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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

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Related Experiment Video

Updated: Jul 24, 2026

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

The POU domain is a bipartite DNA-binding structure.

R A Sturm1, W Herr

  • 1Cold Spring Harbor Laboratory, New York 11724.

Nature
|December 8, 1988
PubMed
Summary

The POU domain in transcription factors is a bipartite DNA-binding structure. Both its POU-specific and homoeo subdomains are essential for DNA binding.

Area of Science:

  • Molecular Biology
  • Genetics
  • Protein Structure

Background:

  • The POU domain is a conserved region in transcription factors like Oct-1, Oct-2, and unc-86.
  • It comprises a POU-specific region and a homoeo domain, linked by a short nonconserved sequence.
  • Homoeobox domains, including the homoeo domain, typically contain a helix-turn-helix motif for DNA binding.

Purpose of the Study:

  • To investigate the DNA-binding capabilities of the POU domain.
  • To determine the functional roles of the POU-specific and homoeo subdomains in DNA binding.
  • To characterize the POU domain as a novel DNA-binding structure.

Main Methods:

  • Sequence analysis to identify conserved regions and relationships.
  • Functional studies on transcription factors containing the POU domain (e.g., Oct-1, Oct-2).

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

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Last Updated: Jul 24, 2026

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

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  • Structural analysis to understand the domain's architecture and interactions.

    • Main Results:

    • The POU domain is a bipartite DNA-binding structure.
    • Both the POU-specific region and the homoeo domain are required for sequence-specific DNA binding.
    • These two subdomains are connected by a flexible linker, forming a novel functional unit.

    Conclusions:

    • The POU domain represents a unique DNA-binding module distinct from previously characterized homoeodomains.
    • The bipartite nature of the POU domain, requiring both subdomains for DNA binding, highlights its specialized function.
    • This finding expands the understanding of transcription factor structure-function relationships and DNA recognition mechanisms.