ArticleBiophysical journal2012
A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- Control and synchronization of rapid nanoscale DNA heat engine by local heating.Science advances · 2025Article
- Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors.Journal of the American Chemical Society · 2023Article
- A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.Journal of the Royal Society, Interface · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency.Molecules (Basel, Switzerland) · 2019Article
- Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies.The journal of physical chemistry. B · 2018Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Tractable RNA-ligand interaction kinetics.BMC bioinformatics · 2017Article
- Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update.Nucleic acids research · 2015Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Folding and unfolding pathways of the human telomeric G-quadruplex.Journal of molecular biology · 2014Article
- Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion.Biopolymers · 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-stranded DNA and RNA hairpin structures with 4-10 nucleotides (nt) in the loop and 5-8 basepairs (bp) in the stem fold on 10-100 μs timescale. In contrast, theoretical estimate of first contact time of two ends of an ideal semiflexible polymer of similar lengths (with persistence length ~2-nt) is 10-100 ns. We propose that this three-orders-of-magnitude difference between these two timescales is a result of roughness in the folding free energy surface arising from intrachain interactions. We present a statistical mechanical model that explicitly includes all misfolded microstates with nonnative Watson-Crick (WC) and non-WC contacts. Rates of interconversion between different microstates are described in terms of two adjustable parameters: the strength of the non-WC interactions (ΔG(nWC)) and the rate at which a basepair is formed adjacent to an existing basepair (k(bp)(+)). The model accurately reproduces the temperature and loop-length dependence of the measured relaxation rates in temperature-jump studies of a 7-bp stem, single-stranded DNA hairpin with 4-20-nt-long poly(dT) loops, with ΔG(nWC) ≈ -2.4 kcal/mol and k(bp)(+) ≥ (1 ns)(-1), in 100 mM NaCl. Thus, our model provides a microscopic interpretation of the slow hairpin folding times as well as an estimate of the strength of intrachain interactions.
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.