Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins

Area of Science:

• Nanotechnology
• Biophysics
• Molecular Motors

Background:

• DNA-nanoparticle motors are artificial nanoscale devices.
• These motors utilize a burnt-bridge Brownian ratchet mechanism.
• Ribonuclease H (RNase H) enzyme drives their motion on RNA-modified surfaces.

Purpose of the Study:

• To investigate the elementary processes governing DNA-nanoparticle motor motion.
• To identify and address the bottlenecks limiting motor speed.
• To optimize motor performance by balancing speed with other parameters.

Main Methods:

• Experimental observation of motor dynamics at varying Ribonuclease H concentrations.
• Kinetic simulation based on motor geometry.
• Engineering the motor to enhance DNA/RNA hybridization rates.

Main Results:

• Slow Ribonuclease H binding was identified as a major bottleneck, causing long pauses.
• Increasing RNase H concentration reduced pause times and increased speed up to 100 nm/s.
• High RNase H concentrations led to decreased processivity, run-length, and unidirectionality.
• A trade-off mechanism between speed and other performance metrics was revealed.
• An engineered motor achieved 30 nm/s speed, 200 processivity, and 3 μm run-length.

Conclusions:

• Optimizing RNase H concentration can enhance motor speed but requires careful balancing.
• Switching the rate-limiting step from RNase H binding to DNA/RNA hybridization is key for improved performance.
• Engineered DNA-nanoparticle motors can achieve performance comparable to biological motor proteins.