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KMID : 0578320090270060657
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Molecules and Cells
2009 Volume.27 No. 6 p.657 ~ p.665
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Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA
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Choi Tae-Suk-Ro
Choi Yong-Chun
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Abstract
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The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature m RNA The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5′ splice sites (5′SS), branch point sequences (BPS) and 3′ splice sites (3′SS) were identified and free energies involved have been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (| lowest | -Kcal) were 5,4, 7,6, 2,1, and 3; i.e., ?18.7 Kcal, ?20.2 Kcal, ?21.0 Kcal, ?24.0 Kcal, ?25.4 Kcal, ?26.4 Kcal and ?28.2 Kcal respectively. These are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding is consistent with the validity of hnRNP formation mechanisms in previous reports.
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KEYWORD
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co-transcriptional folding, Mini-hairpins, snRNAs, U1, U2, U4, U5, U6, splicing, thermodynamics
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