A mathematical model of the Pyrosequencing reaction system
2004 (English)In: Biophysical Chemistry, ISSN 0301-4622, E-ISSN 1873-4200, Vol. 110, no 02-jan, 129-145 p.Article in journal (Refereed) Published
The Pyrosequencing(TM) technology is a newly developed DNA sequencing method that monitors DNA nucleotide incorporation in real-time. A set of coupled enzymatic reactions, together with bioluminescence, detects incorporated nucleotides in the form of light pulses, yielding a characteristic light profile. In this study, a biochemical model of the Pyrosequencing reaction system is suggested and implemented. The model is constructed utilizing an assumption of irreversible Michaelis-Menten rate equations and a constant incorporation efficiency. The kinetic parameters are studied and values are chosen to obtain as reliable simulation results as possible. The results presented here show strong resemblance with real experiments. The model is able to capture the dynamics of a single light pulse with great accuracy, as well as the overall characteristics of a whole pyrogram(TM). The plus- and minus-shift effects observed in experiments are successfully reconstructed by two constant efficiency factors. Furthermore, pulse broadening can partly be explained by apyrase inhibition and successive dilution.
Place, publisher, year, edition, pages
2004. Vol. 110, no 02-jan, 129-145 p.
biochemical modeling, DNA sequencing, enzyme kinetics, Michaelis-Menten, Pyrosequencing technology, dna-polymerase-i, firefly luciferase, solanum-tuberosum, kinetic mechanism, atp, apyrase, bioluminescence, identification, pyrophosphate, processivity
IdentifiersURN: urn:nbn:se:kth:diva-23584DOI: 10.1016/j.bpc.2004.01.010ISI: 000222735700012ScopusID: 2-s2.0-3042642521OAI: oai:DiVA.org:kth-23584DiVA: diva2:342283
QC 20100525 QC 201111012010-08-102010-08-102011-12-21Bibliographically approved