DNA curvature and flexibility in vitro and in vivo

JP Peters, LJ Maher III - Quarterly reviews of biophysics, 2010 - cambridge.org
It has been more than 50 years since the elucidation of the structure of double-helical DNA.
Despite active research and progress in DNA biology and biochemistry, much remains to be …

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

A Arneodo, C Vaillant, B Audit, F Argoul… - Physics Reports, 2011 - Elsevier
Understanding how chromatin is spatially and dynamically organized in the nucleus of
eukaryotic cells and how this affects genome functions is one of the main challenges of cell …

Scaling exponents and probability distributions of DNA end-to-end distance

F Valle, M Favre, P De Los Rios, A Rosa, G Dietler - Physical review letters, 2005 - APS
The scaling of the average gyration radius of polymers as a function of their length can be
experimen<? format?> tally determined from ensemble measurements, such as light …

Local and global effects of strong DNA bending induced during molecular dynamics simulations

J Curuksu, M Zacharias, R Lavery… - Nucleic acids …, 2009 - academic.oup.com
DNA bending plays an important role in many biological processes, but its molecular and
energetic details as a function of base sequence remain to be fully understood. Using a …

Nanoscale morphological analysis of soft matter aggregates with fractal dimension ranging from 1 to 3

F Valle, M Brucale, S Chiodini, E Bystrenova… - Micron, 2017 - Elsevier
While the widespread emergence of nanoscience and nanotechnology can be dated back to
the early eighties, the last decade has witnessed a true coming of age of this research field …

Flexibility of nucleic acids: from DNA to RNA

L Bao, X Zhang, L Jin, ZJ Tan - Chinese Physics B, 2015 - iopscience.iop.org
The structural flexibility of nucleic acids plays a key role in many fundamental life processes,
such as gene replication and expression, DNA-protein recognition, and gene regulation. To …

How acidic amino acid residues facilitate DNA target site selection

KA Hossain, M Kogut, J Słabońska… - Proceedings of the …, 2023 - National Acad Sciences
Despite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly
participate in the base readout, with a strong preference for cytosine. In fact, in the solved …

Small-interfering RNA (siRNA)-based functional micro-and nanostructures for efficient and selective gene silencing

SH Lee, BH Chung, TG Park, YS Nam… - Accounts of chemical …, 2012 - ACS Publications
Because of RNA's ability to encode structure and functional information, researchers have
fabricated diverse geometric structures from this polymer at the micro-and nanoscale. With …

The influence of DNA stiffness upon nucleosome formation

J Virstedt, T Berge, RM Henderson, MJ Waring… - Journal of structural …, 2004 - Elsevier
The rotational and translational positioning of nucleosomes on DNA is dependent to a
significant extent on the physicochemical properties of the double helix. We have …

Probing persistence in DNA curvature properties with atomic force microscopy

J Moukhtar, E Fontaine, C Faivre-Moskalenko… - Physical review …, 2007 - APS
We elaborate on a mean-field extension of the wormlike chain model that accounts for the
presence of long-range correlations (LRC) in the intrinsic curvature disorder of genomic …