ArticleBiopolymers2013
Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.
Article in Biopolymers, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.Scientific reports · 2024Article
- Nanosecond chain dynamics of single-stranded nucleic acids.Nature communications · 2024Article
- Can Hindered Transport Models for Rigid Spheres Predict the Rejection of Single Stranded DNA from Porous Membranes?Membranes · 2022Article
- Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats.Nucleic acids research · 2022Article
- Dataset of normalized probability distributions of virtual bond lengths, bond angles, and dihedral angles for the coarse-grained single-stranded DNA structures.Data in brief · 2022Article
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- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- The role of small-angle scattering in structure-based screening applications.Biophysical reviews · 2018Review
- Martini Coarse-Grained Force Field: Extension to RNA.Biophysical journal · 2017Article
- Persistence Length and Cooperativity Estimation of Single Stranded DNA using FCS Combined with HYDRO Program.Journal of fluorescence · 2017Article
- Visualizing single-stranded nucleic acids in solution.Nucleic acids research · 2017Article
- The impact of base stacking on the conformations and electrostatics of single-stranded DNA.Nucleic acids research · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods.Nucleic acids research · 2016Article
- Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements.Biophysical journal · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with wormlike chain models, but nonbase-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and divalent salt. We report measurements of the form factor and interparticle interactions using SAXS, end-to-end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent molecular dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers.
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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.