Overview on AON design

Methods in Molecular Biology

Volumn 867, Issue , 2012, Pages 117-129

  Aartsma Rus, Annemieke ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Antisense oligonucleotides; Design; Exon skipping; Exonic splicing enhancer; Pre mRNA structure

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; RNA PRECURSOR;

ANIMAL; CHEMISTRY; EXON; GENETICS; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVIEW; RNA SPLICING;

ANIMALS; BASE SEQUENCE; EXONS; HUMANS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES, ANTISENSE; RNA PRECURSORS; RNA SPLICING;

EID: 84859850106     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-767-5_8     Document Type: Review

References (30)

1. Aartsma-Rus A, van Ommen GJ (2007) Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications. RNA 13:1609-1624 (Pubitemid 47481669)
2. Aartsma-Rus A (2010) Antisense-mediated modulation of splicing: therapeutic implications for Duchenne muscular dystrophy. RNA Biol 7:453-461
3. Aartsma-Rus A, Winter CL, Janson AAM et al (2005) Functional analysis of 114 exon-internal AONs for targeted DMD exon skipping: indication for steric hindrance of SR protein binding sites. Oligonucleotides 15:284-297 (Pubitemid 43108225)
4. Aartsma-Rus A, van Vliet L, Hirschi M et al (2009) Guidelines for antisense oligonucleotide design and insight into splice-modulating mechanisms. Mol Ther 17:548-553
5. Aartsma-Rus A, Houlleberghs H, van Deutekom JC et al (2010) Exonic sequences provide better targets for antisense oligonucleotides than splice site sequences in the modulation of Duchenne muscular dystrophy splicing. Oligonucleotides 20:69-77
6. Popplewell LJ, Trollet C, Dickson G et al (2009) Design of phosphorodiamidate morpholino oligomers (PMOs) for the induction of exon skipping of the human DMD gene. Mol Ther 17:554-561
7. Wilton SD, Fall AM, Harding PL et al (2007) Antisense oligonucleotide-induced exon skipping across the human dystrophin gene transcript. Mol Ther 15:1288-1296 (Pubitemid 46965325)
8. Aartsma-Rus A, Singh KH, Fokkema IF et al (2010) Therapeutic exon skipping for dysferlinopathies? Eur J Hum Genet 18:889-894
9. Aartsma-Rus A, van der Maarel S (2010) Reply to Levy et al. Eur J Hum Genet 18:971
10. van Ommen GJ, van Deutekom J, Aartsma-Rus A (2008) The therapeutic potential of antisense-mediated exon skipping. Curr Opin Mol Ther 10:140-149 (Pubitemid 351498876)
11. Aartsma-Rus A, Kaman WE, Bremmer-Bout M et al (2004) Comparative analysis of antisense oligonucleotide analogs for tageted DMD exon 46 skipping in muscle cells. Gene Ther 11:1391-1398 (Pubitemid 39263892)
12. Alter J, Lou F, Rabinowitz A et al (2006) Systemic delivery of morpholino oligonucleotide restores dystrophin expression bodywide and improves dystrophic pathology. Nat Med 12:175-177 (Pubitemid 43214742)
13. Heemskerk H, de Winter C, van Kuik P et al (2010) Preclinical PK and PD studies on 2 ¢-O-methyl-phosphorothioate RNA antisense oligonucleotides in the mdx mouse model. Mol Ther 18:1210-1217
14. Heemskerk HA, De Winter CL, de Kimpe SJ et al (2009) In vivo comparison of 2 ¢-O-methyl phosphorothioate and morpholino antisense oligonucleotides for Duchenne muscular dystrophy exon skipping. J Gene Med 11:257-266
15. Lu QL, Rabinowitz A, Chen YC et al (2005) Systemic delivery of antisense oligoribonucleotide restores dystrophin expression in bodywide skeletal muscles. Proc Natl Acad Sci USA 102:198-203 (Pubitemid 40094452)
16. Malerba A, Thorogood FC, Dickson G et al (2009) Dosing regimen has a significant impact on the efficiency of morpholino oligomer-induced exon skipping in mdx mice. Hum Gene Ther 20:955-965
17. Kurreck J (2003) Antisense technologies. Improvement through novel chemical modifi-cations. Eur J Biochem 270:1628-1644 (Pubitemid 36532522)
18. Sproat BS, Lamond AI, Beijer B et al (1989) Highly efficient chemical synthesis of 2 ¢-O-methyloligoribonucleotides and tetrabiotinylated derivatives; novel probes that are resistant to degradation by RNA or DNA specific nucleases. Nucleic Acids Res 17:3373-3386 (Pubitemid 19120439)
19. De Clercq E, Eckstein F, Sternbach H et al (1969) Interferon induction by and ribonuclease sensitivity of thiophosphate-substituted polyribonucleotides. Antimicrob Agents Chemother 9:187-191
20. Summerton J, Weller D (1997) Morpholino antisense oligomers: design, preparation, and properties. Antisense Nucleic Acid Drug Dev 7:187-195 (Pubitemid 27323077)
21. Heemskerk H, De Winter CL, van Ommen GJ et al (2009) Development of antisense-mediated exon skipping as a treatment for Duchenne muscular dystrophy. Ann N Y Acad Sci 1175:71-79
22. Harding PL, Fall AM, Honeyman K et al (2007) The infl uence of antisense oligonucleotide length on dystrophin exon skipping. Mol Ther 15:157-166 (Pubitemid 46043661)
23. Wee KB, Pramono ZA, Wang JL et al (2008) Dynamics of co-transcriptional pre-mRNA folding infl uences the induction of dystrophin exon skipping by antisense oligonucleotides. PLoS One 3:e1844
24. Mathews DH, Sabina J, Zuker M et al (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911-940 (Pubitemid 29248642)
25. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415 (Pubitemid 37442169)
26. Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3:285-298 (Pubitemid 34279797)
27. Desmet FO, Hamroun D, Lalande M et al (2009) Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67
28. Aartsma-Rus A, Kaman WE, Weij R et al (2006) Exploring the frontiers of therapeutic exon skipping for Duchenne muscular dystrophy by double targeting within one or multiple exons. Mol Ther 14:401-407 (Pubitemid 44184959)
29. Adams AM, Harding PL, Iversen PL et al (2007) Antisense oligonucleotide induced exon skipping and the dystrophin gene transcript: cocktails and chemistries. BMC Mol Biol 8:57
30. Aartsma-Rus A, van Ommen GJ, Kaplan JC (2010) Innovating therapies for muscle diseases. In: Dulac O, Lassonde M, Sarnat H (eds) Handbook of clinical neurology, 3rd series, 3rd edn. Elsevier, Chennai, India