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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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Protein-protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Related Experiment Video

Updated: Mar 11, 2026

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
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G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins.

Subodh Kumar Mishra1, Arpita Tawani1, Amit Mishra2

  • 1Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.

Scientific Reports
|December 2, 2016
PubMed
Summary

The Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is a unique resource detailing protein-G4 interactions. This database aids research into therapeutic targets for cancer and neurological diseases.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • G-quadruplex (G4) structures are formed by nucleic acids and are implicated in various biological processes.
  • Interactions between G4 structures and proteins are crucial for cellular functions and disease development.
  • A centralized resource for G4-protein interactions is needed to facilitate research.

Purpose of the Study:

  • To establish the G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB), a comprehensive platform for G4-protein interactions.
  • To provide detailed information on G4-protein interactions, including protein and nucleic acid details, binding affinities, and experimental techniques.
  • To develop a web-based G-quadruplex predictor tool for identifying potential G4-forming sequences.

Main Methods:

  • Database curation of over 200 entries detailing G4-protein interactions.
  • Inclusion of comprehensive data points: protein/nucleic acid information, binding constants, interacting residues, and PDB IDs.
  • Development of a user-friendly web interface with a G-quadruplex prediction tool.

Main Results:

  • G4IPDB offers a single platform with extensive data on G4-protein interactions.
  • The database includes information on over 200 interactions, covering protein synonyms, UniProt-IDs, organism, target sequences, and binding parameters.
  • A G-quadruplex predictor tool is integrated, analyzing both DNA strands and providing G-scores.

Conclusions:

  • G4IPDB serves as a valuable resource for researchers studying G4-protein interactions.
  • The database and predictor tool can accelerate the discovery and development of novel therapeutics for diseases like cancer and neurological disorders.
  • G4IPDB is freely accessible and will be updated biannually to ensure data relevance.