ArticleNucleic acids research2017
The impact of base stacking on the conformations and electrostatics of single-stranded DNA.
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.
- Genomic sequence context differentially impacts stepwise oxidation by TET enzymes to shape DNA hydroxymethylation landscapes.Nucleic acids research · 2026Article
- smDeepFLUOR: single-molecule deep learning fluorescence classification.Nature communications · 2026Article
- Poly(ADP-ribose) (PAR) exhibits ion-dependent structural properties distinct from RNA.Nucleic acids research · 2026Article
- Aggregation-induced emission of DNA fluorescence as a novel pan-marker of cell death, senescence and sepsisTheranostics · 2026Article
- Excessive Existence of Positively Charged Amino Acids Caused Off-Target Recognition in the Seed Region ofInternational journal of molecular sciences · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions.Nucleic acids research · 2025Article
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 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
- Nucleic Acid-based Electrochemical Sensors Facilitate the Study of DNA Binding by Platinum (II)-based Antineoplastics.Angewandte Chemie (International ed. in English) · 2024Article
- 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
- 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
- Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand.iScience · 2023Review
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- Can Hindered Transport Models for Rigid Spheres Predict the Rejection of Single Stranded DNA from Porous Membranes?Membranes · 2022Article
- Adenine oligomer directed synthesis of chiral gold nanoparticles.Nature communications · 2022Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these 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.