RNA molecules are important cellular molecules and their aptamers are basically are in a wide use these days. Aptamers are peptide molecules that bind to a given specific target molecule. Understanding their basic mechanism, processes and creation of RNA aptamers is where the concept of in silico designing comes into the picture In silico designing of RNA aptamers has gained much achievement due to the use of easy to use and apply bioinformatics tool. These tools contribute to analysis of various aspects in the designing of RNA aptamers like tertiary structure prediction of RNA, protein folding, motif prediction, database search and structure analysis and design.
The databases basically provide a large source for the RNA molecule to be used. Various databases are available throughout the web which help in searching the suitable RNA molecule as per the researcher's need. RNAMotif is one such search tool that searches a database for RNA sequences that match a "motif" provided by the user which describes interactions of secondary structure. A term 'match is quite often used there which implies that the given sequence is capable of adopting the given secondary structure, however it is not intended to be predictive. RNAMotif is an extension of earlier programs rnamot and rnabob and is being widely accepted and used for the purpose it serves.
After that, the structure prediction tools come into the picture that provide basic facilities to design the tertiary structure of the desired RNA molecule. One of them is The Nucleic Acid Simulation Toolkit, also abbreviated as NAST. NAST is a knowledge-based coarse-grained tool for modelling structures of RNA molecules that produces a set of 3D structures. Also, to filter the generated decoy structures, it employs the use of sresidue-resolution experimental data for instance hydroxyl radical footprinting. The software satisfies the data and constraints provided by the users on the basis of following factors:
1. Primary sequence
2. Known or predicted secondary structure
3. Known or predicted tertiary contacts
Its basic functioning follows the following sequence of events: First, it uses an RNA-specific knowledge-based potential to generate large numbers of 3D structures that satisfy the constraints provided by the users. Then it filters these generated structures based on agreement to the available experimental data. As a result, it provides a model of the molecule which satisfies all the known residue-resolution data and also the constraints that has been provided by the user.
Another software that assists in design of RNA structures is BARNACLE. It is a single sequence tertiary structure production software and provides a Python library for the probabilistic sampling of those RNA structures that are compatible with a given nucleotide sequence and are RNA-like on a particular local length scale. Further, FARNA, much like BARNACLE, facilitates single sequence RNA structure prediction and utilises automated de novo prediction of RNA tertiary structures.
A web-based tool for RNA tertiary structure prediction is iFoldRNA that predicts RNA structures by exploiting a model of three beads/ nucleotide by application of molecular dynamics (MD) sampling. It utilizes REMD method or the replica exchange method for the prediction of tertiary structures. It need not require secondary structure inputs for the processing and then rapidly predicts structure of small RNAs that are typically <50nt in size.
Another software, RAGPools or RNA-As-Graph-Pools which is a web server for assisting the design of structured RNA pools used for the application of in vitro selection that suggests the method to build/construct RNA sequence/structure pools with user-specified properties or to be clearer, the parameters and constraints being fed by the user to the system. It provides assistance in analysing resulting distributions and provides a basic tool for designing structured RNA pools with specified target motif distributions and then analysing them. The organisation of RAGPools in RNA pool designer takes the follows sequence of events: first, the user inputs a target motif sequence, then the database takes care of the pie-calculated distribution, the engine linear optimizes them and then the result is obtained in the form of mixing matrix, starting sequence and weight. In a RNA pool analyser, the user inputs a mixing matrix and a starting sequence, the database takes care of the RNA-As-Graph, Engine provides pool generator and topology scanner and then finally, the output is received in the form of motif distribution.
Autodock and DOCK are other softwares that are useful in screening libraries of RNA molecules and possess an ability to dock compounds to RNA molecules. They are being extensively used to screen a library of small molecules in order to find a ligand that would perfectly bind to a specific protein or RNA receptor that has been provided or according to the other parameters.
The in silico designing of RNA aptamers is extensively increasing and the use of bioinformatics tools is rapidly increasing too. Nonetheless one can expect new achievements and discoveries in the future years with respect to the highly developing genomic tools.
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