Conformation of ring single-stranded DNA measured by DNA origami structures

Area of Science:

• Biophysics
• Polymer Physics
• Molecular Biology

Background:

• Measuring the mechanical properties of single-stranded DNA (ssDNA) is crucial but challenging.
• Existing methods for determining ssDNA persistence length have limitations.
• Understanding ssDNA conformation is vital for various biological processes.

Purpose of the Study:

• To develop and validate a novel method for measuring the persistence length of ring ssDNA.
• To overcome the complexities associated with previous measurement techniques.
• To provide a more accurate estimation of ssDNA mechanical properties.

Main Methods:

• Utilized DNA origami nano structures to create ring ssDNA constructs.
• Employed atomic force microscopy (AFM) to capture ssDNA polymer conformations.
• Developed a self-avoiding ring polymer simulation model incorporating minimal energy loop formation for fitting.
• Applied nonparametric estimation statistics to determine persistence length.

Main Results:

• The new method successfully measured ring ssDNA conformations and calculated their radius of gyration.
• A simulation program was developed to fit persistence length to experimental data, accounting for stem-loop formation.
• Calculated persistence length ranged from 1.9-4.4 nm (25-75% loop formation), with a precise value of 2.83 ± 0.63 nm at 50% loop formation.
• This estimation refines previously known persistence length values for ssDNA.

Conclusions:

• The combined approach of DNA origami, AFM, and advanced simulation provides a robust method for measuring ssDNA persistence length.
• The study successfully accounted for intrinsic ssDNA stem-loop structures in the analysis.
• The findings offer improved tools for characterizing ssDNA conformations and mechanical properties, advancing biophysical understanding.