Quantification of siRNA using competitive qPCR

Nucleic Acids Research

Volumn 37, Issue 1, 2009, Pages

  Liu, Wei Li ^a   Stevenson, Mark ^a   Seymour, Leonard W ^a   Fisher, Kerry D ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; HISTIDINE; OLIGOFECTAMINE; POLYMER; PRIMER DNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; E6 PROTEIN, HUMAN PAPILLOMAVIRUS TYPE 16; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; ONCOPROTEIN; REPRESSOR PROTEIN;

AMPLICON; ARTICLE; CONTROLLED STUDY; DNA TEMPLATE; GENE TARGETING; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA INTERFERENCE; RNA PROBE; RNA PROCESSING; RNA SEQUENCE; GENETICS; METHODOLOGY; TUMOR CELL LINE;

HUMAN PAPILLOMAVIRUS;

CELL LINE, TUMOR; DNA PRIMERS; GREEN FLUORESCENT PROTEINS; HUMANS; ONCOGENE PROTEINS, VIRAL; POLYMERASE CHAIN REACTION; REPRESSOR PROTEINS; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 58549113387     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn903     Document Type: Article

References (23)

1. Fire,A., Xu,S., Montgomery,M.K., Kostas,S.A., Driver,S.E. and Mello,C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391, 806-811.
2. Tuschl,T., Zamore,P.D., Lehmann,R., Bartel,D.P. and Sharp,P.A. (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13, 3191-3197.
3. Elbashir,S.M., Harborth.J., Lendeckel.W., Yalcin.A., Weber,K. and Tuschl,T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
4. Soutschek,J., Akine,A., Bramlage,B., Charisse,K., Constien,R., Donoghue,M., Elbashir,S., Geick,A., Hadwiger,P., Harborth, J et al. (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature, 432, 173-178.
5. Zimmermann,T.S., Lec,A.C., Akine,A., Bramlage,B., Bumerot,D., Fedoruk,M.N., Harborth,J. Heyes,J.A., Jeffs,L.B., John,M. et al. (2006) RNAi-mediated gene silencing in non-human primates. Nature, 441, 111-114.
6. Overhoff,M., Wunsche,W. and Sczakiel,G. (2004) Quantitative detection of siRNA and single-stranded oligonucleotides: Relationship between uptake and biological activity of siRNA. Nucleic Acids Res., 32, 070.
7. Chiu,Y.L., Ali,A., Chu,C.Y., Cao,H. and Rana,T.M. (2004) Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells. Chem. Biol., 11, 1165-1175.
8. Chen,A.A., Derfus,A.M., Khetani,S.R. and Bhatia,S.N. (2005) Quantum dots to monitor RNAi delivery and improve gene silencing. Nucleic Acids Res., 33, e190.
9. Heid,C.A., Stevens,J., Livak,K.J. and Williams,P.M. (1996) Real time quantitative PCR. Genome Res., 6, 986-994.
10. Raymond,C.K., Roberts,B.S., Garrett-Engele,P., Lim,L.P. and Johnson,J.M. (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. Rna, 11, 1737-1744.
11. Allawi,H.T., Dahlberg,J.E., Olson,S., Lund,E., Olson,M., Ma,W.P., Takova,J., Neri,B.P. and Lyamichev,V.I. (2004) Quantitation of microRNAs-using a modified Invader assay., RNA, 10, 1153-1161.
12. Chen,C., Ridzon,D.A., Broomer,A.J., Zhou,Z., Lee,D.H., Nguyen,J.T., Barbisin,M., Xu,N.L., Mahuvakar,V.R., Andersen,M.R. et al. (2005) Real-Time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res., 33, e179.
13. Duncan,D.D., Eshoo,M., Esau,C., Freier,S.M. and Lollo,B.A. (2006) Absolute quantitation of microRNAs with a PCR-based assay. Anal. Biochem., 359, 268-270.
14. Jiang,M., Arzumanov,A.A., Gait,M.J. and Milner,J. (2005) A bi-functional siRNA construct induces RNA interference and also primes PCR amplification for its own quantification. Nucleic Acids Res., 33, e151.
15. Stratford,S., Stec,S., Jadhav,V., Seitzer,J., Abrams,M. and Beverly,M. (2009) Examination of real-time polymerase chain reaction methods for the detection and quantification of modified siRNA. Anal. Biochem. 379, 96-104.
16. Piatak,M. Jr, Luk,K.C., Williams,B. and Lifson,J.D. (1993) Quantitative competitive polymerase chain reaction for accurate quantitation of HIV DNA and RNA species. Biotechniques, 14, 70-81.
17. Piatak,M. Jr, Saag,M.S., Yang,L.C., Clark,S.J., Kappes,J.C., Luk,K.C., Hahn,B.H., Shaw,G.M. and Lifson,J.D. (1993) High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science, 259, 1749-1754.
18. Becker-Andre,M. (1991) Quantitative evaluation of mRNA levels. Meth. Mol. Cell. Biol., 2, 189-201.
19. Read,M.L., Singh,S., Ahmed,Z., Stevenson, M., -Briggs,S.S., Oupicky,D., Barrett,L.B., Spice,R., Kendall,M., Berry,M. et al. (2005) A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids. Nucleic Acids Res., 33, e86.
20. Stevenson,M., Ramos-Perez,V., Singh,S., Soliman,M., Preece,J.A., Briggs,S.S., Read,M.L. and Seymour,L.W. (2008) Delivery of siRNA mediated by histidine-containing reducible polycations. J. Control Release, 130, 46-56.
21. Qiagen.com. (2004) Critical Factors for Successful Real-time PCR. Qiagen, Germantown, MD, USA.
22. Shibata,H., Tahira,J. and Hayashi,K. (1995) RNA-primed PCR. Genome Res., 5, 400-403.
23. Stump,M.D., Cherry,J.L. and Weiss,R.B. (1999) The use of modified primers to eliminate cycle sequencing artifacts. Nucleic Acids Res. 27, 4642-4648.