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In Silico mRNA Structure Prediction

All products and services are For Research Use Only and CANNOT be used in the treatment or diagnosis of disease.
Background In Silico Prediction Service Highlights FAQs Published Data


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.

Example of an mRNA structure prediction diagram.

Fig.1 mRNA structure prediction.1

  • 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.

In Silico Prediction Service

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.

The Scope of Creative Biolabs' mRNA structure prediction services.

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.

Inquire About Our Services


  • Advanced Prediction Methods: Utilizes both sequence-based and 3D structure-based assessment routines for accurate mRNA structure prediction.
  • High Accuracy: Incorporates dynamic programming algorithms and folding free energy nearest-neighbor rules to estimate the most stable mRNA conformations.
  • Multiple Sequence Analysis: Improves prediction accuracy using homologous sequences, recognizing conserved structures across RNA families.
  • Comprehensive Services: Offers a complete package including primer design, gene prediction, promoter identification, and interaction analysis.


Q: What is in silico mRNA structure prediction?

A: It involves using computational methods to predict the secondary and tertiary structures of mRNA molecules based on their sequences.

Q: Why is mRNA structure prediction important?

A: Understanding mRNA structure is crucial for studying gene expression, mRNA stability, and interactions with other molecules.

Q: What methods are used for structure prediction?

A: Techniques include dynamic programming algorithms, folding free energy nearest-neighbor rules, and multiple sequence analysis.

Q: In addition to mRNA structural prediction, what other assistance can I receive?

A: Creative Biolabs also offers a range of services including primer design, internet database searches, gene prediction, promoter identification, regulatory element mapping, interaction analysis, multiple sequence alignment, and phylogenetic reconstruction. These services are designed to help clients better utilize data from structural predictions.

Q: What applications benefit from in silico mRNA structure prediction?

A: Applications include the design of mRNA-based vaccines, therapeutics, and the study of mRNA interactions in gene expression and regulation.

Q: How can researchers access these services?

A: Researchers can contact Creative Biolabs to discuss their specific needs and obtain tailored in silico mRNA structure prediction services.

Published Data

This article explores the impact of specific intronic mutations (IVS1nt1G>T and IVS1nt5G>C) on the mRNA structure of the human beta-globin (HBB) gene. These mutations are associated with beta-thalassemia, a severe blood disorder. Using in silico analysis, the study examines how these mutations alter the RNA's secondary and tertiary structures, revealing unique folding characteristics and structural instabilities compared to the wild-type. The findings suggest that these structural changes may affect mRNA stability and function, contributing to the pathogenesis of beta-thalassemia.

Barrier tree diagram of human β-Globin RNA structure.

Fig.3 Barrier tree plot for best RNA structure for the human beta-globin gene.2


  1. Roodashty, Hanieh. Comparison of RNA-folding structures, in-vivo, in-vitro and in-silico. MS thesis. 2019.
  2. Sumantri, Nur Imaniati, et al. "In silico study on RNA structures of intronic mutations of beta-globin gene." F1000Research 9 (2020): 49.
All products and services are For Research Use Only and CANNOT be used in the treatment or diagnosis of disease.