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Nucleic Acids Research, 2003, Vol. 31, No. 14 e72
© 2003 Oxford University Press

mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides

Hong-Yan Zhang1,2, Jianping Mao1, Daixing Zhou1, Yunhe Xu1, Håkan Thonberg1, Zicai Liang*,1 and Claes Wahlestedt1

1 Center for Genomics and Bioinformatics, Karolinska Institutet, 17177, Stockholm, Sweden and 2 United Biotechnologies AB, Sevensvägen 4, 17446, Sundbyberg, Sweden

*To whom correspondence should be addressed. Tel: +46 8 7286371; Fax: +46 8 327934; Email: zicai.liang{at}cgb.ki.se
Correspondence may also be addressed to Claes Wahlestedt. Tel: +46 8 7286629; Fax: +46 8 323950; Email: claes.wahlestedt{at}cgb.ki.se
Present address:
Jianping Mao, Beijing Institute of Radiation Medicine, Beijing, 100850, China

A solution-based method, mRNA accessible site tagging (MAST), has been developed to map the accessible sites of any given mRNA in high throughput fashion. mRNA molecules were immobilized and hybridized to randomized oligonucleotide libraries. Oligonucleotides specifically hybridized to the mRNA were sequenced and found to be able to precisely define the accessible sites of the mRNA. A number of ways were used to validate the accessible sites defined by the MAST process. Mapping of rabbit ß-globin mRNA demonstrates the efficacy and advantage of MAST over other technologies in identifying accessible sites. Antisense oligonucleotides designed according to the accessible site map of human RhoA and Renilla luciferase mRNA result in knockdown effects that are in good correlation with the degrees of accessibility. The MAST methodology can be applied to mRNA of any length using a universal protocol.


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