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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...
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...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

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Related Experiment Video

Updated: Jul 24, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
11:42

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Published on: November 1, 2012

Different interactions used by Cro repressor in specific and nonspecific DNA binding.

Y Takeda, J G Kim, C G Caday

    The Journal of Biological Chemistry
    |July 5, 1986
    PubMed
    Summary

    Chemical modification reveals how Cro repressor binds DNA. Specific lysine residues are protected, defining a DNA-binding region and supporting an alpha-helix interaction model with DNA major grooves.

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    Area of Science:

    • Molecular Biology
    • Biochemistry
    • Structural Biology

    Background:

    • Cro repressor is a key protein in bacteriophage lambda genetic regulation.
    • Understanding its DNA-binding mechanism is crucial for deciphering gene control.
    • Previous models suggested alpha-helices interacting with DNA major grooves.

    Purpose of the Study:

    • To elucidate the precise mode of interaction between Cro repressor and DNA.
    • To identify specific amino acid residues involved in DNA binding.
    • To differentiate interactions with specific versus nonspecific DNA sites.

    Main Methods:

    • Chemical modification of Cro repressor.
    • Protection assays using lysine and tyrosine residues.
    • Analysis of Cro repressor structure in the presence of DNA.

    Main Results:

    • Lysines 32 and 56 were fully protected, while lysines 21, 62, and 63 were partially protected upon DNA binding.
    • Protected lysines mapped to a defined DNA-binding region, supporting alpha-helix interaction with DNA major grooves.
    • Cro-DNA interaction differs for specific and nonspecific sites; nonspecific binding is salt-sensitive (electrostatic), while specific binding is salt-resistant (involving hydrogen bonds and hydrophobic interactions).
    • Tyrosine residue modification indicated conformational changes in Cro repressor upon binding to nonspecific and specific DNA sites.

    Conclusions:

    • The study provides direct experimental evidence for Cro repressor's DNA-binding mode involving alpha-helices in DNA major grooves.
    • The carboxyl-terminal region, including lysines 62 and 63, is involved in DNA binding.
    • Distinct interaction mechanisms exist for specific and nonspecific DNA binding, involving electrostatic and nonelectrostatic forces.
    • Cro repressor undergoes conformational changes upon binding to DNA, varying with site specificity.