Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout")...

DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction

The session explores computational approaches to understanding the fundamental cycle of DNA $ Protein $ DNA by which DNA and proteins co-exist, co-regulate, and co-create each other. There is mounting evidence that DNA structural properties beyond the double helix signiicantly aaect its interactions with proteins and play an important role in a number of biological phenomena ranging from gene r...

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

Enrico Skoruppa, Stefanos K. Nomidis, 2 John F. Marko, and Enrico Carlon KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA (Dated: Januar...

Nonspecific DNA bending and the specificity of protein-DNA interactions.

Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.

In order to define the mean DNA bend angle and distribution of DNA bend angles in the catabolite activator protein (CAP)-DNA complex in solution under standard transcription initiation conditions, we have performed nanosecond time-resolved fluorescence measurements quantifying energy transfer between a probe incorporated at a specific site in CAP, and a complementary probe incorporated at each ...