ArticlePhysical chemistry chemical physics : PCCP2008
Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.
Article in Physical chemistry chemical physics : PCCP, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 32 citations in OpenAlex.
- Molecular Interpretation of Temperature-Induced DNA Melting Monitored through Base Dipole Moment Changes as a Surrogate of the Hypochromic Shift.The journal of physical chemistry letters · 2026Article
- Polymorphic potential of SRF binding site ofRSC advances · 2024Article
- Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.Nucleic acids research · 2015Article
- Dominance of misfolded intermediates in the dynamics of α-helix folding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Observation time scale, free-energy landscapes, and molecular symmetry.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer.Nucleic acids research · 2013Article
- Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.The journal of physical chemistry. B · 2012Article
- Order parameters for macromolecules: application to multiscale simulation.The Journal of chemical physics · 2011Article
- Micrographia of the twenty-first century: from camera obscura to 4D microscopy.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2010Review
- Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.Biophysical journal · 2009Article
- Conformations and coherences in structure determination by ultrafast electron diffraction.The journal of physical chemistry. A · 2009Article
- DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- 4D visualization of embryonic, structural crystallization by single-pulse microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.
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.