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Related Concept Videos

RNA Structure01:23

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Updated: Oct 6, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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VfoldMCPX: predicting multistrand RNA complexes.

Sicheng Zhang1, Yi Cheng1, Peixuan Guo2

  • 1Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA.

RNA (New York, N.Y.)
|January 21, 2022
PubMed
Summary
This summary is machine-generated.

VfoldMCPX accurately predicts the 2D structures and folding stability of multistrand RNA complexes, including those with pseudoknots. This new model enhances understanding of RNA functions and nanostructure design.

Keywords:
RNA pseudoknotfolding thermodynamicsmultistrand RNAsecondary structure

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Area of Science:

  • Computational biology
  • Molecular biology
  • Bioinformatics

Background:

  • Multistrand RNA complexes are crucial for biological processes.
  • Accurate prediction of RNA structure and stability is essential for understanding RNA function and designing RNA nanostructures.
  • Existing models often struggle with complex structures like pseudoknots.

Purpose of the Study:

  • To introduce VfoldMCPX, a novel computational model for predicting the 2D structures and folding stabilities of multistrand RNA complexes.
  • To develop a model capable of accurately handling pseudoknotted RNA structures.
  • To provide an accessible web server for VfoldMCPX.

Main Methods:

  • VfoldMCPX utilizes a partition function-based algorithm.
  • The model incorporates physical loop free energy parameters for enhanced accuracy.
  • It is designed to predict both the native structure and folding stability of RNA complexes.

Main Results:

  • VfoldMCPX demonstrates improved accuracy in predicting structures of multistranded RNA complexes.
  • The model shows particular strength in handling complexes with three or more strands and/or pseudoknots.
  • Extensive tests validate the predictive capabilities of VfoldMCPX.

Conclusions:

  • VfoldMCPX offers a significant advancement in predicting the structure and stability of complex multistrand RNA.
  • The model facilitates a deeper understanding of RNA biological roles and aids in the rational design of RNA nanostructures.
  • The VfoldMCPX web server is available for public use, promoting further research in RNA structure prediction.