Parallel reaction pathways accelerate folding of a guanine quadruplex

Area of Science:

• Molecular Biology
• Biophysics
• Genetics

Background:

• G-quadruplexes (G4s) are crucial four-stranded DNA structures involved in gene regulation and replication.
• G4 sequences can adopt multiple conformations, influencing their biological roles and folding dynamics.
• Understanding G4 folding pathways is key to deciphering their functional mechanisms.

Purpose of the Study:

• To develop and validate an experimental method for quantifying contributions of individual pathways in conformationally heterogeneous G4 folding.
• To investigate the impact of multiple folding pathways on the folding rate of the c-myc Pu22 G-quadruplex.

Main Methods:

• Experimental method based on mutagenesis, thermal hysteresis kinetic experiments, and global analysis.
• Validation using photocaged kinetic NMR experiments.
• Study of the regulatory Pu22 G-quadruplex from the c-myc oncogene promoter.

Main Results:

• The Pu22 G-quadruplex adopts at least four distinct folded isomers.
• Four parallel folding pathways were identified, leading to a 2.5-fold acceleration in the overall folding rate.
• The effective folding rate is significantly faster than the rate of the fastest individual pathway.

Conclusions:

• Multiple parallel pathways can dramatically accelerate G-quadruplex folding.
• This mechanism offers a significant increase in folding efficiency, with potential for accelerations exceeding an order of magnitude for G4s with more isomers.
• The developed method provides a quantitative approach to study complex folding landscapes of G-quadruplexes.