title: Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA.
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.
authors.affiliation: Medical Research Center for Cancer Molecular Therapy, Dong-A University College of Medicine, Busan 602-714, Korea. tsrochoi@uspos.net
authors.forename: Tae Suk
authors.initials: TS
authors.lastname: Ro-Choi
authors.forename: Yong Chun
authors.initials: YC
authors.lastname: Choi
mesh_terms: D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010059:Ovomucin / Q000235:genetics*; D012322:RNA Precursors / Q000737:chemistry* / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics; D017381:Spliceosomes / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites; D012342:RNA, Small Nuclear; C405483:U1 small nuclear RNA; D010059:Ovomucin