ArticlePloS one2013
Structural dynamics of human telomeric G-quadruplex loops studied by molecular dynamics simulations.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- Sequence Determinants of G-Quadruplex Thermostability: Aligning Evidence from High-Precision Biophysics and High-Throughput Genomics.Biomolecules · 2025Review
- The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex.Nucleic acids research · 2021Article
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Journal of chemical theory and computation · 2017Article
- The systematic approach to describing conformational rearrangements in G-quadruplexes.Journal of biomolecular structure & dynamics · 2016Article
- Extended molecular dynamics of a c-kit promoter quadruplex.Nucleic acids research · 2015Article
- Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.Protein & cell · 2015Article
- Flexibility and structural conservation in a c-KIT G-quadruplex.Nucleic acids research · 2015Article
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3 authors.
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Abstract
Loops which are linkers connecting G-strands and supporting the G-tetrad core in G-quadruplex are important for biological roles of G-quadruplexes. TTA loop is a common sequence which mainly resides in human telomeric DNA (hTel) G-quadruplex. A series of molecular dynamics (MD) simulations were carried out to investigate the structural dynamics of TTA loops. We found that (1) the TA base pair formed in TTA loops are very stable, the occupied of all hydrogen bonds are more than 0.95. (2) The TA base pair makes the adjacent G-quartet more stable than others. (3) For the edgewise loop and the diagonal loop, most loop bases are stacking with others, only few bases have considerable freedom. (4) The stabilities of these stacking structures are distinct. Part of the loops, especially TA base pairs, and bases stacking with the G-quartet, maintain certain stable conformations in the simulation, but other parts, like TT and TA stacking structures, are not stable enough. For the first time, spontaneous conformational switches of TTA edgewise loops were observed in our long time MD simulations. (5) For double chain reversal loop, it is really hard to maintain a stable conformation in the long time simulation under present force fields (parm99 and parmbsc0), as it has multiple conformations with similar free energies.
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