ArticleNucleic acids research2017
T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Molecular Basis of pH-Dependent Activity in T7 RNA Polymerase Revealed by Constant pH Replica Exchange Molecular Dynamics.ACS physical chemistry Au · 2026Article
- Article
- Deep learning-guided dual-fitness evolution of T7 RNA polymerase for enhanced stability and activity.Nucleic acids research · 2026Article
- Heterogeneous template-dependent transcription dynamics of T7 RNAP revealed by single-molecule imaging.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Transient interactions modulate the affinity of NF-κB transcription factors for DNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Harnessing Information Thermodynamics: Conversion of DNA Information into Mechanical Work in RNA Transcription and Nanopore Sequencing.Entropy (Basel, Switzerland) · 2024Article
- Bacteriophage RNA polymerases: catalysts for mRNA vaccines and therapeutics.Frontiers in molecular biosciences · 2024Review
- Unveiling the methyl transfer mechanisms in the epigenetic machinery DNMT3A-3 L: A comprehensive study integrating assembly dynamics with catalytic reactions.Computational and structural biotechnology journal · 2023Article
- Automated Path Searching Reveals the Mechanism of Hydrolysis Enhancement by T4 Lysozyme Mutants.International journal of molecular sciences · 2022Article
- Topology and kinetics of R-loop formation.Biophysical journal · 2022Article
- Translocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2's RNA polymerase complexes.Frontiers in molecular biosciences · 2022Article
- Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2.Biophysical journal · 2021Article
- Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition.Nucleic acids research · 2021Article
- Dissecting nucleotide selectivity in viral RNA polymerases.Computational and structural biotechnology journal · 2021Review
- Oxazinomycin arrests RNA polymerase at the polythymidine sequences.Nucleic acids research · 2019Article
- Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control.Nucleic acids research · 2019Article
- A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control.Computational and structural biotechnology journal · 2019Review
- Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.Nucleic acids research · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we studied the complete process of a viral T7 RNA polymerase (RNAP) translocation on DNA during transcription elongation by implementing extensive all-atom molecular dynamics (MD) simulations to construct a Markov state model (MSM). Our studies show that translocation proceeds in a Brownian motion, and the RNAP thermally transits among multiple metastable states. We observed non-synchronized backbone movements of the nucleic acid (NA) chains with the RNA translocation accomplished first, while the template DNA lagged. Notably, both the O-helix and Y-helix on the fingers domain play key roles in facilitating NA translocation through the helix opening. The helix opening allows a key residue Tyr639 to become inserted into the active site, which pushes the RNA-DNA hybrid forward. Another key residue, Phe644, coordinates the downstream template DNA motions by stacking and un-stacking with a transition nucleotide (TN) and its adjacent nucleotide. Moreover, the O-helix opening at pre-translocation (pre-trans) likely resists backtracking. To test this hypothesis, we computationally designed mutants of T7 RNAP by replacing the amino acids on the O-helix with counterpart residues from a mitochondrial RNAP that is capable of backtracking. The current experimental results support the hypothesis.
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