Polymerasebinding

Polymerasebinding refers to the interaction in which a DNA or RNA polymerase enzyme binds to a nucleic acid substrate or to regulatory or accessory proteins that facilitate its engagement with substrate. Binding is a prerequisite for catalysis and often determines the speed, location, processivity, and fidelity of synthesis. In DNA replication, polymerases bind primer–template junctions with the help of sliding clamps and clamp loaders; in transcription, RNA polymerases position themselves at promoter regions with the aid of transcription factors.

Biological context and determinants: Binding can be influenced by DNA sequence and structure, presence of lesions or secondary structures, methylation, and chromatin context in eukaryotes. Protein–protein interactions with accessory factors such as sliding clamps, clamp loaders, and chromatin remodelers can stabilize and orient the polymerase on the nucleic acid. Post-translational modifications of the polymerase or regulatory proteins can modulate affinity and processivity.

Measurement and analysis: Binding affinity and kinetics are studied using biochemical and biophysical methods such as electrophoretic mobility shift assays, surface plasmon resonance, isothermal titration calorimetry, and footprinting techniques. Kinetic assays can provide rates of association and dissociation and inform on processivity.

Regulation and significance: Proper polymerasebinding is essential for accurate genome replication and gene expression. Disruptions in binding can lead to replication stress or transcriptional errors. Therapeutically, strategies that alter polymerase binding to nucleic acids or to accessory factors are explored to inhibit pathogen replication or to affect cancer cell proliferation.