21 April 2016 Synchronization of DNA array replication kinetics
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Abstract
In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.
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Alexey O. Manturov, Anton V. Grigoryev, "Synchronization of DNA array replication kinetics", Proc. SPIE 9917, Saratov Fall Meeting 2015: Third International Symposium on Optics and Biophotonics and Seventh Finnish-Russian Photonics and Laser Symposium (PALS), 991720 (21 April 2016); doi: 10.1117/12.2229623; https://doi.org/10.1117/12.2229623
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