Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Abstract

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA-protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA-protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA-protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased. We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA-protein interactions under the same set of conditions.

Unstructured interactions between peptides and proteins: Exploring the role of sequence motifs in affinity and specificity

“…For example, nonspecific (unstructured) interactions between proteins (or enzymes) and the nucleic acids are important determinants of biological function [3]. The initial, unstructured interactions of proteins with DNA or RNA can help to facilitate binding to specific sites by reducing the dimensionality of diffusion in DNA replication and DNA modification, by forming distorted binding geometries to activate transcription processes, or even by more indirect regulation of gene expression [4][5][6]. While most of these interactions do not involve http the initial formation of specific structures, they can in fact be both quite strong and quite selective in terms of biological function.…”

Self-assembly of DNA networks at the air–water interface over time

“…[23][24][25][26][27] The LB technique is also widely accepted as the most controllable method to transfer a surfactant monolayer from an air-water interface to a solid surface with least loss of the original molecular arrangements. 28,29 Therefore, it is broadly applied for obtaining physiologically compatible templates, 30,31 fabricating nanoscale-ordered chemical sensors, 28 and modifying electrodes or molecular electronic devices 27 with permeation selectivity. 32,33 While the biggest drawback of the LB technique is that it requires the thin film to be an insoluble amphipathic film called a Langmuir film.…”

Interplay of Binding Stoichiometry and Recognition Specificity for the Interaction of MBD2b Protein and Methylated DNA Revealed by Affinity Capillary Electrophoresis Coupled with Laser-Induced Fluorescence Analysis

“…Hence, the multiple binding of MBD2b protein to DNA cooperatively enhances nonspecific interactions with the unmethylated DNA. The nonspecific binding is probably due to the electrostatic interactions between the positively charged residues of MBD2b (p I = 9.32) and the DNA phosphate backbone. − …”