Stability of the i-motif structure is related to the interactions between phosphodiester backbones

Thérèse E. Malliavin, Jocelyne Gau, Karim Snoussi, Jean Louis Leroy

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


The i-motif DNA tetrameric structure is formed of two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. The four phosphodiester backbones forming the structure define two narrow and wide grooves. The short interphosphate distances across the narrow groove induce a strong repulsion which should destabilize the tetramer. To investigate this point, molecular dynamics simulations were run on the [d(C2)]4 and [d(C4)]4 tetramers in 3′E and 5′E topologies, for which the interaction of the phosphodiester backbones through the narrow groove is different. The analysis of the simulations, using the Molecular Mechanics Generalized Born Solvation Area and Molecular Mechanics Poisson-Boltzmann Solvation Area approaches, shows that it is the van der Waals energy contribution which displays the largest relative difference between the two topologies. The comparison of the solvent-accessible area of each topology reveals that the sugar-sugar interactions account for the greater stability of the 3′E topology. This stresses the importance of the sugar-sugar contacts across the narrow groove which, enforcing the optimal backbone twisting, are essential to the base stacking and the i-motif stability. Tighter interactions between the sugars are observed in the case of N-type sugar puckers.

Original languageEnglish (US)
Pages (from-to)3838-3847
Number of pages10
JournalBiophysical journal
Issue number6
StatePublished - Jun 1 2003
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics


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