Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Size and Structure of Viral Genomes

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...

Viruses with RNA Genomes

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...

Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...

Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

Bacterial RNA Polymerase

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

Translesion DNA Polymerases

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

The fidelity control of nucleotide selectivity in SARS-CoV-2 RdRp through amino acid mutations <i>via</i> molecular dynamics simulations.

Physical chemistry chemical physics : PCCP·2025

Same author

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.

PLoS computational biology·2025

Same author

Theoretical Design of Tellurium-Based Two-Dimensional Perovskite Photovoltaic Materials.

Molecules (Basel, Switzerland)·2024

Same author

Correction to "Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations".

The journal of physical chemistry. B·2024

Same author

Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations.

The journal of physical chemistry. B·2024

Same author

Energetic <i>vs.</i> entropic stabilization between a Remdesivir analogue and cognate ATP upon binding and insertion into the active site of SARS-CoV-2 RNA dependent RNA polymerase.

Physical chemistry chemical physics : PCCP·2023

Search research articles

Related Experiment Video

Updated: Nov 2, 2025

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Dissecting nucleotide selectivity in viral RNA polymerases.

Chunhong Long¹, Moises Ernesto Romero², Daniel La Rocco³

¹School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.

Computational and Structural Biotechnology Journal

|June 9, 2021

Summary

This study reviews viral polymerases, focusing on SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and nucleotide selection mechanisms. Understanding these viral enzymes aids in designing effective antiviral therapeutics against coronaviruses.

Keywords:

Fidelity control Kinetic modeling Molecular dynamics (MD) simulation Nucleotide selection RNA dependent RNA polymerase (RdRp)RNA/DNA polymerase (RNAP/DNAP)

More Related Videos

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

Related Experiment Videos

Last Updated: Nov 2, 2025

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

Area of Science:

Biochemistry
Structural Biology
Virology

Background:

Designing effective antiviral therapeutics against SARS-CoV-2 is critical.
Viral polymerases are conserved targets for drug development.
Understanding nucleotide selection by viral polymerases is key to antiviral design.

Purpose of the Study:

To review structural and computational insights into viral polymerases related to SARS-CoV-2 RdRp.
To elucidate mechanisms of nucleotide substrate and drug analog selection.
To compare SARS-CoV-2 RdRp with other polymerases for potential drug targeting.

Main Methods:

Literature review of structural biology and computational studies.
Comparative analysis of RdRps from Polio virus, Hepatitis C virus, and SARS-CoV-2.
Examination of phage T7 RNA polymerase and human mitochondrial RNAP.
Inclusion of viral phi29 DNA polymerase for functional comparison.

Main Results:

Key residues and structural motifs for nucleotide selectivity identified in viral RdRps.
Structural and biochemical characteristics of SARS-CoV-2 RdRp elucidated.
Insights into stepwise nucleotide selectivity from T7 RNAP and phi29 DNA polymerase.
Human mitochondrial RNAP identified as a non-targetable homolog.

Conclusions:

Structural and mechanistic understanding of viral polymerases informs antiviral drug design.
Comparative analysis highlights conserved and unique features of SARS-CoV-2 RdRp.
Fidelity control mechanisms, like proofreading, are crucial for viral genome synthesis.