In Silico mRNA Structure Prediction

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  • In Silico mRNA Structure Prediction

    In silico prediction and modeling is an important tool used to obtain RNA secondary structure. This method is either a sequence-based prediction or 3D structure-based assessment routines. As an undoubted leader in mRNA services, Creative Biolabs has developed a delicate mRNA modeling platform for RNA 3D structure prediction, analysis, and manipulation.

    Significance of mRNA Structure Prediction

    mRNAs are important intermediary molecules that carry codes from the DNA in the nucleus to the sites of protein synthesis in the ribosomes in the cytoplasm. The functions of mRNA are strongly dependent on its sequence and the three-dimensional (3D) structure, so an appropriate recognition of its structure is of great importance. Usually, the 3D shape of mRNA molecule is designated by its secondary structure which represents the base-pairing interactions within the molecule. Therefore, a prediction & analysis of the mRNA secondary structure is a crucial step in the functional characterization of mRNA. RNA structure probing approaches mainly include in vivo, in vitro and in silico. Amongst, in silico method is the most promising and economical method to obtain RNA secondary structure on the basis of either sequence prediction or 3D structure assessment routines.

    mRNA structure prediction. Fig.1 mRNA structure prediction. (Roodashty, 2019)

    In silico Studies of RNA Folding

    In silico prediction and modeling of RNA structure is an important tool to provide additional insight into mRNA structure and function.

    • RNA structure prediction from one sequence in silico
    • RNA structure prediction from sequence alone often uses dynamic programming algorithms to efficiently search the set of possible structures and folding free energy nearest-neighbor rules to estimate folding stability. The lowest free energy conformation signifies the most probable structure at equilibrium.

    • RNA structure prediction from multiple sequences in silico
    • The accuracy of in silico prediction can be dramatically improved by using multiple RNA homologous sequences, commonly called an RNA family, because the structure is generally conserved to a greater extent than sequence for RNAs.

    Services at Creative Biolabs

    Creative Biolabs has integrated our expertise in mRNA biological research with advances in computational algorithms to develop a delicate mRNA modeling platform for in silico computational mRNA structure prediction. Our services can be provided as a stand-alone item or a complete package, including but not limited to primer design, internet database searches, gene prediction, promoter identification, regulatory elements mapping, interaction analysis, multiple sequences alignment, phylogenetic reconstruction, and a wide variety of other functions.

    <em>In silico</em> services of mRNA structure prediction at Creative Biolabs. Fig.2 In silico services of mRNA structure prediction at Creative Biolabs.

    A number of in silico methods have been developed to predict RNA secondary structure. With deep and broad expertise in mRNA therapeutics studies, Creative Biolabs is devoted to offering mRNA secondary structure prediction services using in silico methods to get new insights in mRNA structure and related functions. If you are interested in our services, please feel free to contact us.


    1. Roodashty, Hanieh. Comparison of RNA-folding structures, in-vivoin-vitro and in-silico. MS thesis. 2019.
    For Research Use Only.