Energetically biased DNA motor containing a thermodynamically stable partial strand displacement state

Area of Science:

• Biochemistry
• Molecular Biology
• Synthetic Biology

Background:

• Tuning DNA kinetics traditionally involves altering toehold lengths and DNA concentrations.
• Improving the completion probability of strand displacement reactions is a key factor for enhanced DNA kinetics.

Purpose of the Study:

• To explore a novel strategy for enhancing DNA strand displacement kinetics by manipulating energetic biases.
• To introduce a synthetic nucleotide, inosine, into DNA motor devices to modulate reaction kinetics.

Main Methods:

• Design and construction of a toehold DNA motor device incorporating inosine at specific nucleotide sites.
• Investigation of the impact of inosine inclusion on DNA strand displacement reaction kinetics and completion probability.
• Analysis of energetic biases to control the stability of partially displaced states.

Main Results:

• The inclusion of inosine successfully modulated the kinetics of the DNA strand displacement process.
• The synthetic nucleotide enabled tuning of energetic biases, allowing the device to stabilize in a partially displaced state.
• Demonstrated a complementary strategy to existing methods for improving DNA kinetics.

Conclusions:

• Energetic biases are a powerful tool for altering DNA strand displacement kinetics.
• The use of synthetic nucleotides like inosine offers a new avenue for designing and optimizing DNA motor devices.
• This work expands the toolkit for controlling DNA-based molecular machines.