ArticleScientific reports2016
Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Polymeric Properties of Telomeric G-Quadruplex Multimers: Effects of Chemically Inert Crowders.Biomacromolecules · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter.Nucleic acids research · 2024Article
- Uncertainties in Markov State Models of Small Proteins.Journal of chemical theory and computation · 2023Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study.Molecules (Basel, Switzerland) · 2018Article
- Article
- Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.Nucleic acids research · 2017Article
- StreAM-[Formula: see text]: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.Algorithms for molecular biology : AMB · 2017Article
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8 authors.
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Abstract
Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.
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