Structure-Encoded Oxidation Enables Nucleotide-Resolved RNA Editing, Conjugation, and Structural Probing

Area of Science:

• Chemical Biology
• RNA Biology
• Molecular Biology

Background:

• RNA oxidation is common in biological stress and disease.
• Current methods for RNA oxidation often lack nucleotide-level precision.
• Existing techniques rely on proximity or specific ligands for targeting.

Purpose of the Study:

• To demonstrate RNA secondary structure as a programmable tool for site-selective RNA oxidation.
• To develop a method for nucleotide-resolved control over guanosine oxidation.
• To explore applications of structure-guided RNA oxidation.

Main Methods:

• Defining structure-reactivity rules for guanosine oxidation based on loop geometry and oxidant.
• Developing LOCAL (Localized Oxidation Constrained at Loops), a DNA-programmed, postsynthetic RNA oxidation method.
• Utilizing selected oxidants and RNA secondary structure to direct oxidation.

Main Results:

• Established practical rules linking RNA secondary structure to guanosine oxidation site and lesion type.
• Developed LOCAL for precise, nucleotide-resolved guanosine oxidation in transcribed RNAs.
• Demonstrated LOCAL's utility in oxidative base editing, RNA bioconjugation, and structural probing.

Conclusions:

• RNA secondary structure can be leveraged for programmable, site-selective RNA oxidation.
• LOCAL provides a versatile tool for nucleotide-resolved RNA modification and analysis.
• Structure-encoded RNA oxidation expands the toolkit for chemical biology and RNA research.