  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.
