Analysis of Accordion DNA Stretching Revealed by The Gold Cluster Ruler

TL;DR

This paper investigates the accordion-like stretching behavior of DNA revealed by gold cluster ruler measurements, explaining discrepancies with previous observations through cluster interactions and ion effects.

Contribution

It introduces a model accounting for cluster exclusion volume and long-range repulsion to reconcile experimental data with prior findings.

Findings

DNA exhibits correlated stretching over 80 base pairs.

Cluster interactions influence DNA length measurements.

Long-range repulsion explains observed discrepancies.

Abstract

A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it revealed that the DNA length fluctuations are strikingly strong and correlated over at least 80 base pair steps. In other words, the DNA behaves as accordion bellows, with distant fragments stretching and shrinking concertedly. This hypothesis, however, disagrees with earlier experimental and computational observations. This Letter shows that the discrepancy can be rationalized by taking into account the cluster exclusion volume and assuming a moderate long-range repulsion between them. The long-range interaction can originate from an ion exclusion effect and cluster polarization in close proximity to the DNA surface.