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Related Experiment Video

Updated: Jul 5, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Probing RNA structure and function by nucleotide analog interference mapping.

Jesse C Cochrane¹, Scott A Strobel

¹Yale University, New Haven, Connecticut, USA.

Current Protocols in Nucleic Acid Chemistry

|April 23, 2008

Summary

Nucleotide analog interference mapping (NAIM) identifies crucial RNA functional groups. This method uses modified nucleotides to pinpoint sites affecting RNA structure and function, aiding molecular studies.

Related Experiment Videos

Last Updated: Jul 5, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Area of Science:

Molecular Biology
Biochemistry
RNA Structure and Function

Background:

RNA molecules play critical roles in various biological processes.
Understanding the structure-function relationships of RNA is essential for deciphering its biological roles.
Existing methods may not allow for simultaneous identification of multiple functional groups.

Purpose of the Study:

To describe the methodology of Nucleotide Analog Interference Mapping (NAIM).
To highlight the versatility of NAIM in identifying diverse RNA functional elements.
To provide an overview of the analogs, techniques, and data analysis involved in NAIM.

Main Methods:

Random incorporation of phosphorothioate-tagged nucleotides and analogs into RNA via in vitro transcription.
Utilizing phosphorothioate tags to mark substitution sites and assess impact on RNA structure/function.
Expansion of NAIM to NAIS (hydrogen bonding pairs), ionizable groups, metal ion ligands, and QNAIM (protein binding energetics).

Main Results:

NAIM enables simultaneous, individual identification of structurally and catalytically important RNA functional groups.
The technique successfully maps modifications affecting RNA structure and function.
NAIM has been extended to analyze hydrogen bonding, ionizable groups, metal ion coordination, and protein-RNA interactions.

Conclusions:

NAIM is a powerful and versatile technique for comprehensive functional group analysis in RNA.
The method provides detailed insights into RNA structure-function relationships.
NAIM and its extensions offer valuable tools for RNA research.