When fully extended, one copy of the three billion base pair human genome reaches a
length of over two meters. Yet, it must be packaged into the nucleus of a cell with an average …

The nucleosomal subunit organization of chromatin provides a multitude of functions.
Nucleosomes elicit an initial∼ 7-fold linear compaction of genomic DNA. They provide a …

The recognition of specific DNA sequences by proteins is thought to depend on two types of
mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily …

Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …

Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome
placement, usually measured by quantifying protection of DNA from enzymatic digestion …

We present a set of protocols showing how to use the 3DNA suite of programs to analyze,
rebuild and visualize three-dimensional nucleic-acid structures. The software determines a …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Nucleosome positioning plays a key role in genomic regulation by defining histone–DNA
context and by modulating access to specific sites. Moreover, the histone–DNA register …

The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and
occlude the DNA from access to most DNA-binding proteins. An understanding of the …

It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …