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

Biophysical Journal
Thérèse E MalliavinJean-Louis Leroy

Abstract

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-mo...Continue Reading

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Citations

Aug 29, 2006·Nucleic Acids Research·Souvik ModiYamuna Krishnan
Apr 11, 2009·Briefings in Bioinformatics·William B LangdonAndrew P Harrison
Dec 24, 2013·Biophysical Journal·Raghvendra Pratap SinghFabrizio Cleri
May 12, 2016·Nucleic Acids Research·Hala Abou AssiMasad J Damha
Aug 8, 2015·Chemical Communications : Chem Comm·Henry Albert DayZoë Ann Ella Waller
May 21, 2015·Nanoscale·Saheli Halder, Yamuna Krishnan
Oct 31, 2007·Angewandte Chemie·Niti KumarMichael Petersen
Sep 9, 2011·Chemical Society Reviews·Jungkweon Choi, Tetsuro Majima
Feb 5, 2019·Nucleic Acids Research·Petra ŠkolákováMichaela Vorlíčková
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Aug 12, 2004·Journal of the American Chemical Society·Jirí SponerPavel Hobza
Dec 17, 2004·Journal of the American Chemical Society·Pascale HazelStephen Neidle
Oct 1, 2021·Chemical Reviews·Eric LargyValérie Gabelica

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