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A more recent version of this article appeared on December 13, 2002
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M207030200v1
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Papers In Press, published online ahead of print October 11, 2002
J. Biol. Chem, 10.1074/jbc.M207030200
Submitted on July 13, 2002
Revised on September 10, 2002
Accepted on October 11, 2002

DNA binding properties of human Pol gamma B

Jose A. Carrodeguas, Kevin G. Pinz, and Daniel F. Bogenhagen

Department of Pharmacology, SUNY at Stony Brook, Stony Brook, NY 11794-8651

Corresponding Author: dan{at}pharm.sunysb.edu

We have recently reported the crystal structure of the accessory subunit of mitochondrial DNA polymerase, pol gamma B, and identified a region of the protein involved in DNA binding. The DNA employed in previous studies was presumed to be single-stranded since it was generated by single-sided PCR. Further characterization of this DNA indicated that, due to a strand transfer event during synthesis by single-sided PCR, the DNA adopts a double-stranded hairpin conformation under native conditions. We used a series of double and single-stranded oligonucleotides of different lengths to confirm that human pol gamma B prefers to bind double-stranded DNA longer than 40 bp with little apparent sequence specificity. Site-specific deletion mutagenesis identified clusters of basic residues in two surface loops required for DNA binding located on opposite sides of the symmetrical pol gamma B dimer. A heterodimer of pol gamma B that contains one mutant and one wild-type DNA binding region was shown to be unable to bind double-stranded DNA, suggesting that a single DNA molecule must contact both DNA binding sites in the pol gamma B dimer. The ability to bind double-stranded DNA is not essential for pol gamma B stimulation of pol gamma A activity in vitro, but may play a role in DNA replication or repair.


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