ArticleNucleic acids research2013
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Polymeric Properties of Telomeric G-Quadruplex Multimers: Effects of Chemically Inert Crowders.Biomacromolecules · 2025Article
- 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
- Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.International journal of molecular sciences · 2023Article
- Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.The journal of physical chemistry. B · 2022Article
- New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes.Molecules (Basel, Switzerland) · 2021Review
- Polarizable Molecular Dynamics Simulations of TwoJournal of chemical theory and computation · 2020Article
- Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2020Review
- Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail.PLoS computational biology · 2019Article
- Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.Nucleic acids research · 2018Article
- Mesoscopic model for DNA G-quadruplex unfolding.Scientific reports · 2017Article
- Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.Biophysical journal · 2017Article
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Journal of chemical theory and computation · 2017Article
- Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations.ACS omega · 2017Article
- Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad-a common structural unit of G-quadruplex DNA.Nucleic acids research · 2016Article
- Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.Nucleic acids research · 2015Article
- Extended molecular dynamics of a c-kit promoter quadruplex.Nucleic acids research · 2015Article
- Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes.Nucleic acids research · 2015Article
- Loop flexibility in human telomeric quadruplex small-molecule complexes.Nucleic acids research · 2015Article
- Flexibility and structural conservation in a c-KIT G-quadruplex.Nucleic acids research · 2015Article
- Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats.Nucleic acids research · 2014Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.
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