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Proofreading

Proofreading

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.
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PCR

Lagging Strand Synthesis

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

DNA Isolation

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

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Related Experiment Video

Updated: Jun 9, 2025

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

Direct and indirect selection in a proofreading polymerase.

Kabir Husain^1,2, Vedant Sachdeva², Riccardo Ravasio²

¹Department of Physics and Astronomy, University College London, United Kingdom.

Biorxiv : the Preprint Server for Biology

|October 28, 2024

Summary

This summary is machine-generated.

This study explores how mutation rates evolve, finding that higher mutation rates offer long-term benefits by increasing beneficial mutations but incur short-term costs due to reduced polymerase activity. These trade-offs create complex evolutionary dynamics.

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Last Updated: Jun 9, 2025

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Published on: June 19, 2018

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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

Area of Science:

Evolutionary biology
Molecular evolution
Genetics

Background:

Evolvability traits are influenced by indirect selection, impacting long-term evolutionary trajectories rather than immediate individual fitness.
Studying evolvability traits is challenging due to confounding direct fitness effects of unknown magnitude.
Mutation rates are key traits influencing evolvability, but their evolution is complex.

Purpose of the Study:

To theoretically and experimentally investigate the evolution of mutation rates in proofreading polymerases.
To disentangle direct and indirect selection pressures on mutation rates.
To understand the fitness consequences of varying mutation rates over different timescales.

Main Methods:

Theoretical modeling of evolutionary dynamics.
Experimental evolution studies using proofreading polymerases.
Analysis of direct and indirect fitness effects associated with mutation rates.

Main Results:

Mutagenic polymerases show a long-term advantage through accelerated beneficial mutation acquisition.
A trade-off exists between mutation rates and polymerase activity, leading to a short-term fitness penalty.
Fitness effects operate on different timescales, preventing a single metric for mutator allele fitness.
Unusual evolutionary dynamics observed include kinetic exclusion and Rock-Paper-Scissors dynamics.

Conclusions:

The evolution of mutation rates is shaped by a complex interplay of short-term and long-term fitness consequences.
Anticorrelations between mutation rates and short-term fitness can drive novel evolutionary dynamics.
Findings have implications for understanding the evolution of mutation rates and broader evolutionary principles.