2awv: Difference between revisions
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[[Image:2awv.gif|left|200px]] | [[Image:2awv.gif|left|200px]] | ||
'''NMR Structural Analysis of the dimer of 5MCCTCATCC''' | {{Structure | ||
|PDB= 2awv |SIZE=350|CAPTION= <scene name='initialview01'>2awv</scene> | |||
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'''NMR Structural Analysis of the dimer of 5MCCTCATCC''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2AWV is a [ | 2AWV is a [[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== | ==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:// | 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: Protein complex]] | ||
[[Category: Canalia, M.]] | [[Category: Canalia, M.]] | ||
[[Category: Leroy, J L.]] | [[Category: Leroy, J L.]] | ||
[[Category: dimer]] | [[Category: dimer]] | ||
[[Category: hemiprotonated cc+ | [[Category: hemiprotonated cc+ pair]] | ||
[[Category: i-motif]] | [[Category: i-motif]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:54:50 2008'' | ||
Revision as of 13:54, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
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
2AWV is a Protein complex structure of sequences from [1]. 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
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