Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules

TL;DR

This paper models how local defects like kinks and flexible hinges in short DNA molecules affect their mechanical properties, providing predictions useful for experimental DNA studies.

Contribution

It introduces a transfer-matrix method to predict mechanical responses of DNA with local defects, advancing understanding of DNA mechanics at the molecular level.

Findings

Defects cause measurable shifts in DNA extension and persistence length.

Predictions assist in designing experiments for DNA-protein interaction studies.

Mechanical responses vary with defect type and thermal excitation.

Abstract

We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer or plasmon resonance technique, and the traditional biochemistry cyclization probability measurements.