Kinetics of the triplex-duplex transition in DNA

Area of Science:

• Biophysical Chemistry
• Molecular Biology
• Structural Biology

Background:

• Understanding DNA triplex folding and unfolding kinetics is crucial for gene regulation and therapeutic applications.
• Previous studies have lacked detailed kinetic insights into the intermediate states of triplex formation.

Purpose of the Study:

• To investigate the folding and unfolding kinetics of DNA triplexes at the single-molecule level.
• To elucidate the mechanism of triplex formation and identify potential kinetic traps.

Main Methods:

• Single-molecule fluorescence resonance energy transfer (smFRET) was employed to monitor triplex folding/unfolding.
• Analysis of dwell-time distributions in high-FRET (folded) and low-FRET (unfolded) states.

Main Results:

• Triplexes exhibit marginal stability at neutral pH, with comparable dwell times in folded and unfolded states.
• Dwell-time distributions indicate complex folding pathways, requiring multi-exponential fitting for the folded state and single-exponential for the unfolded state.
• The data supports a model involving metastable states that can trap the folding process.

Conclusions:

• DNA triplex folding is a complex process influenced by metastable intermediates.
• The proposed kinetic model accurately describes the observed FRET data and macroscopic folding timescales.
• These findings provide a deeper understanding of DNA structure dynamics and stability.