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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'''
| + | ===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).
| + | The line below this paragraph, {{ABSTRACT_PUBMED_16204453}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 16204453 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_16204453}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Hemiprotonated cc+ pair]] | | [[Category: Hemiprotonated cc+ pair]] |
| | [[Category: I-motif]] | | [[Category: I-motif]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:34:09 2008'' | + | |
| | + | ''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
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
