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Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Sequence-dependent force response during peeling of single-stranded DNA from graphite.

Suresh Manohar¹, Anand Jagota

¹Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|April 7, 2010

Summary

We analyzed the statistical thermodynamics of peeling single-stranded DNA (ssDNA) from graphite. Models predict steady peeling force and sequence-dependent force spikes, offering insights into ssDNA adhesion.

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Area of Science:

Statistical thermodynamics
Polymer physics
Surface science
Biophysics

Background:

Understanding the adhesion of single-stranded DNA (ssDNA) to surfaces is crucial for various applications, including DNA sequencing and nanotechnology.
Previous studies have explored DNA-surface interactions, but a detailed statistical thermodynamic analysis of the peeling process from specific substrates like graphite is lacking.

Purpose of the Study:

To analyze the statistical thermodynamics of peeling single-stranded DNA (ssDNA) from a graphite surface.
To model ssDNA as a polymer chain adsorbed to a frictionless substrate using established polymer physics models.
To predict the force response during ssDNA peeling under different experimental controls (force vs. displacement) and relate it to adhesion properties.

Main Methods:

Utilized three polymer chain models: freely jointed chain (FJC), wormlike chain (WLC), and rotational isomeric state (RIS).
Applied recently measured experimental parameters for ssDNA and graphite interactions.
Performed theoretical analysis under both force-controlled and displacement-controlled conditions.

Main Results:

All three models predict a steady peeling force under force control, consistent with experimental observations.
For finite-length chains, a prediction of measurable force spikes under displacement control was made.
Derived exact closed-form results for the FJC model, establishing relationships between peeling force and adhesion free energy.

Conclusions:

The study provides a robust theoretical framework for understanding ssDNA-graphite peeling dynamics.
Predicted force spikes under displacement control may serve as a method to probe ssDNA sequence information.
The findings offer valuable insights into DNA-surface interactions and potential for sequence-specific adhesion measurements.