Binding Selectivity of RecA to a single stranded DNA, a computational approach

摘要: Homologous recombination (HR) is the major DNA double strand break repair pathway which maintains genomic integrity. It fundamental for survivability and functionality of all organisms. One initial steps in HR formation nucleoprotein filament composed by a single stranded chain surrounded recombinases protein. The orchestrates search an undamaged homologue, as template process. Our theoretical study was aimed at elucidating selectivity interaction between monomer enzyme Escherichia coli, EcRecA, bacterial homologue human Rad51, with series oligonucleotides nine bases length. complex, equilibrated 20 ns Langevian dynamics, inserted periodic box 8 A buffer water molecules explicitly described TIP3P model. absolute binding free energies are calculated implicit solvent using Poisson-Boltzmann (PB) generalized Born (GB) accessible surface area, MM-PB(GB)SA solute entropic contribution also normal mode analysis. results underline how significant energy due to Arg196, critical amino acid activity enzyme. revealed affinity EcRecA significantly higher toward dT9 rather than dA9, expected from experimental results.