Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu srovnávací studie, časopisecké články, práce podpořená grantem
PubMed
18606615
PubMed Central
PMC2528177
DOI
10.1093/nar/gkn421
PII: gkn421
Knihovny.cz E-zdroje
- MeSH
- benzothiazoly MeSH
- chinoliny MeSH
- diaminy MeSH
- fluorescenční barviva analýza MeSH
- kvartérní amoniové sloučeniny chemie MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- organické látky analýza MeSH
- polymerázová řetězová reakce metody MeSH
- teplota MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- benzothiazoly MeSH
- chinoliny MeSH
- diaminy MeSH
- fluorescenční barviva MeSH
- kvartérní amoniové sloučeniny MeSH
- organické látky MeSH
- SYBR Green I MeSH Prohlížeč
Tetraalkylammonium (TAA) derivatives have been reported to serve as stabilizers of asymmetrical cyanine dyes in aqueous solutions and to increase the yield and efficiency of polymerase chain reaction (PCR) detected by end-point analysis. In this study, we compared the ability of various TAA derivatives (with alkyl chain ranging from 1 to 5 carbons) and some other compounds to serve as enhancers of real-time PCR based on fluorescence detection from intercalating dye SYBR Green I (SGI). Our data indicate that TAA chlorides and some other TAA derivatives serve as potent enhancers of SGI-monitored real-time PCR. Optimal results were obtained with 10-16 mM tetrapropylammonium chloride. The effect of TAA compounds was dependent on the nature of counter ions present and composition of the reaction mixtures used. Based on measurements of SGI-generated fluorescence signal in the presence of PCR-amplified DNA fragments, oligonucleotide primers and/or various additives, we propose that TAA-derivatives reduce the binding of SGI to oligonucleotide primers and thus enhance primer-template interactions during annealing phase. Furthermore, these compounds serve as stabilizers of SGI-containing PCR mixtures. The combined data indicate that TAA derivatives might be a new class of additives contributing to robustness of real-time PCR monitored by asymmetrical cyanine dye SGI.
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Bustin SA. A-Z of Quantitative PCR. La Jolla: International University Line; 2004.
Dieffenbach CW, Dveksler GS. PCR primer. A laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 1995.
Baskaran N, Kandpal RP, Bhargava AK, Glynn MW, Bale A, Weissman SM. Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Res. 1996;6:633–638. PubMed
Sidhu MK, Liao MJ, Rashidbaigi A. Dimethyl sulfoxide improves RNA amplification. BioTechniques. 1996;21:44–47. PubMed
Jung M, Muche JM, Lukowsky A, Jung K, Loening SA. Dimethyl sulfoxide as additive in ready-to-use reaction mixtures for real-time polymerase chain reaction analysis with SYBR Green I dye. Anal. Biochem. 2001;289:292–295. PubMed
Chakrabarti R, Schutt CE. The enhancement of PCR amplification by low molecular-weight sulfones. Gene. 2001;274:293–298. PubMed
Chakrabarti R, Schutt CE. Novel sulfoxides facilitate GC-rich template amplification. BioTechniques. 2002;32:866–873. PubMed
Weissensteiner T, Lanchbury JS. Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. BioTechniques. 1996;21:1102–1108. PubMed
Hengen PN. Optimizing multiplex and LA-PCR with betaine. Trends Biochem. Sci. 1997;22:225–226. PubMed
Sarkar G, Kapelner S, Sommer SS. Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res. 1990;18:7465. PubMed PMC
Comey CT, Jung JM, Budowle B. Use of formamide to improve amplification of HLA DQ alpha sequences. BioTechniques. 1991;10:60–61. PubMed
Chakrabarti R, Schutt CE. The enhancement of PCR amplification by low molecular weight amides. Nucleic Acids Res. 2001;29:2377–2381. PubMed PMC
