Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes
| Autor: | Kasra Zandi, Nawwaf Kharma, Samia Djerroud, Sabrine Najeh, Jonathan Perreault |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0303 health sciences Hammerhead ribozyme biology Computer science viruses Ribozyme RNA Computational biology biology.organism_classification computer.software_genre 01 natural sciences Inverse folding 03 medical and health sciences Synthetic biology RNA Sequence biology.protein Computer Aided Design Nucleic acid structure Pseudoknot computer VS ribozyme 030304 developmental biology 010606 plant biology & botany |
| Zdroj: | Methods in Molecular Biology ISBN: 9781071607152 |
| Popis: | Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|