ArticleNucleic acids research2011
Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 70 citations in OpenAlex.
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.Nature communications · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.bioRxiv : the preprint server for biology · 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
- Selective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex.Inorganic chemistry · 2023Article
- Bimodular Antiparallel G-Quadruplex Nanoconstruct with Antiproliferative Activity.Molecules (Basel, Switzerland) · 2019Article
- Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations.Molecules (Basel, Switzerland) · 2019Article
- Putative Mechanisms Underlying High Inhibitory Activities of Bimodular DNA Aptamers to Thrombin.Biomolecules · 2019Article
- Quantifying MgPolymers · 2018Article
- Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.Nucleic acids research · 2018Article
- Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.Nucleic acids research · 2017Article
- Advances in the development of aptamer drug conjugates for targeted drug delivery.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology · 2017Review
- Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations.ACS omega · 2017Article
- Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery.Biochemistry. Biokhimiia · 2016Article
- The systematic approach to describing conformational rearrangements in G-quadruplexes.Journal of biomolecular structure & dynamics · 2016Article
- Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.Nucleic acids research · 2015Article
- 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
- Tuning supramolecular G-quadruplexes with mono- and divalent cations.Supramolecular chemistry · 2015Article
- DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.Journal of molecular modeling · 2014Article
- An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation.The journal of physical chemistry. B · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.
Indexed as
Identifiers
What OpenQuestion holds
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.