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Detection and Quantification of RNA Modifications on RNA-DNA Hybrids Using SID-UPLC-MS/MS
Marta Starczak1, Abdulkadir Abakir2, Alexey Ruzov3
1Department of Clinical Biochemistry, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland.
Methods in Molecular Biology (Clifton, N.J.)
|June 15, 2022
Summary
R-loops, structures of RNA and DNA, can cause genomic instability. This study introduces a method to quantify RNA modifications within these structures, aiding in understanding their biological roles.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- R-loops are three-stranded nucleic acid structures (RNA-DNA hybrid and single-stranded DNA).
- They are implicated in genomic instability and regulation of eukaryotic cellular processes.
- RNA modifications on RNA-DNA hybrids may influence R-loop biology.
Purpose of the Study:
- To present a protocol for the quantitative analysis of RNA modifications on RNA-DNA hybrids.
- To enable further investigation into the role of RNA modifications in R-loop metabolism.
Main Methods:
- Stable-isotope dilution ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (SID-UPLC-MS/MS).
- This method allows for quantitative analysis of RNA modifications within R-loops.
Main Results:
- A novel protocol for quantifying RNA modifications on RNA-DNA hybrids was successfully developed.
- The method is suitable for integration with other techniques for comprehensive R-loop analysis.
Conclusions:
- The presented SID-UPLC-MS/MS protocol is a valuable tool for studying RNA modifications in R-loops.
- This technique can elucidate the functional significance of RNA modifications in R-loop-associated biological processes and genomic stability.
