Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

Genetics and Molecular Biology

Volumn 30, Issue 4, 2007, Pages 1206-1208

  Pereira, Tiago Campos ^a   Bittencourt, Vinícius D'Ávila Pascoal ^a   Secolin, Rodrigo ^a   de Souza Rocha, Cristiane ^a   de Godoy Maia, Ivan ^b   Lopes Cendes, Iscia ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

RNAi; siRNA; siRNA design; Software

Indexed keywords

DOUBLE STRANDED RNA; SMALL INTERFERING RNA;

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; ENERGY; GENE FUNCTION; GENE IDENTIFICATION; GENE SILENCING; GIBBS FREE ENERGY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MOLECULAR BIOLOGY; NUCLEOTIDE SEQUENCE; ONLINE ANALYSIS; RNA ANALYSIS; RNA INTERFERENCE;

EID: 37649018871     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572007000600030     Document Type: Article

References (14)

1. Brummelkamp TR, Bernards R and Agami R (2002) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2:243-247.
2. Elbashir SM, 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.
3. Fedoriw AM, Stein P, Svoboda P, Schultz RM and Bartolomei MS (2004) Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 303:238-240.
4. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE and Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811.
5. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M and Ahringer J (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408:325-330.
6. Gitlin L, Karelsky S and Andino R (2002) Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 418:430-434.
7. Holen T, Amarzguioui M, Wiiger MT, Babaie E and Prydz H (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res 30:1757-1766.
8. Khvorova A, Reynolds A and Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216.
9. Mohmmed A, Dasaradhi PV, Bhatnagar RK, Chauhan VS and Malhotra P (2003) In vivo gene silencing in Plasmodium berghei - A mouse malaria model. Biochem Biophys Res Commun. 309:506-511.
10. Ogita S, Uefuji H, Yamaguchi Y, Koizumi N and Sano H (2003) Producing decaffeinated coffee plants. Nature 423:823.
11. Pei Y and Tuschl T. (2006) On the art of identifying effective and specific siRNAs. Nat Methods 3:670-6.
12. Rand TA, Petersen S, Du F and Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123:621-619.
13. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N and Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199-208.
14. Xia H, Mao Q, Eliason SL, Harper SQ, Martins IH, Orr HT, Paulson HL, Yang L, Kotin RM and Davidson BL (2004) RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia. Nat Med 10:816-820.