Probing Protein Motions for Sequence Fidelity Control or Information Detection along DNA

In template-based polymerization or transcription elongation, fidelity is mainly controlled by RNA polymerase (RNAP) selectivity. Although it is understood that RNAP operates in non-equilibrium nucleotide addition cycles to improve accuracy, it is not clear how it communicates with DNA template to assist cognate nucleotide incorporation. We have combined kinetic modeling with all-atom molecular dynamics (MD) simulation to show most critical residue motions supporting the nucleotide 'recognition' and selectivity, from phage T7 to SARS-CoV-2 viral replication. The atomistic MD simulations are also useful in demonstrating hydrogen bonding (HB) interaction at the protein-DNA interface. The rate-limiting collective HB dynamics is revealed in our recent work showing spontaneous stepping of a transcription factor (TF) protein along DNA. Modeled to coarse-grained level, protein-DNA electrostatics maintain significant impacts, for example, with the TF protein preferentially associating with one DNA strand in facilitated diffusion. Additionally, we have found that the protein-DNA associations can be notably impacted by protein rotation or re-orientation, which lead to a hierarchical free energy landscape of protein diffusion and dissociation along DNA for target search.