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Transcription Attenuation in Prokaryotes

Transcription Attenuation in Prokaryotes

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Related Experiment Video

Updated: May 27, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Attenuation of loop-receptor interactions with pseudoknot formation.

Kirill A Afonin¹, Yen-Ping Lin, Erin R Calkins

¹Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.

Nucleic Acids Research

|November 15, 2011

Summary

Natural RNA structures prefer A/U-rich sequences to avoid folding traps. This study shows G/C-rich RNA receptors can be trapped in pseudoknots, explaining evolutionary preferences and aiding synthetic biology designs.

Related Experiment Videos

Last Updated: May 27, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Area of Science:

Molecular Biology
Structural Biology
RNA Biology

Background:

RNA tetraloops mediate long-range interactions in natural RNAs.
In vitro selected GNRA tetraloop/receptor interactions are often G/C-rich, unlike natural A/U-rich counterparts.
Evolutionary preference for A/U-rich sequences may prevent folding traps in larger RNA contexts.

Purpose of the Study:

Investigate the hypothesis that natural RNA evolution favors A/U-rich GNRA receptors to avoid folding traps.
Examine how G/C content in GNRA receptors affects their ability to form alternative intramolecular structures (pseudoknots).
Provide design principles for RNA-based attenuator devices.

Main Methods:

In vitro investigation of riboswitches with natural and artificial GNRA receptors.
Native gel-shift assays to determine interaction extents.
Co-transcriptional assembly to study RNA folding and interactions.

Main Results:

The extent of attenuation in riboswitches is correlated with the G/C content of the GNRA receptor.
G/C-rich GNRA receptors are more prone to being trapped in alternative intramolecular pseudoknots.
This trapping mechanism prevents intermolecular GNRA/receptor interactions.

Conclusions:

The G/C content of GNRA receptors influences their structural behavior and interaction potential.
Evolutionary selection may favor A/U-rich GNRA receptors to ensure proper RNA folding and function.
Findings offer insights into RNA structural evolution and guide the design of synthetic RNA devices.