Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA
| Autor: | Yong Chun Choi, Tae Suk Ro-Choi |
|---|---|
| Rok vydání: | 2009 |
| Předmět: |
Stereochemistry
RNA Splicing Molecular Sequence Data Plasma protein binding Biology Ovomucin RNA Small Nuclear RNA Precursors Animals Nucleotide splice Molecular Biology chemistry.chemical_classification RNA recognition motif Base Sequence Intron RNA Cell Biology General Medicine Molecular biology chemistry RNA splicing Spliceosomes Nucleic Acid Conformation Thermodynamics RNA Splice Sites Precursor mRNA Chickens |
| Zdroj: | Molecules and cells. 27(6) |
| ISSN: | 0219-1032 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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