Computer-Aided Design of RNA Origami Structures
| Autor: | Steffen M. Sparvath, Ebbe Sloth Andersen, Cody Geary |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Riboswitch Nanostructure biology Computer science Aptamer Ribozyme RNA 02 engineering and technology Computational biology 021001 nanoscience & nanotechnology Non-coding RNA Small molecule DNA sequencing 03 medical and health sciences Synthetic biology chemistry.chemical_compound 030104 developmental biology chemistry RNA polymerase Helix biology.protein Nanomedicine 0210 nano-technology Protein secondary structure |
| Zdroj: | Methods in Molecular Biology ISBN: 9781493964529 |
| Popis: | RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order. |
| Databáze: | OpenAIRE |
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