Yanling Yang, who just graduated with a Ph.D. from my lab, has a paper in the just published November issue of Biophysical Chemistry. The entire issue of the journal celebrates the 25th Anniversary of a conference called “The Gibbs Conference on Biothermodynamics”, and each of the papers is from the laboratory of one of the organizers of one of the previous 25 annual meetings (I co-organized #24). Despite the restricted invitation list, however, all the papers were peer reviewed (some quite viciously according to reports) and some required several months of revisions to qualify for the issue.
Our lab’s contribution focuses on how the thermodynamics of binding of DNA polymerases different DNA structures might influence the balance between replication and repair in the cell. Yanling examined DNA molecules with normal replication start sites, along with DNA molecules with nicks and gaps between bases, and DNA molecules with mismatches near the polymerase binding site. One of the major questions was: do the “same” enzymes from two different organisms (in this case the Pol I DNA polymerases from E. coli and Thermus aquaticus) actually perform the “same” functions in the two different organisms? The thermodynamic results of this paper suggest that there are some serious differences between these two “homologous” enzymes, such that the E. coli enzyme is more advanced in being able to recognize different DNA structures.
The schematic below illustrates this in cartoon fashion by illustrating how Klentaq (from Thermus aquaticus) sees a primer-template (i.e. a “normal” replication start site) as being equal to a DNA with a gap in it. In contrast, Klenow (from E. coli) binds the primer-template DNA with much higher affinity than it binds the gapped DNA.
The paper compares the binding preferences among a large number of different DNA structures, and consistently finds that the E. coli enzyme is capable of distinguishing among all these DNAs (and binding to them with differing affinities), while the T. aquaticus enzyme sees and binds to almost every DNA exactly equivalently. We spend some time discussing how this might shift the balance between repair and replication in the two different organisms, and discussing how evolutionary time has made this enzyme more subtle and sophisticated in its DNA substrate choices.
As always, if your institution does not have access to the paper and you would like a copy, I will be happy to send you one.