Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA |
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Authors: | Tae Suk Ro-Choi Yong Chun Choi |
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Institution: | (1) Medical Research Center for Cancer Molecular Therapy, Dong-A University College of Medicine, Busan, 602-714, Korea;(2) Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA;(3) Present address: Retirees at 4147 Martinshire Dr., Houstion, Texas 77025, USA |
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Abstract: | 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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