Silencing gene expression by targeting chromosomal DNA with antigene peptide nucleic acids and duplex RNAs

Nature Protocols

Volumn 1, Issue 1, 2006, Pages 436-443

  Janowski, Bethany A ^a   Hu, Jiaxin ^a   Corey, David R ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED RNA; PEPTIDE NUCLEIC ACID;

ARTICLE; CHEMISTRY; CHROMOSOME; GENE SILENCING; GENETIC TRANSFECTION; METHODOLOGY; TRANSCRIPTION INITIATION SITE;

CHROMOSOMES; DNA; GENE SILENCING; PEPTIDE NUCLEIC ACIDS; RNA, DOUBLE-STRANDED; TRANSCRIPTION INITIATION SITE; TRANSFECTION;

EID: 33748337330     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.64     Document Type: Article

References (35)

1. Kaihatsu, K., Janowski, B.A. & Corey, D.R. Recognition of duplex DNA by oligonucleotides and peptide nucleic acids. Chem. Biol. 11, 749-758 (2002).
2. Janowski, B.A. et al. Inhibiting transcription of chromosomal DNA using antigene peptide nucleic acids. Nat. Chem. Biol. 1, 210-215 (2005).
3. Janowski, B.A. et al. Inhibiting gene expression at transcription start sites in chromosomal DNA by antigene RNAs. Nat Chem. Biol. 1, 216-222 (2005).
4. Knauert, M.P. & Glazer, P.M. Triplex forming oligonucleotides: sequence-specific: Tools for gene targeting. Hum. Mol. Gen. 10 2243-2251 (2001).
5. Besch, R., Giovannangeli, C., Schuh, T., Kammerbauer, C. & Degitz, K. Characterization and quantification of triple helix formation in chromosomal DNA. J. Mol. Biol. 341, 979-989 (2004).
6. Dervan, P.B. & Edelson, B.S. Recognition of the DNA minor groove by pyrrole-imidizole polyamides. Curr. Opin. Struct. Biol. 13, 284-299 (2003).
7. Dudouet, B. et al. Accessibility of nuclear chromatin by DNA binding polyamides. Chem. Biol. 10, 859-867 (2003).
8. Nielsen, P.G., Egholm, M., Berg, R.H. & Buchardt, O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254, 1497-1500 (1991).
9. Hamilton, S.E., Simmons, C.G., Kathriya, I. & Corey, D.R. Cellular delivery of peptide nucleic acids and inhibition of human telomerase. Chem. Biol. 6, 343-351 (1999).
10. Doyle, D.F., Braasch, D.A, Simmons, C.G., Janowski, B.A. & Corey, D.R. Intracellular delivery and inhibition of gene expression by peptide nucleic acids. Biochemistry 40, 53-64 (2001).
11. Kaihatsu, K., Huffman, K.E. & Corey, D.R. Cellular uptake, localization, and inhibition of gene expression by PNAs and PNA-peptide conjugates. Biochemistry 43, 14340-14347 (2004).
12. Turner, J.J. et al. Cell-penetrating peptide conjugates of peptide nucleic acids (PNA) as inhibitors of HIV-1 Tat-dependent trans-activation in cells. Nucleic Acids Res. 30, 6837-6849 (2005).
13. Albertshofer, K. et al. Structure-activity relationship study on a simple cationic peptide motif for cellular delivery of antisense peptide nucleic acid. J. Med. Chem. 48, 6741-6749 (2005).
14. Maier, M.A. et al. Evaluation of basic amphipathic peptides for cellular delivery of antisense peptide nucleic acids. J. Med. Chem. 49, 2534-2542 (2006).
15. Shiraishi, T. et al. Calcium ions effectively enhance the effect of antisense peptide nucleic acids conjugated to cationic tat and oligoarginine peptides. Chem. Biol. 12, 923-929 (2005).
16. Abes, S. et al. Endosome trapping Limits the efficiency of splicing correction by PNA-oligolysine conjugates. J. Control. Release 110, 595-604 (2006).
17. Nielsen, P.E. Addressing the challenges of cellular delivery and bioavailability of peptide nucleic acids (PNA). Q. Rev. Biophys. 39, 1-6 (2006).
18. Morris, K.V., Chan, S.W., Jacobsen, S.E. & Looney, D.J. Small-interfering RNA-induced transcriptional silencing in human cells. Science 305, 1289-1292 (2004).
19. Ting, A.H. et al. Short double-stranded RNA induces transcriptional gene silencing in human cells in the absence of DNA methylation. Nat. Genet. 37, 906-910 (2005).
20. Castanotto, D. et al. Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1 promoter in Hela cells. Mol. Ther. 12 179-183 (2005).
21. Suzuki, K. et al. Prolonged transcriptional silencing and CpG methylation induced by siRNAs targeted to the HIV-1 promoter region. J. RNAi Gene Silencing 1, 66-78 (2005).
22. Zhang, M.-X. et al. Regulation of endothelial nitric oxide synthase by small RNA. Proc. Natl. Acad. Sci. USA 102, 16967-16972 (2005).
23. Weinberg, M.S. et al. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12, 256-262 (2006).
24. Corey, D.R. Regulating mammalian transcription with RNA. Trends Biochem. Sci. 30, 655-658 (2005).
25. Morris, K.V. Therapeutic potential of siRNA-mediated transcriptional gene silencing. Biotechniques 40, S7-S13 (2006).
26. Greenberg, M. in Current Protocols in Molecular Biology 4, 10.1-4.10.11 (1987).
27. Braasch, D.A. & Corey, D.R. Synthesis, analysis, purification, and intracellular delivery of peptide nucleic acids. Methods 23, 97-107 (2001).
28. Mayfield, L.D. & Corey, D.R. Automated synthesis of peptide nucleic acids (PNAs) and peptide nucleic acid-peptide conjugates. Anal. Biochem. 268, 401-404 (1999).
29. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
30. Crooke, S.T. Evaluating the mechanism of action of antiproliferative antisense drugs. Antisense Nucleic. Acid Drug Dev. 10, 123-126 (2000).
31. Editorial. Wither RNAi? Nat. Cell Biol. 5, 489-490 (2003).
32. Kastner, P. et al. Two distinct estrogen-regulated promoters generate transcripts encoding the two functionally different human progesterone receptor isoforms A and B. EMBO J. 9, 1603-1614 (1990).
33. Misrahi, M. et al. Structure of the human progesterone receptor gene. Biochim. Biophys. Acta 1216, 289-292 (1993).
34. Hashimoto, S. et al. 5′-End SAGE for the analysis of transcriptional start sites. Nat. Biotechnol. 22, 1146-1149.
35. Yamashita, R. et al. DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res. D86-D89 (2006).