Velocity of DNA during translocation through a solid-state nanopore

Area of Science:

• Nanotechnology
• Molecular Biology
• Biophysics

Background:

• Understanding DNA translocation through solid-state nanopores is crucial for single-molecule sensing and sequencing.
• The dynamics of DNA propagation through nanopores remain poorly understood.

Purpose of the Study:

• To investigate the local velocity of different segments of DNA during translocation.
• To determine the impact of DNA unfolding on translocation dynamics.
• To quantify the error introduced by assuming constant translocation velocity.

Main Methods:

• Utilized linear double-stranded DNA molecules constructed via DNA origami.
• Incorporated markers at known positions along the DNA molecules.
• Measured local translocation velocities of DNA segments in real-time.

Main Results:

• Observed substantial intramolecular velocity fluctuations, attributed to changing drag forces during DNA unfolding.
• Detected an increased local translocation velocity towards the end of the process, indicative of speeding up as the DNA unfolds.
• Quantified the uncertainty in determining DNA feature positions based on temporal location.

Conclusions:

• DNA translocation through nanopores is characterized by complex dynamics, not a constant velocity.
• The unfolding of DNA significantly influences its translocation speed.
• Assuming constant velocity leads to inaccuracies in positioning DNA features during nanopore analysis.