Dynamics of β and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure Journal Article


Authors: Yao, N.; Hurwitz, J.; O'Donnell, M.
Article Title: Dynamics of β and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure
Abstract: 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 β 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 β 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 β 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 β 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.
Keywords: nonhuman; dna synthesis; molecular dynamics; hela cells; dna; double stranded dna; protein processing; escherichia coli; base pairing; dna structure; models, molecular; binding sites; dna primers; cycline; single stranded dna; dna, single-stranded; nucleic acid conformation; oligonucleotide; protein dna interaction; oligodeoxyribonucleotides; proliferating cell nuclear antigen; dna template; dna directed dna polymerase gamma; templates, genetic; restriction mapping; dna polymerase iii; humans; priority journal; article
Journal Title: Journal of Biological Chemistry
Volume: 275
Issue: 2
ISSN: 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology  
Date Published: 2000-01-14
Start Page: 1421
End Page: 1432
Language: English
DOI: 10.1074/jbc.275.2.1421
PUBMED: 10625694
PROVIDER: scopus
DOI/URL:
Notes: Export Date: 18 November 2015 -- Source: Scopus
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  1. Jerard Hurwitz
    206 Hurwitz