ArticleNucleic acids research2017
Visualizing single-stranded nucleic acids in solution.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- The Distinct Structural Propensities of Poly-C, A, and U Single-Stranded RNA.Biomacromolecules · 2026Article
- Kinetics, thermodynamics, and mechanisms of PMO interactions from computational molecular modeling.Molecular therapy. Nucleic acids · 2026Article
- Nucleotide-Specific RNA Conformations and Dynamics as Precursors to Ribonucleoprotein Condensates.Journal of the American Chemical Society · 2025Article
- 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
- Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- Studies of DNA 'Breathing' by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3)The journal of physical chemistry. B · 2023Article
- An enhanced biophysical screening strategy to investigate the affinity of ASOs for their target RNA.RSC chemical biology · 2023Article
- Driving forces of the complex formation between highly charged disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Three-Dimensional Modeling of CpG DNA Binding with Matrix Lumican Shows Leucine-Rich Repeat Motif Involvement as in TLR9-CpG DNA Interactions.International journal of molecular sciences · 2023Article
- Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM.Nucleic acids research · 2023Article
- Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding.Nucleic acids research · 2023Article
- DNA Oligonucleotides as Antivirals and Vaccine Constituents against SARS Coronaviruses: A Prospective Tool for Immune System Tuning.International journal of molecular sciences · 2023Article
- Post-genomic platform for development of oligonucleotide vaccines against RNA viruses: diamond cuts diamond.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2022Article
- Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.RNA (New York, N.Y.) · 2022Article
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats.Nucleic acids research · 2022Article
- Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein-ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.
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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.