ArticleBiophysical journal2003
Stability of the I-motif structure is related to the interactions between phosphodiester backbones.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Unraveling G-Quadruplex and i-Motif Coexistence Within a Double-Stranded DNA.Angewandte Chemie (International ed. in English) · 2026Article
- Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs.Molecules (Basel, Switzerland) · 2024Review
- Structural Motifs at the Telomeres and Their Role in Regulatory Pathways.Biochemistry · 2024Review
- Replication-induced DNA secondary structures drive fork uncoupling and breakage.The EMBO journal · 2023Article
- Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations.International journal of molecular sciences · 2023Article
- Crystal Structure of an i-Motif from the HRAS Oncogene Promoter.Angewandte Chemie (International ed. in English) · 2023Article
- Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.Nucleic acids research · 2021Article
- A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription.Nucleic acids research · 2019Article
- Systematic investigation of sequence requirements for DNA i-motif formation.Nucleic acids research · 2019Article
- DNAComputational and structural biotechnology journal · 2019Article
- i-Motif DNA: structural features and significance to cell biology.Nucleic acids research · 2018Article
- Stabilization of i-motif structures by 2'-β-fluorination of DNA.Nucleic acids research · 2016Article
- Reversible DNA i-motif to hairpin switching induced by copper(II) cations.Chemical communications (Cambridge, England) · 2015Article
- Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC 4Y m) Monitored with Electrospray Ionization Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2015Article
- The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules.Journal of the American Chemical Society · 2014Article
- Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation.Biophysical journal · 2013Article
- Biophysical characterization of an ensemble of intramolecular i-motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence.Biophysical journal · 2010Article
- The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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-motif stability. Tighter interactions between the sugars are observed in the case of N-type sugar puckers.
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