We review molecular dynamics simulations of nucleic acids, including those completed from
1995 to 2000, with a focus on the applications and results rather than the methods. After the …

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 …

Abstract The 1.9-Å-resolution crystal structure of the nucleosome core particle containing
147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented …

Publisher Summary This chapter discusses the structure and function of DNA. DNA occupies
a critical role in cells, because it is the source of all intrinsic genetic information. Chemically …

A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the
Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical …

We describe a very accurate addition (called structure X here) to the B-DNA dodecamer
family of X-ray structures. Our results confirm the observation of Drew and Dickerson [(1981) …

DNA bending in 86 complexes with sequence-specific proteins has been examined using
normal vector plots, matrices of normal vector angles between all base pairs in the helix, and …

We describe herein a computationally intensive project aimed at carrying out molecular
dynamics (MD) simulations including water and counterions on B-DNA oligomers containing …

Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers
containing all 136 unique tetranucleotide basepair steps are reported. The objective is to …

▪ Abstract Is it by design or by default that water molecules are observed at the interfaces of
some protein-DNA complexes? Both experimental and theoretical studies on the …