Dimethyl sulfoxide improves sensitivity and specificity of RT-PCR and QRT-PCR amplification of low-expressed transgenes

Archives of Biological Sciences

Volumn 64, Issue 3, 2012, Pages 865-876

  Simonović, Ana ^a   Trifunović, Milana ^a   Raspor, M ^a   Cingel, A ^a   Bogdanović, Milica ^a   Dragicevic M ^a   Subotić, Angelina ^a  

^a UNIVERSITY OF BELGRADE   (Serbia)

Author keywords

Bovine serum albumin; Dimethyl sulfoxide; Ethylene glycol; Formamide; Glycerol; PCR additives; PCR enhancers; qPCR optimization; Trehalose; Tween 20

Indexed keywords

EID: 84867841466     PISSN: 03544664     EISSN: None     Source Type: Journal    
DOI: 10.2298/ABS1203865S     Document Type: Article

References (43)

1. Bachmann, B., Luke, W. and G. Hunsmann (1990). Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic Acids Res. 18(5), 1309.
2. Baskaran, N., Kandpal, R. P., Bhargava, A. K., Glynn, M. W., Bale, A. and S. M. Weissman (1996). Uniform amplification of a mixture of deoxyribonucleic acids with varying GC content. Genome Res. 6, 633-638.
3. Bookstein, R., Lai, C. C., To, H., and W. H. Lee (1990). PCR-based detection of a polymorphic BamHI site in intron 1 of the human retinoblastoma (RB) gene. Nucleic Acids Res. 18(6), 1666.
4. Carninci, P., Nishiyama, Y., Westover, A., Itoh, M., Nagaoka, S., Sasaki, N., et al. (1998). Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full-length cDNA. Proc. Natl. Acad. Sci. U S A 95, 520-524.
5. Chakrabarti, R., and C. E. Schutt (2001a). The enhancement of PCR amplification by low molecular weight amides. Nucleic Acids Res. 29(11), 2377-2381.
6. Chakrabarti, R., and C. E. Schutt (2001b). The enhancement of PCR amplification by low molecular-weight sulfones. Gene. 274(1-2), 293-298.
7. Chakrabarti, R., and C. E. Schutt (2002). Novel sulfoxides facilitate GC-rich template amplification. Biotechniques. 32(4), 866 - 874.
8. Chevet, E., Lemaître, G., and M. D. Katinka (1995). Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res. 23(16), 3343-3344.
9. Demeke, T., and R. P. Adams (1992). The effects of plant polysaccharides and buffer additives on PCR. Biotechniques. 12(3), 332-334.
10. Frackman, S., Kobs, G., Simpson, D. and D. Storts (1998). Betaine and DMSO: enhancing agents for PCR. Promega Notes 65, 27.
11. Gašić, K., Hernandez, A., and S.S. Korban (2004). RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA library construction. Plant Mol. Biol. Rep. 22, 437a-437g.
12. Gelfand, D.H. and T.J. White (1990). Thermostable DNA Polymerases. In: PCR Protocols: A Guide to Methods and Applications, (Eds. M.A. Innis, D.H. Gelfand, J.J. Sninsky, and T.J. White), 129-141. Academic Press, San Diego, CA.
13. Giambernardi, T. A., Rodeck, U., and R. J. Klebe (1998). Bovine serum albumin reverses inhibition of RT-PCR by melanin. Biotechniques. 25(4), 564-566.
14. Hengen, P. N. (1997). Optimizing multiplex and LA-PCR with betaine. Trends in Biochemical Sciences 22(6), 225-226.
15. Henke, W., Herdel, K., Jung, K., Schnorr, D., and S. A. Loening (1997). Betaine improves the PCR amplification of GCrich DNA sequences. Nucleic Acids Res. 25, 3957-3958.
16. Hung, T., Mak, K., and K. Fong (1990). A specificity enhancer for polymerase chain reaction. Nucleic Acids Res. 18(16), 4953.
17. Jung, M., Muche, J. M., Lukowsky, A., Jung, K., and S. A. Loening (2001). Dimethyl sulfoxide as additive in ready-to-use reaction mixtures for real-time polymerase chain reaction analysis with SYBR Green I dye. Anal. Biochem. 289(2), 292-295.
18. Kitade, Y., Ootsuka, S., Iitsuka, O. and N. Saga (2003). Effect of DMSO on PCR of Porphyra yezoensis (Rhodophyta) gene. Journal of Applied Phycology 15, 555-557.
19. Klatser, P. R., Kuijper, S., van Ingen, C. W., and A. H. Kolk. (1998). Stabilized, freeze-dried PCR mix for detection of mycobacteria. J. Clin. Microbiol. 36, 1798-800.
20. Kovárová, M., and P. Dráber (2000). New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res. 28(13), E70.
