Coordinated Residue Motions at the Enzyme–Substrate Interface Promote DNA Translocation in Polymerases

The translocation of DNA in polymerase (Pol) enzymes is a critical step for Pol-mediated nucleic acid polymerization, essential for storing and transmitting genetic information in all living organisms. During this process, the newly elongated double-stranded DNA has to shift along the Pol enzyme to recreate the initial configuration at the metal-aided reactive center, where nucleotide addition can occur recurrently at every catalytic cycle. Double-stranded DNA translocation, therefore, allows the enzyme to add one more nucleotide to the growing strand, complementary to the template strand, without the enzyme dissociating from the DNA. Yet, the dynamic mechanism by which the Pol·DNA complex accomplishes DNA translocation remains poorly understood at the atomistic level. Here, leveraging recent structural data on DNA polymerase η (Polη), we elucidate its translocation mechanism, which we show to occur via an enzyme motion where the shift of Polη is asynchronous along the two DNA strands. Through equilibrium molecular dynamics and deep-learning-guided enhanced sampling simulations, we found that such a mechanism relies precisely on a set of positively charged residues of the enzyme that operate in a coordinated way at the Polη·DNA interface. Moving like screen wipers, such a dynamic mechanism of these residues promotes DNA translocation. These findings now offer new avenues to comprehend further such a complex yet fundamental dynamic process for DNA polymerization.