Kinetics of an RNA conformational switch

Area of Science:

• Molecular Biology
• Biophysics
• RNA Structure Dynamics

Background:

• The spliced leader RNA in Leptomonas collosoma exhibits two stable, competing secondary structures with similar free energies.
• External factors, such as short complementary oligonucleotides, can influence and potentially alter these RNA structures.

Purpose of the Study:

• To investigate the kinetics of the structural switch in Leptomonas collosoma spliced leader RNA induced by complementary oligonucleotides.
• To elucidate the mechanism underlying this rapid RNA structural transition.

Main Methods:

• Utilized stopped-flow rapid-mixing techniques to monitor fast kinetic processes.
• Employed temperature-jump (T-jump) relaxation spectroscopy to study the thermodynamics and kinetics of structural changes.
• Measured the rates of structural switching at varying oligonucleotide concentrations.

Main Results:

• The structural switch between competing RNA conformations can be rapidly induced by complementary oligonucleotides.
• At high oligonucleotide concentrations, the rate of RNA structural transition becomes the rate-limiting step, occurring within a fraction of a second.
• The observed low activation energy suggests a concerted mechanism, likely involving branch migration.

Conclusions:

• Short oligonucleotides effectively control RNA secondary structure dynamics in Leptomonas collosoma.
• The rapid, low-activation energy process points towards a branch migration mechanism for RNA structural switching.
• Understanding these dynamics is crucial for RNA function and regulation in trypanosomatids.