Mathematical model of real-time PCR kinetics

Biotechnology and Bioengineering

Volumn 92, Issue 3, 2005, Pages 346-355

  Gevertz, Jana L ^a,c   Dunn, Stanley M ^a   Roth, Charles M ^a,b  

^a RUTGERS UNIVERSITY   (United States)

^b The State University of New Jersey   (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

Gene expression; Mathematical modeling; PCR efficiency

Indexed keywords

FLUORESCENCE; GENES; MATHEMATICAL MODELS; PARAMETER ESTIMATION; REAL TIME SYSTEMS;

GENE EXPRESSION; MATHEMATICAL MODELING; PCR EFFICIENCY;

ENZYME KINETICS;

ACCURACY; ARTICLE; BIOPHYSICS; GENE EXPRESSION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PARAMETER; PERIODICITY; PREDICTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SIMULATION;

COMPUTER SIMULATION; DNA; IN SITU HYBRIDIZATION, FLUORESCENCE; KINETICS; MODELS, CHEMICAL; MODELS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 27744483352     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/bit.20617     Document Type: Article

References (21)

1. Freeman WM, Walker SJ, Vrana KE. 1999. Quantitative RT-PCR: Pitfalls and potential. Biotechniques 26(1):112-122, 124-125.
2. Goidin D, Mamessier A, Staquet MJ, Schmitt D, Berthier-Vergnes O. 2001. Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Anal Biochem 295(1):17-21.
3. Halford WP, Falco VC, Gebhardt BM, Carr DJ. 1999. The inherent quantitative capacity of the reverse transcription-polymerase chain reaction. Anal Biochem 266(2):181 -191.
4. Hsu JT, Das S, Mohapatra S. 1997. Polymerase chain reaction engineering. Biotechnol Bioeng 55:359-366.
5. Jayaraman A, Yarmush ML, Roth CM 2000. Dynamics of gene expression in rat hepatocytes under stress. Metabolic Eng 2:239-251.
6. Kainz P. 2000. The PCR plateau phase-Towards an understanding of its limitations. Biochim Biophys Acta 1494(1-2):23-27.
7. Liu W, Saint DA 2002. A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Anal Biochem 302(1):52-59.
8. Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402-408.
9. Peirson SN, Butler JN Foster RG. 2003. Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis. Nucleic Acids Res 31(14):e73.
10. Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45.
11. Plum GE, Breslauer KJ Roberts RW. 1999. Thermodynamics and kinetics of nucleic acid association/dissociation and folding processes. Comprehensive natural products chemistry. Oxford, UK: Elsevier Science Ltd. 7, ch. 2:15-33.
12. Qiagen. 2002. HotStar Taq PCR Handbook. Valencia, CA.
13. Ramakers C, Ruijter JM, Deprez RH, Moorman AF. 2003. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339(1):62-66.
14. Roth CM. 2002. Quantifying gene expression. Curr Issues Mol Biol 4(3):93 - 100.
15. Rutledge RG, Cote C. 2003. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res 31(16):e93.
16. Sambrook J, Russell DW. 2001. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
17. Schmittgen TD, Zakrajsek BA. 2000. Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods 46(1-2):69-81.
18. Schnell S, Mendoza C. 1997. Theoretical description of the polymerase chain reaction. J Theor Biol 188(3):313-318.
19. Stagliano KE, Carchman E, Deb S. 2003. Real-time polymerase chain reaction quantitation of relative expression of genes modulated by p53 using SYBR green I. Methods Mol Biol 234:73-91.
20. Tichopad A, Dilger M, Schwarz G, Pfaffl MW. 2003. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res 31(20):e122.
21. Tinoco I., Sauer K, Wang JC, Puglisi JD. 2001. Physical chemistry: Principles and applications in biological sciences. Upper Saddle River, NJ: Prentice Hall.