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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Viral RNA structure analysis using DMS-MaPseq.

Phillip Tomezsko1, Harish Swaminathan2, Silvi Rouskin2

  • 1Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Program in Virology, Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA.

Methods (San Diego, Calif.)
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Summary
This summary is machine-generated.

This review highlights chemical probing and next-generation sequencing for analyzing viral RNA structures. Dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq) offers a robust method for studying RNA structures in various environments.

Keywords:
Chemical probingDMS-MaPseqDimethyl sulfateNext-generation sequencingRNA structure

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Area of Science:

  • Virology
  • Molecular Biology
  • Genomics

Background:

  • RNA structure is crucial for viral replication and host factor interaction in both RNA and DNA viruses.
  • Chemical probing combined with next-generation sequencing advances RNA structure analysis.

Purpose of the Study:

  • To review recent viral RNA structural studies using chemical probing and next-generation sequencing.
  • To highlight the advantages and applications of dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq).

Main Methods:

  • Utilizing chemical probing techniques to analyze RNA structure.
  • Employing next-generation sequencing for high-throughput structural data acquisition.
  • Detailed protocol for whole-genome DMS-MaPseq in HIV-1 infected cells.

Main Results:

  • DMS-MaPseq is a robust assay applicable to RNA in vitro, in cell, and in virion.
  • The study presents the structure of HIV-1 TAR as determined by DMS-MaPseq.
  • Demonstrates the utility of DMS-MaPseq in understanding viral RNA dynamics.

Conclusions:

  • DMS-MaPseq is a powerful tool for investigating viral RNA structures.
  • This method can reveal how viral RNA structures change in different cellular environments and upon interaction with host factors.
  • Advances in sequencing technologies enhance the study of viral RNA structure and function.