Distribution of label spacings for genome mapping in nanochannels

TL;DR

This paper develops a theoretical model to explain the distribution of label spacings in genome mapping experiments using nanochannels, accounting for conformational hairpins that affect label positions.

Contribution

It introduces a novel theory for label spacing distributions in nanochannel genome mapping, addressing the effects of DNA hairpins on measurement accuracy.

Findings

The model explains heavy tails in label spacing distributions.

Conformational hairpins significantly influence label position variability.

The theory aligns with experimental observations of label spacing distributions.

Abstract

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.