Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and
processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister …

This paper considers how enzymes that catalyze reactions at specific DNA sites have been
engineered to overcome the problem of competitive inhibition by excess nonspecific binding …

Interaction of regulatory DNA binding proteins with their target sites is usually preceded by
binding to nonspecific DNA. This speeds up the search for the target site by several orders of …

We developed a knowledge-based statistical energy function for protein− ligand, protein−
protein, and protein− DNA complexes by using 19 atom types and ad istance-scale f inite i …

Background: Site-specific protein-DNA complexes vary greatly in structural properties and in
the thermodynamic strategy for achieving an appropriate binding free energy. A better …

We study theoretical “design principles” for transcription factor (TF)–DNA interaction in
bacteria, focusing particularly on the statistical interaction of the TFs with the genomic …

Salmonella bacteriophage repressor Mnt belongs to the ribbon–helix–helix class of
transcription factors. Previous SELEX results suggested that interactions of Mnt with …

Protein–DNA interactions play a central role in transcriptional regulation and other biological
processes. Investigating the mechanism of binding affinity and specificity in protein–DNA …

The control and function of RNA are governed by the specificity of RNA binding proteins.
Here, we describe a method for global unbiased analysis of RNA-protein interactions that …

Until now, it has been reasonably assumed that specific base-pair recognition is the only
mechanism controlling the specificity of transcription factor (TF)− DNA binding. Contrary to …