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Related Concept Videos

RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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RNA Structure01:23

RNA Structure

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Overview
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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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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Protein Folding01:25

Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Related Experiment Video

Updated: Jan 17, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.

Xunxun Wang1, Zouchenyu Zhou1, Shixiong Yu1

  • 1Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.

Nucleic Acids Research
|January 14, 2026
PubMed
Summary

We developed TiRNA, a new method for predicting RNA structures and stability in solutions. TiRNA accurately forecasts RNA folding and thermal stability from sequences or secondary structures, outperforming existing methods.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Molecular Biology

Background:

  • RNA molecules perform vital biological functions, including gene regulation and catalysis.
  • RNA structure and stability are crucial for function but are sensitive to ionic conditions.
  • Predicting RNA structures and stability in ionic solutions remains a significant challenge.

Purpose of the Study:

  • To develop a computational method for accurate prediction of RNA folding and three-dimensional (3D) structure.
  • To incorporate temperature and ion effects into RNA structure and stability simulations.
  • To enable reliable prediction of RNA structures and thermal stability from sequence or secondary structure information.

Main Methods:

  • Developed TiRNA, a coarse-grained simulation method accounting for temperature and ion effects.
  • Applied TiRNA to predict RNA folding and 3D structures, including complex motifs like pseudoknots and multi-way junctions.
  • Validated TiRNA's predictions against experimental data and compared performance with existing state-of-the-art methods.

Main Results:

  • TiRNA successfully predicted the 3D structures of various RNAs, including those with complex topological features.
  • The method accurately predicted the thermal stability of RNAs under different ionic conditions.
  • TiRNA demonstrated superior performance compared to existing methods in predicting both structure and stability solely from sequence data.
  • Predictions were also reliable when starting from secondary structure information.

Conclusions:

  • TiRNA offers a robust and accurate approach for simulating RNA folding and predicting 3D structures and thermal stability in ionic solutions.
  • The method's ability to utilize sequence or secondary structure as input enhances its versatility.
  • TiRNA represents a significant advancement in computational tools for RNA structure and function research.