Use of microarrays in transfection of mammalian cells with dicer-digested small interfering RNAs

Analytical Biochemistry

Volumn 374, Issue 2, 2008, Pages 417-422

  Fujimoto, Hiroyuki ^a   Kato, Koichi ^a   Iwata, Hiroo ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Endoribonuclease digested siRNA; Self assembled monolayer; Transfection cell microarray

Indexed keywords

BIOASSAY; CYTOLOGY; MAMMALS; PROTEINS; RNA; SELF ASSEMBLED MONOLAYERS; TRANSCRIPTION;

CELL MICROARRAY; DOUBLE-STRANDED RNA (DSRNA); ENDORIBONUCLEASE; ENHANCED GREEN FLUORESCENT PROTEIN; HIGH THROUGHPUT SCREENING; HIGH-THROUGHPUT ANALYSIS; MICROPATTERNED SUBSTRATES; SMALL INTERFERING RNA (SIRNA);

MOLECULAR BIOLOGY;

COMPLEMENTARY DNA; DOUBLE STRANDED RNA; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; RIBONUCLEASE; SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENE FUNCTION; GENE SILENCING; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MAMMAL CELL; MOLECULAR INTERACTION; NONHUMAN; PLASMID; PRIORITY JOURNAL; REACTION OPTIMIZATION; RNA ANALYSIS;

MAMMALIA;

EID: 39149104019     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2007.12.029     Document Type: Article

References (22)

1. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., and Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
2. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohmann M., Welchman D.P., Zipperlen P., and Ahringer J. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 (2003) 231-237
3. Ziauddin J., and Sabatini D.M. Microarrays of cells expressing defined cDNAs. Nature 411 (2001) 107-110
4. Yamauchi F., Kato K., and Iwata H. Micropatterned, self-assembled monolayers for fabrication of transfected cell microarrays. Biochim. Biophys. Acta 1672 (2004) 138-147
5. Yamauchi F., Kato K., and Iwata H. Spatially and temporally controlled gene transfer by electroporation into adherent cells on plasmid DNA-loaded electrodes. Nucleic Acids Res. 32 (2004) e187
6. Yoshikawa T., Uchimura E., Kishi M., Funeriu D.P., Miyake M., and Miyake J. Transfection microarray of human mesenchymal stem cells and on-chip siRNA gene knockdown. J. Controlled Release 96 (2004) 227-232
7. Mousses S., Caplen N., Cornelison R., Weaver D., Basik M., Hautaniemi S., Elkahloun A.G., Lotufo R.A., Choudary E.R., Suh E., and Kallioniemi O. RNAi microarray analysis in cultured mammalian cells. Genome Res. 13 (2003) 2341-2347
8. Kumar R., Conklin D.S., and Mittal V. High-throughput selection of effective RNAi probes for gene silencing. Genome Res. 13 (2003) 2333-2340
9. Fujimoto H., Yoshizako S., Kato K., and Iwata H. Fabrication of cell-based arrays using micropatterned alkanethiol monolayers for the parallel silencing of specific genes by small interfering RNA. Bioconj. Chem. 17 (2006) 1404-1410
10. Reynolds A., Leake D., Boese Q., Scaringe S., Marshall W.S., and Khvorova A. Rational siRNA design for RNA interference. Nat. Biotechnol. 22 (2004) 326-330
11. Pei Y., and Tuschl T. On the art of identifying effective and specific siRNAs. Nat. Methods 3 (2006) 670-676
12. Yang D., Buchholz F., Huang Z., Goga A., Chen C.-Y., Brodsky F.M., and Bishop J.M. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc. Natl. Acad. Sci. USA 99 (2002) 9942-9947
13. Myers J.W., Jones J.T., Meyer T., and Ferrell J.E. Recombinant dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat. Biotechnol. 21 (2003) 324-328
14. Buchholz F., Kittler R., Slabicki M., and Theis M. Enzymatically prepared RNAi libraries. Nat. Methods 3 (2006) 696-700
15. Kittler R., Putz G., Pelletier L., Poser I., Heninger A.K., Drechsel D., Fischer S., Konstantinova I., Habermann B., Grabner H., Yaspo M.L., Himmelbauer H., Korn B., Neugebauer K., Pisabarro M.T., and Buchholz F. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432 (2004) 1036-1040
16. Tarlov M.J., Burgess D.R.F., and Gillen G. UV photopatterning of alkanethiolate monolayers self-assembled on gold and silver. J. Am. Chem. Soc. 115 (1993) 5305-5306
17. Lechardeur D., Sohn K.-J., Haardt M., Joshi P.B., Monck M., Graham R.W., Beatty B., Squire J., O'Brodovich H., and Lukacs G.L. Metabolic instability of plasmid DNA in the cytosol: A potential barrier to gene transfer. Gene Ther. 6 (1999) 482-497
18. Zhu C., and Jiang W. Cell cycle-dependent translocation of PRC1 on the spindle by Kif4 is essential for midzone formation and cytokinesis. Proc. Natl. Acad. Sci. USA 102 (2005) 343-348
19. Xuan B., Qian Z., Hong J., and Huang W. EsiRNAs inhibit hepatitis B virus replication in mice model more efficiently than synthesized siRNAs. Virus Res. 118 (2006) 150-155
20. Birmingham A., Anderson E.M., Reynolds A., Ilsley-Tyree D., Leake D., Fedorov Y., Baskerville S., Maksimova E., Robinson K., Karpilow J., Marshall W.S., and Khvorova A. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods 3 (2006) 199-204
21. Lin X., Ruan X., Anderson M.G., McDowell J.A., Kroeger P.E., Fesik S.W., and Shen Y. siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res. 33 (2005) 4527-4535
22. Jackson A.L., Burchard J., Schelter J., Chau B.N., Cleary M., Lim L., and Linsley P.S. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12 (2005) 1179-1187