NMR Structural Analysis of the dimer of 5MCCTCATCC==
At slightly acidic pH, the association of two d(5mCCTCACTCC) strands, results in the formation of an i-motif dimer. Using NMR methods, we, investigated the structure of [d(5mCCTCACTCC)]2, the internal motion of, the base pairs stacked in the i-motif core, the dimer formation and, dissociation kinetics versus pH. The excellent resolution of the 1H and, 31P spectra provided the determination of dihedral angles, which together, with a large set of distance restraints, improve substantially the, definition of the sugar-phosphate backbone by comparison with previous NMR, studies of i-motif structures. [d(5mCCTCACTCC)]2 is built by intercalation, of two symmetrical hairpins held together by six symmetrical C*C+ pairs, and by pair T7*T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The, base pair intercalation order is, C9*C9+/5mC1*5mC1+/C8*C8+/C2*C2+/T7.T7/C6*C6+/C4*C4+. The T3 bases are, flipped out in the wide grooves. The core of the structure includes four, long-lived pairs whose lifetimes at 15 degrees C range from 100 s (C8*C8+), to 0.18 s (T7*T7). The formation rate and the lifetime of, [d(5mCCTCACTCC)]2 were measured between pH 6.8 and 4.8. The dimer, formation rate is three to four magnitude orders slower than that of a, B-DNA duplex. It depends on pH, as it must occur for a bimolecular process, involving non cooperative association of neutral and protonated residues., In the range of pH investigated, the dimer lifetime, 500 s at 0 degrees C, pH 6.8, varies approximately as 10(-pH).
<StructureSection load='2awv' size='340' side='right'caption='[[2awv]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2awv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AWV FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MCY:5-METHYL-2-DEOXYCYTIDINE'>MCY</scene></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=2awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2awv OCA], [https://pdbe.org/2awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2awv RCSB], [https://www.ebi.ac.uk/pdbsum/2awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2awv ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
At slightly acidic pH, the association of two d(5mCCTCACTCC) strands results in the formation of an i-motif dimer. Using NMR methods, we investigated the structure of [d(5mCCTCACTCC)]2, the internal motion of the base pairs stacked in the i-motif core, the dimer formation and dissociation kinetics versus pH. The excellent resolution of the 1H and 31P spectra provided the determination of dihedral angles, which together with a large set of distance restraints, improve substantially the definition of the sugar-phosphate backbone by comparison with previous NMR studies of i-motif structures. [d(5mCCTCACTCC)]2 is built by intercalation of two symmetrical hairpins held together by six symmetrical C*C+ pairs and by pair T7*T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The base pair intercalation order is C9*C9+/5mC1*5mC1+/C8*C8+/C2*C2+/T7.T7/C6*C6+/C4*C4+. The T3 bases are flipped out in the wide grooves. The core of the structure includes four long-lived pairs whose lifetimes at 15 degrees C range from 100 s (C8*C8+) to 0.18 s (T7*T7). The formation rate and the lifetime of [d(5mCCTCACTCC)]2 were measured between pH 6.8 and 4.8. The dimer formation rate is three to four magnitude orders slower than that of a B-DNA duplex. It depends on pH, as it must occur for a bimolecular process involving non cooperative association of neutral and protonated residues. In the range of pH investigated, the dimer lifetime, 500 s at 0 degrees C, pH 6.8, varies approximately as 10(-pH).


==About this Structure==
Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC).,Canalia M, Leroy JL Nucleic Acids Res. 2005 Oct 4;33(17):5471-81. Print 2005. PMID:16204453<ref>PMID:16204453</ref>
2AWV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC)., Canalia M, Leroy JL, Nucleic Acids Res. 2005 Oct 4;33(17):5471-81. Print 2005. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16204453 16204453]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 2awv" style="background-color:#fffaf0;"></div>
[[Category: Canalia, M.]]
== References ==
[[Category: Leroy, J.L.]]
<references/>
[[Category: dimer]]
__TOC__
[[Category: hemiprotonated cc+ pairs]]
</StructureSection>
[[Category: i-motif]]
[[Category: Large Structures]]
 
[[Category: Canalia M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:11:41 2008''
[[Category: Leroy J-L]]
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