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2awv

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{{STRUCTURE_2awv| PDB=2awv | SCENE= }}
{{STRUCTURE_2awv| PDB=2awv | SCENE= }}
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'''NMR Structural Analysis of the dimer of 5MCCTCATCC'''
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===NMR Structural Analysis of the dimer of 5MCCTCATCC===
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==Overview==
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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).
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{{ABSTRACT_PUBMED_16204453}}
==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=2AWV OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA].
==Reference==
==Reference==
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[[Category: Hemiprotonated cc+ pair]]
[[Category: Hemiprotonated cc+ pair]]
[[Category: I-motif]]
[[Category: I-motif]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:40:01 2008''

Revision as of 11:40, 28 July 2008

Image:2awv.png

Template:STRUCTURE 2awv

NMR Structural Analysis of the dimer of 5MCCTCATCC

Template:ABSTRACT PUBMED 16204453

About this Structure

Full experimental information is available from OCA.

Reference

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

Page seeded by OCA on Mon Jul 28 14:40:01 2008

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