Hybridization of antisense oligonucleotides with alpha-sarcin loop region of Escherichia coli 23S rRNA
| Autor: | Vladislav A. Petyuk, Valentin V. Vlassov, Marina A. Zenkova, Roman N. Serikov |
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| Rok vydání: | 2004 |
| Předmět: |
Base pair
Molecular Sequence Data medicine.disease_cause Biochemistry Fungal Proteins 23S ribosomal RNA Endoribonucleases Genetics medicine Escherichia coli Nucleic acid structure Heteroduplex formation Equilibrium constant Base Sequence Chemistry Oligonucleotide RNA General Medicine Oligonucleotides Antisense Molecular biology Kinetics RNA Bacterial RNA Ribosomal 23S Molecular Medicine Nucleic Acid Conformation Thermodynamics |
| Zdroj: | Nucleosides, nucleotidesnucleic acids. 23(6-7) |
| ISSN: | 1525-7770 |
| Popis: | Binding of complementary oligonucleotides (ONs) with alpha-sarcin loop region (2638-2682) of Escherichia coli 23S rRNA was investigated. Four of the tested pentadecanucleotides efficiently bound to target sequences with association rate and equilibrium constants approximately 10(3) M(-1)s(-1) and 10(7) M(-1), respectively. ON S5 (CGAGAGGACCGGAGU) complementary to the sequence 2658-2672 displayed the highest affinity to the target. Activation energy for binding of ON S5 was measured to be 11 kcal/mol; this value corresponds to approximately 10% of the calculated enthalpy of the local RNA structure unfolding in the presence of this oligonucleotide. The activation energy value is evidence for the heteroduplex formation to occur via strand displacement pathway; the initiation of heteroduplex formation requires disruption of 1-2 base pairs in RNA hairpin. |
| Databáze: | OpenAIRE |
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