Statistical properties of metastable intermediates in DNA unzipping

TL;DR

This study investigates the size distribution of metastable intermediates during DNA unzipping using optical tweezers, revealing power-law behavior and the influence of single-stranded DNA compliance on detection sensitivity.

Contribution

It provides the first detailed analysis of the size distribution of unzipping intermediates and quantifies how DNA compliance affects experimental resolution.

Findings

Unzipping region sizes follow a power-law distribution.

Regions smaller than 10 bp are often undetected due to DNA compliance.

Single nucleotide compliance limits force probe sensitivity to discriminate individual base pairs.

Abstract

We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed following a power law, ranging from one base pair up to more than a hundred base pairs. We find that a large fraction of unzipping regions smaller than 10 bp are seldom detected because of the high compliance of the released single stranded DNA. We show how the compliance of a single nucleotide sets a limit value around 0.1 N/m for the stiffness of any local force probe aiming to discriminate one base pair at a time in DNA unzipping experiments.