Kinetics of biopolymerization on nucleic acid templates

@article{MacDonald1968KineticsOB,
  title={Kinetics of biopolymerization on nucleic acid templates},
  author={Carolyn T. MacDonald and Julian H. Gibbs and Allen C. Pipkin},
  journal={Biopolymers},
  year={1968},
  volume={6}
}
The kinetics of biopolymerization on nucleic acid templates is discussed. The model introduced allows for the simultaneous synthesis of several chains, of a given type, on a common template, e.g., the polyribosome situation. Each growth center [growing chain end plus enzyme(s)] moves one template site at a time, but blocks L adjacent sites. Solutions are found for the probability nj(t) that a template has a growing center that occupies the sites j — L + 1,…, j at time t. Two special sets of… Expand
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References

SHOWING 1-8 OF 8 REFERENCES
The kinetics of multicenter macromolecule growth along a template.
TLDR
The extended kinetic theory of polymer replication on linear, effectively single stranded templates is extended to the case of several simultaneously growing chains, suggesting that experimental discrimination between one and two chain replication by direct analysis of the dispersion is not feasible except for relatively large conversions. Expand
Polymerization kinetics of biological macromolecules on templates.
A kinetics of formation of polymers on linear templates is developed which is applicable to the synthesis of biological macromolecules. Two extreme situations are given theoretical treatment. InExpand
Capacity of T4 DNA to serve as template for purified Escerichia coli RNA polymerase.
TLDR
A model is proposed which assumes a limited number of specific starting sites for RNA polymerase on the native T4 DNA molecule, suggesting that both polymerase and starting sites on the DNA are heterogeneous with respect to their mutual binding affinities. Expand
Kinetics of synthesis and/or conformational changes of biological macromolecules
The analogy, in both the thermodynamics and the kinetics, of reversible polymerizations on templates (in the case wherein these are catalyzed by exoenzymes) to helix–coil transitions (in the caseExpand
THE REPLICATION OF DNA IN ESCHERICHIA COLI.
  • M. Meselson, F. Stahl
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1958
TLDR
A method was developed for the detection of small density differences among macromolecules and the distribution of the heavy nitrogen isotope N15 among molecules of DNA following the transfer of a uniformly N15-labeled, exponentially growing bacterial population to a growth medium containing the ordinary nitrogen isotopes. Expand
THE VISUALIZATION OF POLYRIBOSOMAL STRUCTURE.
TLDR
Polyribosomes from rabbit reticulocytes have been studied in the electron microscope using positive- and negative-staining techniques and the relation between the polyribosome and the length of the messenger RNA for hemoglobin is discussed. Expand
AN ESTIMATE OF THE SIZE OF THE RIBOSOMAL SITE FOR MESSENGER RNA BINDING.
  • M. Takanami, G. Zubay
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1964