Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments

Clinical Chemistry

Volumn 60, Issue 2, 2014, Pages 334-340

  Montgomery, Jesse L ^a   Wittwer, Carl T ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; BETAINE; CALCIUM; CESIUM; COBALT; DIMETHYL SULFOXIDE; DNA POLYMERASE; FORMAMIDE; GLYCEROL; LITHIUM; MANGANESE; NUCLEOTIDE; POTASSIUM; PROPYLENE GLYCOL; REAGENT; SODIUM; ZINC; DNA; DNA DIRECTED DNA POLYMERASE; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; FLUORESCENT DYE; MONOVALENT CATION;

ACCURACY; ADSORPTION; ARTICLE; BIOCHEMICAL EQUIPMENT; DNA DETERMINATION; FLUORESCENCE; MELTING POINT; REAL TIME POLYMERASE CHAIN REACTION; TEMPERATURE; CHEMISTRY; DEVICES; HEAT; PROCEDURES; TIME;

CATIONS, MONOVALENT; DNA; DNA-DIRECTED DNA POLYMERASE; FLUORESCENT DYES; HOT TEMPERATURE; INDICATORS AND REAGENTS; REAL-TIME POLYMERASE CHAIN REACTION; TIME FACTORS;

EID: 84893514221     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2013.212829     Document Type: Article

References (20)

1. Kasas S, Thomson NH, Smith BL, Hansma HG, Zhu X, Guthold M, et al. Escherichia coli RNA polymerase activity observed using atomic force microscopy. Biochemistry 1997;36:461-8.
2. Schafer DA, Gelles J, Sheetz MP, Landick R. Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 1991;352:444-8.
3. Wuite GJ, Smith SB, Young M, Keller D, Bustamante C. Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 2000;404:103-6.
4. Johnson RS, Strausbauch M, Cooper R, Register JK. Rapid kinetic analysis of transcription elongation by Escherichia coli RNA polymerase. J Mol Biol 2008;381:1106-13.
5. Gong P, Campagnola G, Peersen OB. A quantitative stopped-flow fluorescence assay for measuring polymerase elongation rates. Anal Biochem 2009;391:45-55.
6. Tang GQ, Anand VS, Patel SS. Fluorescence-based assay to measure the real-time kinetics of nucleotide incorporation during transcription elongation. J Mol Biol 2011;405:666-78.
7. Montgomery JL, Rejali N, Wittwer CT. Stoppedflow DNA polymerase assay by continuous monitoring of dNTP incorporation by fluorescence. Anal Biochem 2013;441:133-9.
8. Matsuno H, Niikura K, Okahata Y. Direct monitoring kinetic studies of DNA polymerase reactions on a DNA-immobilized quartz-crystal microbalance. Chemistry 2001;7:3305-12.
9. Griep MA. Fluorescence recovery assay: a continuous assay for processive DNA polymerases applied specifically to DNA polymerase III holoenzyme. Anal Biochem 1995;232:180-9.
10. Mestas SP, Sholders AJ, Peersen OB. A fluorescence polarization-based screening assay for nucleic acid polymerase elongation activity. Anal Biochem 2007;365:194-200.
11. Suarez AS, Stefan A, Lemma S, Conte E, Hochkoeppler A. Continuous enzyme-coupled assay of phosphate- or pyrophosphate-releasing enzymes. Biotechniques 2012;53:99-103.
12. Kallansrud G, Ward B. A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients. Anal Biochem 1996;236:134-8.
13. Mao F, Leung WY, Xin X. Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 2007;7:76.
14. Olive DM, Simsek M, Al-Mufti S. Polymerase chain reaction assay for detection of human cytomegalovirus. J Clin Microbiol 1989;27:1238-42.
15. Watanabe M, Abe K, Aoki M, Kameya T, Itoyama Y, Shoji M, et al. A reproducible assay of polymerase chain reaction to detect trinucleotide repeat expansion of Huntington's disease and senile chorea. Neurol Res 1996;18:16-8.
16. Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology 1993;11:1026-30.
17. Gelfand DH. Taq DNA polymerase. In: Erlich HA, ed. PCR technology: principles and applications for DNA amplification. New York: Macmillan Publishers; 1989. p 17-22.
18. Landre PA, Gelfand DH, Watson RM. The use of cosolvents to enhance amplification by the polymerase chain reaction. In: Innis MA, Gelfand DH, Sninsky JJ, eds. PCR strategies. San Diego: Academic Press; 1995. p 3-16.
19. Wittwer CT, Kusukawa N. Real-time PCR and melting analysis. In: Persing DH, ed. Molecular microbiology: diagnostic principles and practice. 2nd ed. Washington (DC): ASM Press; 2011. p 63-83.
20. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003;49:853-60.