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Related Experiment Video

Updated: Oct 21, 2025

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Witnessing the structural evolution of an RNA enzyme.

Xavier Portillo¹, Yu-Ting Huang², Ronald R Breaker^1,3

¹Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.

|September 9, 2021

Summary

This summary is machine-generated.

Directed evolution created an RNA polymerase ribozyme capable of synthesizing complex RNAs. This ribozyme evolved a new structure, enhancing its catalytic activity and demonstrating RNA

Keywords:

RNA polymerase biochemistry chemical biology molecular evolution none ribozyme

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Nanomanipulation of Single RNA Molecules by Optical Tweezers

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DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

DNAzyme-dependent Analysis of rRNA 2’-O-Methylation

Published on: September 16, 2019

Area of Science:

Molecular Biology
RNA Catalysis
Directed Evolution

Background:

RNA polymerase ribozymes are crucial for synthesizing functional RNAs.
Directed evolution has been employed to enhance ribozyme capabilities.
Understanding RNA structural dynamics is key to improving catalytic function.

Purpose of the Study:

To investigate the structural and functional evolution of an RNA polymerase ribozyme.
To elucidate the mechanisms underlying improved catalytic activity through structural rearrangement.
To explore the evolutionary trajectory and potential for further optimization of ribozyme polymerase activity.

Main Methods:

Directed evolution of an RNA polymerase ribozyme.
Site-directed mutagenesis and structural probing.
Deep sequencing analysis to track evolutionary changes.

Main Results:

The ribozyme evolved the ability to synthesize complex functional RNAs, including its ancestor.
A major structural rearrangement occurred in the catalytic core, forming a novel tertiary element near the active site.
Progressive stabilization of this new structure correlated with enhanced catalytic activity, with multiple evolutionary paths converging on this solution.

Conclusions:

RNA tertiary structural remodeling can be experimentally induced and optimized.
The evolving ribozyme escaped a local fitness optimum, achieving a new, higher fitness landscape.
This study demonstrates the potential for significant improvements in artificial ribozyme polymerase activity.