Chevet E, Lemaitre G, Katinka MD. Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res. 1995;23:3343–3344. PubMed PMC
Hung T, Mak K, Fong K. A specificity enhancer for polymerase chain reaction. Nucleic Acids Res. 1990;18:4953. PubMed PMC
Kovárová M, Dráber P. New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res. 2000;28:e70. PubMed PMC
Watanabe M, Abe K, Aoki M, Kameya T, Itoyama Y, Shoji M, Ikeda M, Iizuka T, Hirai S. A reproducible assay of polymerase chain reaction to detect trinucleotide repeat expansion of Huntington's disease and senile chorea. Neurol. Res. 1996;18:16–18. PubMed
Pomp D, Medrano JF. Organic solvents as facilitators of polymerase chain reaction. BioTechniques. 1991;10:58–59. PubMed
Bachmann B, Luke W, Hunsmann G. Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Res. 1990;18:1309. PubMed PMC
Varadaraj K, Skinner DM. Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases. Gene. 1994;140:1–5. PubMed
Carninci P, Nishiyama Y, Westover A, Itoh M, Nagaoka S, Sasaki N, Okazaki Y, Muramatsu M, Hayashizaki Y. Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. Proc. Natl Acad. Sci USA. 1998;95:520–524. PubMed PMC
Spiess A-N, Muellr N, Ivell R. Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of Taq polymerase by the disaccharide trehalose. Clin. Chem. 2004;50:1256–1259. PubMed
Nath K, Sarosy JW, Hahn J, Di Como CJ. Effects of ethidium bromide and SYBR Green I on different polymerase chain reaction systems. J. Biochem. Biophys. Methods. 2000;42:15–29. PubMed
Wu M, White HW, Kusukawa N, Stein TM. Stabilization of highly sensitive nucleic acid stains in aqueous solutions, US6365341. 2002
Zeng Z, Clark SM, Mathies RA, Glazer AN. Improved stability and electrophoretic properties of preformed fluorescent cationic dye-DNA complexes in a taps-tetrapentylammonium buffer in agarose slab gels. Anal. Biochem. 1997;252:110–114. PubMed
Zipper H, Brunner H, Bernhagen J, Vitzthum F. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 2004;32:e103. PubMed PMC
Dráber P, Zikán J, Vojtíšková M. Establishment and characterization of permanent murine hybridomas secreting monoclonal anti-Thy-1 antibodies. J. Immunogenet. 1980;7:455–474. PubMed
Scalice ER, Sharkey DJ, Daiss JL. Monoclonal antibodies prepared against the DNA polymerase from Thermus aquaticus are potent inhibitors of enzyme activity. J. Immunol. Methods. 1994;172:147–163. PubMed
Dráberová L, Dráber P. Functional expression of the endogenous Thy-1 gene and the transfected murine Thy-1.2 gene in rat basophilic leukemia cells. Eur. J. Immunol. 1991;21:1583–1590. PubMed
Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der NJ. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 1990;28:495–503. PubMed PMC
Wolff R, Gemmill R. Purifying and Analyzing Genomic DNA. In: Birren B, Green ED, Klapholz S, Myers RM, Roskams J, editors. Genome Analysis: A Laboratory Manual. Cold Spring Harbor, New York, NY: Cold Spring Harbor Laboratory Press; 1997. pp. 1–81.
Melchior WB, Jr, Von Hippel PH. Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc. Natl Acad. Sci USA. 1973;70:298–302. PubMed PMC
Jacobs KA, Rudersdorf R, Neill SD, Dougherty JP, Brown EL, Fritsch EF. The thermal stability of oligonucleotide duplexes is sequence independent in tetraalkylammonium salt solutions: application to identifying recombinant DNA clones. Nucleic Acids Res. 1988;16:4637–4650. PubMed PMC
Monis PT, Giglio S, Saint CP. Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal. Biochem. 2005;340:24–34. PubMed
Karsai A, Muller S, Platz S, Hauser MT. Evaluation of a homemade SYBR green I reaction mixture for real-time PCR quantification of gene expression. BioTechniques. 2002;32:790–796. PubMed PMC
1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer