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Replication forks in both prokaryotic and eukaryotic systems pause at random sites due to depletion of dNTP pools, DNA damage, tight binding nonhistone proteins or unusual DNA sequences and/or structures, in a mostly non-polar fashion. However, there is also physiologically programmed replication termination at sequence-specific authentic replication termini. Here, the structure and functions of programmed replication termini, their mechanism of action and their diverse physiological functions in prokaryotes and eukaryotes have been reviewed., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

We expressed the carboxy-terminal portion of the E2 open reading frame (ORF)-encoded protein of human papillomavirus type 16 (HPV-16) and purified it to near homogeneity. Using DNase I footprinting techniques, we show that like the homologous protein from bovine papillomavirus type 1 (BPV-1), HPV-18, HPV-11, it binds DNA at the enhancer consensus motif ACCN6GGT. Base and phosphate backbone contact points were determined using methylation protection and interference and ethylation interference assays. This HPV-16 E2 DNA-binding domain protein contacts the site at the outermost conserved GG residues which is similar to the interaction of the BPV-1 E2 system. However, there are many fewer phosphate backbone contacts. Using gel retardation assays, the HPV-16 E2 protein interaction with the consensus motif was characterized further based on the specific sequence of the noncontacted, nonconserved internal bases. Affinity of this E2 protein for the consensus site increased dramatically with an A.T-rich core sequence. Like the homologous BPV-1 protein, HPV-16 E2 protein induces DNA bending at its binding site. Furthermore, examination of the DNA region containing a single consensus motif far upstream from the major promoter, P97, revealed naturally bent DNA that was further bent upon interaction with the HPV-16 E2 protein.

The transcriptional trans-activator E2 protein from bovine papillomavirus type 1 has been shown to bind to the DNA consensus sequence ACCN6GGT. We have produced the DNA-binding domain of the E2 protein as a recombinant protein in Escherichia coli. The E2 DNA-binding domain was purified as two different molecular weight forms. Using these purified proteins, we show that two molecules of the E2 protein bind to a single DNA consensus binding site.