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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.
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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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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Assessment of Nucleic Acid Structure Prediction in CASP16.

Rachael C Kretsch1, Alissa M Hummer2,3, Shujun He2,4

  • 1Biophysics Program, Stanford University School of Medicine, Stanford, California, USA.

Proteins
|October 30, 2025
PubMed
Summary

Accurate 3D nucleic acid structure prediction remains challenging, with CASP16 results showing poor performance for novel RNA structures. Top predictions relied on human expertise and existing templates, highlighting areas for improvement in computational biology.

Keywords:
CASP16DNA structureRNA structuredeep learningmultiple sequence alignmentnucleic‐acid ligand structurenucleic‐acid protein complex structurestructure prediction

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate 3D nucleic acid structure prediction is crucial for understanding biological functions.
  • The CASP16 (Critical Assessment of Structure Prediction) competition assessed the state-of-the-art in nucleic acid structure prediction.

Purpose of the Study:

  • To evaluate the accuracy of blind 3D nucleic acid structure predictions in CASP16.
  • To compare the performance of automated servers versus human expert predictors.
  • To assess the prediction accuracy of nucleic acid complexes and interactions.

Main Methods:

  • Blind prediction submissions for 42 diverse nucleic acid targets.
  • Evaluation of predictions using metrics like TM-scores.
  • Analysis of performance based on template availability and prediction methods.

Main Results:

  • Overall prediction performance was generally poor, especially for novel RNA structures (no predictions > 0.8 TM-score).
  • Top-performing groups (Vfold, GuangzhouRNA-human, KiharaLab) were human expert predictors.
  • Accuracy depended heavily on the availability of 3D structure templates; template-free modeling showed limited success.
  • Consistent recovery of complex structural features like pseudoknots and non-canonical pairs remained a challenge.
  • Prediction accuracy for nucleic acid complexes was also poor without templates.

Conclusions:

  • Current computational methods struggle with accurate de novo 3D nucleic acid structure prediction.
  • Human expertise and template-based modeling are currently superior for nucleic acid structure prediction.
  • Significant advancements are needed to improve the prediction of complex nucleic acid structures and interactions.