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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

RNA crosslinking methods.

Michael E Harris¹, Eric L Christian

¹Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University Schoolof Medicine, Cleveland, Ohio, USA.

Methods in Enzymology

|October 16, 2010

Summary

This summary is machine-generated.

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RNA-RNA crosslinking reveals proximity of functional groups in complex RNA structures. This method aids in interpreting structural data and designing experiments using photoaffinity reagents.

Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

RNA structure and function are critical in biological processes.
Understanding RNA-RNA proximity is essential for deciphering complex ribonucleoprotein interactions.
Existing methods for structural analysis require complementary techniques to validate RNA proximity.

Purpose of the Study:

To provide an overview of protocols and experimental considerations for RNA-RNA crosslinking.
To detail the use of long- and short-range photoaffinity reagents for RNA structural studies.
To guide researchers in obtaining accurate structural information through crosslinking.

Main Methods:

Overview of protocols for RNA-RNA crosslinking using photoaffinity reagents.

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Quantitative Detection of DNA-Protein Crosslinks and Their Post-Translational Modifications

Quantitative Detection of DNA-Protein Crosslinks and Their Post-Translational Modifications

Published on: April 21, 2023

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Last Updated: Jun 8, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Quantitative Detection of DNA-Protein Crosslinks and Their Post-Translational Modifications

Quantitative Detection of DNA-Protein Crosslinks and Their Post-Translational Modifications

Published on: April 21, 2023

Strategies for random and site-specific incorporation of crosslinking agents into RNA.

Methods for isolating crosslinked products and mapping crosslinked sites.

Assessment of crosslinking data for structural interpretation.

Main Results:

RNA-RNA crosslinking is a rapid method to evidence functional group proximity in complex RNAs.
Successful crosslinking depends on reagent placement, reaction conditions, and mapping techniques.
Photoaffinity reagents offer versatile strategies for both random and site-specific crosslinking.
The described methods facilitate the physical contextualization of RNA structures.

Conclusions:

RNA-RNA crosslinking is a powerful technique for probing RNA structure and interactions.
Careful consideration of experimental parameters is crucial for accurate structural determination.
This overview serves as a guide for implementing and interpreting RNA-RNA crosslinking experiments.
The method enhances the interpretation of structural data from complementary biochemical and biophysical techniques.