ArticleNucleic acids research2013
Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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.
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Who cites it
23 citing papers in PubMed, 52 citations in OpenAlex.
- MACRO-MOLECULAR CROWDING FAVORS WRITHE IN UNWOUND DNA.bioRxiv : the preprint server for biology · 2026Article
- Alexidine, identified as a Z-DNA inducer by the NanoZ screening platform, acts as a transcriptional regulator.Nucleic acids research · 2026Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats.Nucleic acids research · 2022Article
- Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.The journal of physical chemistry. B · 2020Article
- Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases.ACS chemical neuroscience · 2018Article
- E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats.Nucleic acids research · 2018Article
- A B-Z junction induced by an A … A mismatch in GAC repeats in the gene for cartilage oligomeric matrix protein promotes binding with the hZαThe Journal of biological chemistry · 2017Article
- Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats.Biophysical journal · 2017Article
- Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases.ACS chemical neuroscience · 2017Article
- Assessing the Current State of Amber Force Field Modifications for DNA.Journal of chemical theory and computation · 2016Article
- Article
- Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation.PLoS computational biology · 2015Article
- Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study.Nucleic acids research · 2014Article
- Role of microscopic flexibility in tightly curved DNA.The journal of physical chemistry. B · 2014Article
- Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.Journal of chemical theory and computation · 2014Article
- Thermodynamics of Deca-alanine Folding in Water.Journal of chemical theory and computation · 2014Article
- Investigation of B-Z transitions with DNA oligonucleotides containing 8-methylguanine.Artificial DNA, PNA & XNA · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of DNA, to Z-DNA is accomplished. Due to the complexity of the B-Z-DNA transition, experimental and computational studies have resulted in several different, apparently contradictory models. Here, we use molecular dynamics simulations coupled with state-of-the-art enhanced sampling techniques operating through non-conventional reaction coordinates, to investigate the B-Z-DNA transition at the atomic level. Our results show a complex free energy landscape, where several phenomena such as over-stretching, unpeeling, base pair extrusion and base pair flipping are observed resulting in interconversions between different DNA conformations such as B-DNA, Z-DNA and S-DNA. In particular, different minimum free energy paths allow for the coexistence of different mechanisms (such as zipper and stretch-collapse mechanisms) that previously had been proposed as independent, disconnected models. We find that the B-Z-DNA transition--in absence of other molecular partners--can encompass more than one mechanism of comparable free energy, and is therefore better described in terms of a reaction path ensemble.
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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.