ArticleJournal of the American Chemical Society2011
Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 70 citations in OpenAlex.
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- How loop lengths shape topological preferences of two-tetrad G-quadruplexes.Nucleic acids research · 2026Article
- Sequence Determinants of G-Quadruplex Thermostability: Aligning Evidence from High-Precision Biophysics and High-Throughput Genomics.Biomolecules · 2025Review
- Large-Scale Conformational Analysis Explains G-Quadruplex Topological Landscape.The journal of physical chemistry. B · 2025Article
- Towards improved anticancer properties of the G-quadruplex-forming T40231 aptamer through increased flexibility of nucleoside residues.Scientific reports · 2025Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- Mechanistic insights into multiple-step transport of mitochondrial ADP/ATP carrier.Computational and structural biotechnology journal · 2022Article
- The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex.Nucleic acids research · 2021Article
- Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment.Chembiochem : a European journal of chemical biology · 2021Review
- Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes.Molecules (Basel, Switzerland) · 2021Article
- Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Mechanical diversity and folding intermediates of parallel-stranded G-quadruplexes with a bulge.Nucleic acids research · 2021Article
- Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back.Nucleic acids research · 2020Article
- Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail.PLoS computational biology · 2019Article
- Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52.Molecules (Basel, Switzerland) · 2019Article
- Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.Nucleic acids research · 2018Article
- Encoding canonical DNA quadruplex structure.Science advances · 2018Article
- Interaction between G-Quadruplex and Zinc Cationic Porphyrin: The Role of the Axial Water.Scientific reports · 2017Article
- Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations.Biophysical journal · 2017Article
- Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence-structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT(2), dT(3), dTTA, and dT(4)] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The work also provides new insight into G-quadruplex folding and stability. This includes reporting the observed instability of the left propeller loop, which extends the rules for G-quadruplex folding. We also suggest a plausible explanation why human telomere sequences predominantly form hybrid-I and hybrid-II type structures in K(+) solution. Overall, our calculation results indicate that short loops generally are less stable than longer loops, and we hypothesize that the extreme stability of sequences with very short loops could possibly derive from the formation of parallel multimers. The results suggest that free energy differences, estimated from MD and free energy analysis with current force fields and simulation protocols, are able to complement experiment and to help dissect and explain loop sequence, loop length, and G-tract length and orientation influences on G-quadruplex structure.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.