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Mismatch Repair

Mismatch Repair

Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

Mismatch Repair

Mismatch Repair

¹H NMR: Complex Splitting

¹H NMR: Complex Splitting

A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: Jun 25, 2026

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

Published on: March 31, 2010

Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis.

Shayantani Mukherjee¹, Sean M Law, Michael Feig

¹Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.

Biophysical Journal

|March 4, 2009

Summary

This summary is machine-generated.

DNA mismatch repair proteins MutS and MSH2-MSH6 share common dynamic features. Correlated motions suggest a long-range allostery pathway crucial for DNA repair initiation and recognition.

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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

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Last Updated: Jun 25, 2026

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

Published on: March 31, 2010

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

Area of Science:

Molecular biology
Genetics
Biophysics

Background:

Postreplication DNA mismatch repair maintains genomic integrity in all organisms.
Bacterial MutS and eukaryotic MSH2-MSH6 initiate repair by recognizing DNA mismatches.
Existing crystal structures offer limited insight into the dynamic mechanisms of mismatch recognition.

Purpose of the Study:

To investigate the molecular dynamics of MutS and MSH2-MSH6 during DNA mismatch repair.
To elucidate the mechanism of long-range allostery in mismatch recognition and repair initiation.
To propose a molecular-level model for the DNA mismatch recognition cycle.

Main Methods:

Normal-mode calculations were performed on MutS and MSH2-MSH6, both with and without DNA.
Analysis focused on protein flexibilities, correlated motions, and domain interactions.
Results were interpreted in conjunction with existing experimental data.

Main Results:

MutS and MSH2-MSH6 exhibit similar protein flexibilities and dynamic characteristics.
A correlated motion pathway exists between the lever and ATPase domains, facilitating long-range allostery.
Changes in DNA-binding domains are coupled to ATPase sites, explaining mismatch recognition.

Conclusions:

The study reveals common dynamic principles governing DNA mismatch repair in prokaryotes and eukaryotes.
A molecular mechanism for long-range allostery in mismatch recognition and repair initiation is proposed.
Distinct conformational states are identified for different stages of the DNA mismatch repair cycle.