Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion

Abstract

Many DNA-interacting proteins diffuse on DNA to perform their biochemical functions. Processivity factors diffuse on DNA to permit unimpeded elongation by their associated DNA polymerases, but little is known regarding their rates and mechanisms of diffusion. The processivity factor of herpes simplex virus DNA polymerase, UL42, unlike ''sliding clamp'' processivity factors that normally form rings around DNA, binds DNA directly and tightly as a monomer, but can still diffuse on DNA. To investigate the mechanism of UL42 diffusion on DNA, we examined the effects of salt concentration on diffusion coefficient. Ensemble studies, employing electrophoretic mobility shift assays on relatively short DNAs, showed that off-rates of UL42 from DNA depended on DNA length at higher but not lower salt concentrations, consistent with the diffusion coefficient being salt-dependent. Direct assays of the motion of single fluorescently labeled UL42 molecules along DNA revealed increased diffusion at higher salt concentrations. Remarkably, the diffusion coefficients observed in these assays were Ϸ10 4 -fold higher than those calculated from ensemble experiments. Discrepancies between the single-molecule and ensemble results were resolved by the observation, in single-molecule experiments, that UL42 releases relatively slowly from the ends of DNA in a salt-dependent manner. The results indicate that UL42 ''hops'' rather than ''slides,'' i.e., it microscopically dissociates from and reassociates with DNA as it diffuses rather than remaining so intimately associated with DNA that cation condensation on the phosphate backbone does not affect its motion. These findings may be relevant to mechanisms of other processivity factors and DNA-binding proteins.herpes simplex virus ͉ linear diffusion D NA polymerases are central to DNA replication. Most replicative DNA polymerases include accessory subunits that promote replication of long stretches of DNA without dissociating from the template. The best known of these processivity factors are the ''sliding clamps'' (reviewed in ref. 1), which include polymerase subunits of bacteria, eukaryotes, and archaea that form multimeric rings around DNA with the aid of ATP-dependent clamp-loaders. These rings then tether their cognate catalytic subunits to DNA, permitting processive DNA synthesis.A variety of cellular and viral polymerases include processivity subunits that do not use ATP or other proteins for loading onto DNA. Of these, herpes simplex virus (HSV) UL42 is one of the best characterized. This protein's structure resembles that of a monomer of the sliding clamp proliferating cell nuclear antigen (2), yet UL42 binds directly to DNA as a monomer with relatively high affinity (apparent dissociation constant (K d ) in the nanomolar range) (3-5). This direct binding of DNA by UL42 tethers the catalytic subunit of HSV DNA polymerase (Pol) to DNA, thereby enabling processivity (3,(5)(6)(7).An important attribute of processivity factors is their ability to diffuse on DNA. Such diffusion permits teth...

Mutations That Increase DNA Binding by the Processivity Factor of Herpes Simplex Virus Affect Virus Production and DNA Replication Fidelity

“…There is evidence that processivity subunits of other herpesviruses play roles in gene expression, especially late in infection (17,38). It has recently been shown that UL42 diffuses on DNA by a "hopping" rather than a "sliding" mechanism (21). It was speculated that hopping could permit movements of UL42 around proteins bound to DNA, which in turn could be beneficial for a role for UL42 in gene expression.…”

Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

“…The ability to observe, in real time, interactions of a single protein with a single DNA molecule allows for the detection of transient intermediates and kinetic details that are difficult to obtain with ensemble-averaging biochemical assays. Single-molecule techniques have been used to study diffusion of a variety of proteins along DNA, such as transcription factors (12,13), DNA repair factors (14,15), processivity factors (16,17), RNA polymerases (18)(19)(20), and restriction enzymes (21). In this report, we present single-molecule imaging experiments that visualize the interaction of individual T7 DNA polymerases with DNA, demonstrate that the protein complex diffuses along duplex DNA, and show that a change in the diffusional mode of T7 DNA polymerase is mediated by the binding of its processivity factor, thioredoxin.…”

Direct Visualization of Single-Molecule DNA-Binding Proteins Along DNA to Understand DNA-Protein Interactions

“…With this platform, dynamics of many single-molecule proteins have been uncovered. These include dynamics of single-protein polymers along DNA (Greene & Mizuuchi, 2002;Han & Mizuuchi, 2010;Tan et al, 2007) and one-dimensional diffusion of many DNA-binding protein molecules, for example, a base-excision DNA-repair protein along DNA (Blainey et al, 2006;Etson et al, 2010;Kochaniak et al, 2009;Komazin-Meredith et al, 2008;Tafvizi et al, 2011). A comparison of one-dimensional diffusion constants as a function of protein size with theoretical predictions indicates that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix (Blainey et al, 2009).…”