21. Kreader, C. A. (1996). Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol. 62(3), 1102-1106.
22. Liu, Y. S., Thomas, R. J., and W. A. Phillips (1995). Single-step direct PCR amplification from solid tissues. Nucleic Acids Res. 23(9), 1640.
23. McConlogue, L., Brow, M. A., and M. A. Innis (1988). Structureindependent DNA amplification by PCR using 7-deaza-2'-deoxyguanosine. Nucleic Acids Res. 16(20), 9869.
24. Melchior, W. B. Jr, and P. H. Von Hippel (1973). Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc. Natl. Acad. Sci. U S A 70(2), 298-302.
25. Meyer, P. (1998). Stabilities and instabilities in tranagene expression. In Transgenic Plant Research, (Ed. K. Lindsey), 263-275. Harwood Academic Publishers, Switzerland.
26. Mizuno, Y., Carninci, P., Okazaki, Y., Tateno, M., Kawai, J., Amanuma, H., Muramatsu, M., and Y. Hayashizaki (1999). Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display. Nucleic Acids Res. 27(5), 1345-1349.
27. Multer, G. L. and K. A. Boynton (1995). PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies. Nucl. Acids Res. 23 (8), 1411-1418.
28. Nagai, M., Yoshida, A., and N. Sato (1998). Additive effects of bovine serum albumin, dithiothreitol, and glycerol on PCR. Biochem. Mol. Biol. Int. 44(1), 157-163.
29. Pääbo, S., Gifford, J. A. and A. C. Wilson (1988). Mitochondrial DNA sequences from a 7000-year old brain. Nucleic Acid Res. 16(20), 9775 - 9787.
30. Ramussen, R., Morrison, T., Herrmann, M. and C. Wittwer (1998). Quantitative PCR by Continuous Fluorescence Monitoring of a Double Strand DNA Specific Binding Dye. Biochemica 2, 8-11.
31. Raspor, M., Motyka, V., Žižková, E., Dobrev. P.I., Trávničková. A., Zdravković-Korać, S., Simonović, A., Ninković, S. and I. C. Dragićević. (2012): Cytokinin profiles of AtCKX2-overexpressing potato plants and the impact of altered cytokinin homeostasis on tuberization in vitro. J Plant Growth Regul. DOI 10.1007/s00344-011-9255-3.
32. Rees, W. A., Yager, T. D., Korte, J., and P. H. von Hippel. (1993). Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry. 32(1), 137-144.
33. Sarkar, G., Kapelner, S., and S. S. Sommer (1990). Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res. 18(24), 7465.
34. Shaik, G. M., Dráberová, L., Dráber, P., Boubelík, M., and P. Dráber (2008). Tetraalkylammonium derivatives as realtime PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I. Nucleic Acids Res. 36(15), e93.
35. Sidhu, M. K., Liao, M. J., and A. Rashidbaigi (1996). Dimethyl sulfoxide improves RNA amplification. Biotechniques 21(1), 44-47.
36. Sorokin V.A., Gladchenko G.O., Valeev V.A., Sysa I.V., Petrova L.G. and Y.P. Blagoi. (1997). Effect of salt and organic solvents on DNA thermal stability and structure. Journal of Molecular Structure 408-409, 237-240.
37. Spiess, A. N., Mueller, N., and R. Ivell (2004). Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of taq polymerase by the disaccharide trehalose. Clin. Chem. 50(7), 1256-1259.
38. Turner, S. L., and F. J. Jenkins (1995). Use of deoxyinosine in PCR to improve amplification of GC-rich DNA. Biotechniques. 19(1), 48-52.
39. van Leeuwen, W., Ruttink, T., Borst-Vrenssen, A. W., van der Plas, L. H., and A. R. van der Krol. (2001). Characterization of position-induced spatial and temporal regulation of transgene promoter activity in plants. J. Exp. Bot. 52(358), 949-959.
40. Varadaraj, K., and D. M. Skinner (1994). Denaturants or cosolvents improve the specificity of PCR amplification of a GC-rich DNA using genetically engineered DNA polymerases. Gene 140 (1), 1-5.
41. Weissensteiner, T., and J. S. Lanchbury (1996). Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. Biotechniques 21, 1102-1108.
42. Winship, P.R. (1989). An improved method for directly sequencing PCR amplified material using dimethyl sulfoxide. Nucleic Acids Res. 17(3), 1266.
43. Zhang, Z., Yang, X., Meng, L., Liu, F., Shen, C., and W. Yang (2009). Enhanced amplification of GC-rich DNA with two organic reagents. Biotechniques. 47(3), 775-779.