Pauses at positions of secondary structure during in vitro replication of single-stranded fd bacteriophage DNA by T4 DNA polymerase

Since bacteriophage T4 DNA polymerase is unable to use duplex DNA molecules as templates (B. Alberts, J. Barry, M. Brittner, M. Davies, H. Hama-Inaba, C. C. Liu, D. Mace, L. Moran, C. F. Morris, J. Piperno, and N. Sinha, 1977, in Nucleic Acids and Protein Recognition, Vogel, H. J., ed., pp. 31–63, Academic Press, New York), a technique involving synchronous and uniquely primed synthesis of DNA on the single-stranded fd DNA by the T4 DNA polymerase has been developed to probe regions exhibiting secondary structure on this genome. As the polymerase proceeds, the template secondary structure acts as a kinetic barrier to delay the continuous chain extension catalyzed by this enzyme. These kinetic pause sites can be mapped by denaturing agarose gel electrophoresis of replication intermediates and used to generate a secondary structure map. Using this method, we are able to establish a list including at least seven plausible stable helical regions in fd DNA. Two of the most stable secondary structures have been mapped near fd sequence positions 3350 and 5650, respectively. The latter has been reported to be the region where fd DNA replication begins (C. P. Gray, R. Sommer, C. Polke, E. Beck, and H. Schaller, 1978, Proc. Nat. Acad. Sci. USA, 75, 50–53). However, the biological function associated with the former has yet to be investigated. Following a two-state model, we estimate the first-order rate constant for progression through the duplex regions near position 5650 in fd DNA to be about 0.042 min^?1 for fd DNA synthesis by the T4 DNA polymerase under our reaction conditions. A 7.5-fold increase in this rate constant is obtained upon the addition of the T4 DNA helix destabilizing protein (i.e., gene 32 protein). The general pattern of our secondary structure map agrees well with a computer search for duplex regions on the fd genome. Both the stability and the size of a stable secondary structure at a particular position on the fd template determine the time that the newly made DNA molecules spend at that site. A structure with a stem of less than 8 base pairs does not interrupt significantly the procession of the T4 DNA polymerase during the process of fd DNA synthesis.