2awv
From Proteopedia
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[[Image:2awv.gif|left|200px]] | [[Image:2awv.gif|left|200px]] | ||
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| - | + | {{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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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AWV OCA]. | |
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/16204453 16204453] | 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://www.ncbi.nlm.nih.gov/pubmed/16204453 16204453] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Canalia, M.]] | [[Category: Canalia, M.]] | ||
[[Category: Leroy, J L.]] | [[Category: Leroy, J L.]] | ||
| - | [[Category: | + | [[Category: Dimer]] |
| - | [[Category: | + | [[Category: Hemiprotonated cc+ pair]] |
| - | [[Category: | + | [[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 | + | |
Revision as of 16:34, 3 May 2008
NMR Structural Analysis of the dimer of 5MCCTCATCC
Overview
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
Full crystallographic 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 Sat May 3 19:34:09 2008
