title: A mathematical model of the Pyrosequencing reaction system.
abstract: The Pyrosequencing 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 trade mark. 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.
authors.affiliation: PSCI/SANS, Department of Numerical Analysis and Computer Science, Royal Institute of Technology (KTH), SE-100 44 Stockholm, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Svantesson
authors.forename: Pål O
authors.initials: PO
authors.lastname: Westermark
authors.forename: Jeanette Hellgren
authors.initials: JH
authors.lastname: Kotaleski
authors.forename: Baback
authors.initials: B
authors.lastname: Gharizadeh
authors.forename: Anders
authors.initials: A
authors.lastname: Lansner
authors.forename: Pål
authors.initials: P
authors.lastname: Nyrén
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D007700:Kinetics; D008027:Light; D008962:Models, Theoretical; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA