2AWV

NMR Structural Analysis of the dimer of 5MCCTCATCC

Summary for 2AWV

• Entry DOI: 10.2210/pdb2awv/pdb
• Related: 1Q2T 1RME
• Descriptor: 5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3' (1 entity in total)
• Functional Keywords: i-motif, hemiprotonated cc+ pairs, dimer, dna
• Total number of polymer chains: 2
• Total formula weight: 5091.55

Authors

Canalia, M.,Leroy, J.-L. (deposition date: 2005-09-02, release date: 2005-09-20, Last modification date: 2024-05-29)

Primary citation

Canalia, M.,Leroy, J.-L.
Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC).
Nucleic Acids Res., 33:5471-5481, 2005

PubMed Abstract: 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).

PubMed: 16204453
DOI: 10.1093/nar/gki843

Experimental method

SOLUTION NMR