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J Biol Chem, Vol. 275, Issue 2, 1421-1432, January 14, 2000
From the Chromosomal replicases of cellular organisms
utilize a ring shaped protein that encircles DNA as a mobile tether for
high processivity in DNA synthesis. These "sliding clamps" have
sufficiently large linear diameters to encircle duplex DNA and are
perhaps even large enough to slide over certain DNA secondary
structural elements. This report examines the Escherichia
coli
Dynamics of
and Proliferating Cell Nuclear Antigen Sliding
Clamps in Traversing DNA Secondary Structure*
§,
**
Joan and Sanford I. Weill Graduate School of
Medical Sciences of Cornell University, Microbiology Department, New
York, New York 10021, the § Rockefeller University and the
Howard Hughes Medical Institute, Laboratory of DNA Replication,
New York, New York 10021, and the ¶ Graduate Program in Molecular
Biology, Memorial Sloan-Kettering Cancer Center,
New York, New York 10021
and human proliferating cell nuclear antigen clamps for
their ability to slide over various DNA secondary structures. The
results show that these clamps are capable of traversing a
13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5'
tail, and a 15-mer bubble within the duplex. However, upon increasing
the size of these structures (20-nucleotide loop, 12-base pair
stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding
motion of the and proliferating cell nuclear antigen over these
elements is halted. Studies of the E. coli replicase, DNA
polymerase III holoenzyme, in chain elongation with the clamp
demonstrate that upon encounter with an oligonucleotide annealed in its
path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs
even when the oligonucleotide contains a secondary structure element,
provided the clamp can traverse the structure. However, upon
encounter with a downstream oligonucleotide containing a large internal
secondary structure, the holoenzyme clears the obstacle by strand
displacing the oligonucleotide from the template. Implications of these
protein dynamics to DNA transactions are discussed.
*
This work was supported by National Institutes of Health
Grant 38839.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
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