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Related Concept Videos

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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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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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the

Ofer Kimchi1,2, Michael P Brenner3, Lucy J Colwell4

  • 1School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. okimchi@princeton.edu.

Methods in Molecular Biology (Clifton, N.J.)
|January 27, 2023
PubMed
Summary

LandscapeFold predicts RNA and DNA secondary structures by enumerating all possible folds using polymer physics. This algorithm estimates configurational entropy, including complex pseudoknots, and is adjustable by users.

Keywords:
Free energy landscapeMinimum free energy structurePolymer physics theoryPseudoknotStructure enumeration

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Biophysics

Background:

  • Accurate prediction of nucleic acid secondary structures is crucial for understanding their function.
  • Existing methods may face challenges with complex structures like pseudoknots.

Purpose of the Study:

  • To detail the LandscapeFold algorithm for secondary structure prediction of RNA and DNA.
  • To explain its application and user-adjustable parameters.

Main Methods:

  • Direct enumeration of all possible secondary structures for up to two nucleic acid sequences.
  • Application of a polymer physics model to estimate configurational entropy.
  • Inclusion of complex pseudoknot structures in the analysis.

Main Results:

  • LandscapeFold provides a method for comprehensive secondary structure prediction.
  • The algorithm's flexibility allows for user-defined adjustments.
  • Code availability facilitates further research and application.

Conclusions:

  • LandscapeFold offers a robust approach to predicting nucleic acid secondary structures.
  • The algorithm's ability to handle pseudoknots enhances its utility.
  • Open-source availability promotes accessibility and development in the field.