ArticleBiophysical journal2008
Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 39 citations in OpenAlex.
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field.Journal of chemical theory and computation · 2023Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.ACS omega · 2020Article
- Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence.Nucleic acids research · 2020Article
- Dehydrated DNA in B-form: ionic liquids in rescue.Nucleic acids research · 2018Article
- Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier.European biophysics journal : EBJ · 2018Article
- Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity.European biophysics journal : EBJ · 2016Article
- The Influence of DNA Configuration on the Direct Strand Break Yield.Computational and mathematical methods in medicine · 2015Article
- A histone-like protein induces plasmid DNA to form liquid crystals in vitro and gene compaction in vivo.International journal of molecular sciences · 2013Article
- Radioprotective effects produced by the condensation of plasmid DNA with avidin and biotinylated gold nanoparticles.Radiation and environmental biophysics · 2012Article
- The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Journal of biosciences · 2012Review
- Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.Journal of biosciences · 2012Article
- Structural determinants of photoreactivity of triplex forming oligonucleotides conjugated to psoralens.Journal of nucleic acids · 2010Article
- Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA.The journal of physical chemistry. B · 2009Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG)(2), d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity. UVRR results, obtained under similar conditions, suggest that the transition involves a series of intermediate forms between A and B. Cooperative and distinct transitions were observed for the bases and the sugars. Independent MD simulations on d(CGCGAATTCGCG)(2) show a spontaneous change from the A to B form in aqueous solution and describe a kinetic model that agrees well with UVRR results. Based on these observations, we predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B to A at reduced water activity. These results indicate that a quasiergodic sampling of the solvent distribution may be a problem in going from B to A at reduced water activity in the course of an MD simulation.
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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.