For mRNA Accessible Sites Screening: A Comparative Study by Using MAST and Computational Prediction

MAO Jian ping 1)* , Zicai LIANG 2) , MAO Bing zhi 1)

Chinese Journal of Biochemistry and Molecular Biology ›› 2004, Vol. 20 ›› Issue (03) : 399-407.

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PDF(314 KB)
Chinese Journal of Biochemistry and Molecular Biology ›› 2004, Vol. 20 ›› Issue (03) : 399-407.
Article

For mRNA Accessible Sites Screening: A Comparative Study by Using MAST and Computational Prediction

  • MAO Jian ping 1)* , Zicai LIANG 2) , MAO Bing zhi 1)
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Abstract

Selecting the target sites of the mRNA has been a major challenge in antisense drug research. Two accessible target sites of rabbit ( Oryctolagus cuniculus )β globin mRNA fragment were obtained by using MAST. From the lowest free energy (Δ G 37 ) structure folded by RNAstructure3 71, two sites were achieved by oligo walking and were identical to those obtained from MAST. Moreover, they were the same with those ones reported by combinatorial oligonucleotide arrays hybridization. For green fluorescence protein(GFP), four accessible target sites were obtained by MAST. Antisense oligonucleotides designed to these sites were tested to be effective in vitro. By using oligo walking function of RNAstructure3 71, 3 among the 8 recommended sites were similar with 3 sites of MAST selected. The validating of sites computer aid predicted among many recommended ones need to be tested in vitro and it would work more difficultly if for long sequence length gene. But it is yet helpful to target sites screening and antisense designing. Effective antisense oligonucleotides could be designed based on sequence data from MAST. MAST is a simplified protocol and could screen mRNAs of any size, and be a good tool in antisense drugs designing.

Key words

mRNA / RNAstructure3 71 / MAST / β globin / GFP / accessible site / antisense RNA

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MAO Jian ping 1)* , Zicai LIANG 2) , MAO Bing zhi 1). For mRNA Accessible Sites Screening: A Comparative Study by Using MAST and Computational Prediction[J]. Chinese Journal of Biochemistry and Molecular Biology, 2004, 20(03): 399-407

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