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Related Concept Videos

Nucleic Acids02:43

Nucleic Acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
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Nucleic acids02:43

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Biosynthesis of Nucleic Acids01:28

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Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
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Nucleic Acid Structure01:25

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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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Nucleic Acids and Nucleotides01:20

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
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VeriNA3d: an R package for nucleic acids data mining.

Diego Gallego1,2, Leonardo Darré1,3, Pablo D Dans1

  • 1Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology.

Bioinformatics (Oxford, England)
|July 10, 2019
PubMed
Summary
This summary is machine-generated.

veriNA3d is a new R package designed for analyzing nucleic acid structures, particularly complex RNA. It enables flexible, high-throughput data mining of structural databases, filling a critical gap in bioinformatics tools.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Chemistry

Background:

  • Analyzing complex nucleic acid structures, especially RNA, is crucial for understanding biological function.
  • Existing tools may lack the flexibility and throughput for large-scale structural database mining.

Purpose of the Study:

  • To introduce veriNA3d, an R package for comprehensive analysis of nucleic acid structural data.
  • To provide tools for both single-structure analysis and high-throughput mining of structural datasets.

Main Methods:

  • Development of an R package, veriNA3d.
  • Implementation of functions for analyzing single and multiple mmCIF/PDB structures.
  • Integration with public and local structural data repositories.

Main Results:

  • veriNA3d offers flexible and high-throughput analysis capabilities for nucleic acid structural data.
  • The package supports the examination of complex RNA structures.
  • It facilitates data mining across extensive structural databases.

Conclusions:

  • veriNA3d addresses a need for efficient and adaptable tools in nucleic acid structural bioinformatics.
  • The package enhances the ability to analyze and mine large collections of structural data, particularly for RNA.