Experimental and computational analysis of DNA unwinding and polymerization kinetics.
DNA unwinding and polymerization are complex processes involving many intermediate species in the reactions. Our understanding of these processes is limited because the rates of the reactions or the existence of intermediate species is not apparent without specially designed experimental techniques and data analysis procedures. In this chapter we describe how pre-steady state and single-turnover measurements analyzed by model-based methods can be used for estimating the elementary rate constants. Using the hexameric helicase and the DNA polymerase from bacteriophage T7 as model systems, we provide stepwise procedures for measuring the kinetics of the reactions they catalyze based on radioactivity and fluorescence. We also describe analysis of the experimental measurements using publicly available models and software gfit ( http://gfit.sf.net ).
Pandey
Manjula
M
Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ, USA.
Levin
Mikhail K
MK
Patel
Smita S
SS
D001681:Biological Assay / Q000295:instrumentation / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004265:DNA Helicases / Q000737:chemistry / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D007700:Kinetics; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D012984:Software
D004247:DNA; D004259:DNA-Directed DNA Polymerase; D004265:DNA Helicases