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Mathematical modelling and analysis of the pyrosequencing reaction system
KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
2005 (English)Licentiate thesis, comprehensive summary (Other scientific)
Place, publisher, year, edition, pages
Stockholm: Numerisk analys och datalogi , 2005. , 41 p.
Series
Trita-NA, ISSN 0348-2952 ; 0535
Keyword [en]
apyrase, bioluminescence, DNA polymerase, DNA sequencing, enzyme kinetics, Klenow fragment, mathematical modelling, Michaelis-Menten, pyrosequencing
National Category
Computer Science
Identifiers
URN: urn:nbn:se:kth:diva-524ISBN: 91-7178-177-3 (print)OAI: oai:DiVA.org:kth-524DiVA: diva2:14285
Presentation
2005-10-27, sal 4523, KTH, Lindstedtsvägen 5, Stockholm, 13:00
Supervisors
Note
QC 20101222Available from: 2005-11-29 Created: 2005-11-29 Last updated: 2010-12-22Bibliographically approved
List of papers
1. A mathematical model of the Pyrosequencing reaction system
Open this publication in new window or tab >>A mathematical model of the Pyrosequencing reaction system
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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
Abstract [en]

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.

Keyword
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
National Category
Computer Science
Identifiers
urn:nbn:se:kth:diva-23584 (URN)10.1016/j.bpc.2004.01.010 (DOI)000222735700012 ()2-s2.0-3042642521 (Scopus ID)
Note
QC 20100525 QC 20111101Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2011-12-21Bibliographically approved
2. An Investigation of the Apyrase Stepin the Pyrosequencing Model:Combining Experiments and Simulations.
Open this publication in new window or tab >>An Investigation of the Apyrase Stepin the Pyrosequencing Model:Combining Experiments and Simulations.
2005 (English)Report (Other academic)
Place, publisher, year, edition, pages
Stockholm: KTH, 2005. 19 p.
Series
Trita-NA, ISSN 0348-2952 ; P0509
National Category
Computer Science
Identifiers
urn:nbn:se:kth:diva-27753 (URN)
Note
QC 20101222Available from: 2010-12-22 Created: 2010-12-22 Last updated: 2010-12-22Bibliographically approved
3. Towards an Improved Polymerase Descriptionin the Pyrosequencing Model.
Open this publication in new window or tab >>Towards an Improved Polymerase Descriptionin the Pyrosequencing Model.
2005 (English)Report (Other academic)
Place, publisher, year, edition, pages
Stockholm: KTH, 2005. 10 p.
Series
Trita-NA, ISSN 0348-2952 ; P0510
National Category
Computer Science
Identifiers
urn:nbn:se:kth:diva-27754 (URN)
Note
QC 20101222Available from: 2010-12-22 Created: 2010-12-22 Last updated: 2010-12-22Bibliographically approved

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