Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics

Area of Science:

• Biotechnology
• Nucleic Acid Nanotechnology
• Molecular Biology

Background:

• Strand displacement reactions are fundamental to nucleic acid nanotechnology.
• DNA-based systems are well-understood, but RNA/DNA hybrid systems lack kinetic data.
• This limits the development of RNA-based therapeutics and diagnostics.

Purpose of the Study:

• To characterize the kinetics of RNA/DNA hybrid strand displacement reactions.
• To investigate the impact of sequence composition and design parameters on reaction rates.
• To establish design principles for predictable RNA/DNA hybrid reaction networks.

Main Methods:

• Characterized 22 RNA/DNA hybrid and 11 DNA/DNA strand displacement systems.
• Varied parameters such as toehold length and branch migration domain length.
• Analyzed reaction rates and sequence-dependent effects on kinetics.

Main Results:

• Differences in RNA-DNA vs. DNA-DNA duplex stability significantly affect strand displacement rates (up to 3 orders of magnitude).
• Kinetics are strongly sequence-dependent, influenced by the purine content of RNA strands.
• RNA invaders are favored with high purine content and disfavored with low purine content.

Conclusions:

• The stability and sequence composition of RNA/DNA hybrids critically influence strand displacement kinetics.
• These findings provide foundational principles for designing complex nucleic acid systems with predictable dynamics.
• Enables advancement in RNA-based nanotechnology for diagnostics and therapeutics.