ArticleBiophysical journal2014
Sequence-dependent elasticity and electrostatics of single-stranded DNA: signatures of base-stacking.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Effect of Polymer Structure on the Thermodynamics of Polyelectrolyte Complex Micelle Formation.Macromolecules · 2026Article
- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- 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
- Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability.RSC advances · 2024Article
- Article
- Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors.Biosensors · 2023Article
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- A modular spring-loaded actuator for mechanical activation of membrane proteins.Nature communications · 2022Article
- Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA.RSC advances · 2022Article
- KAS-seq: genome-wide sequencing of single-stranded DNA by NNature protocols · 2022Review
- Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression.Frontiers in microbiology · 2022Article
- Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex.Chemical science · 2021Article
- Sugar-Pucker Force-Induced Transition in Single-Stranded DNA.International journal of molecular sciences · 2021Article
- Optical tweezers in single-molecule biophysics.Nature reviews. Methods primers · 2021Article
- Electrophoretic Mobility of DNA in Solutions of High Ionic Strength.Biophysical journal · 2020Article
- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- DNA sequence-dependent chromatin architecture and nuclear hubs formation.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer's rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼-0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration.
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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.