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- Svantesson, AnnaKTH,Numerisk analys och datalogi, NADA (author)
A mathematical model of the Pyrosequencing reaction system
- Article/chapterEnglish2004
Publisher, publication year, extent ...
- Elsevier BV,2004
- printrdacarrier
Numbers
- LIBRIS-ID:oai:DiVA.org:kth-23584
- https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-23584URI
- https://doi.org/10.1016/j.bpc.2004.01.010DOI
Supplementary language notes
- Language:English
- Summary in:English
Part of subdatabase
- SwePubSwePub
Classification
Notes
- QC 20100525 QC 20111101
- 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.
Subject headings and genre
- NATURVETENSKAP Data- och informationsvetenskap Datavetenskap hsv//swe
- NATURAL SCIENCES Computer and Information Sciences Computer Sciences hsv//eng
- 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
- Computer science
- Datalogi
Added entries (persons, corporate bodies, meetings, titles ...)
- Westermark, Pål. O.KTH,Numerisk analys och datalogi, NADA(Swepub:kth)u144azrf (author)
- Hellgren Kotaleski, JeanetteKTH,Numerisk analys och datalogi, NADA(Swepub:kth)u13pnwqn (author)
- Gharizadeh, BabackKTH,Bioteknologi(Swepub:kth)u1u8iiq0 (author)
- Lansner, AndersKTH,Numerisk analys och datalogi, NADA(Swepub:kth)u12s8cr8 (author)
- Nyrén, PålKTH,Bioteknologi(Swepub:kth)u134qr82 (author)
- KTHNumerisk analys och datalogi, NADA (creator_code:org_t)
Related titles
- In:Biophysical Chemistry: Elsevier BV110:02-jan, s. 129-1450301-46221873-4200
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