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Related Concept Videos

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...
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...
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...
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...
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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

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Related Experiment Video

Updated: May 31, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity.

Itamar Sela1, David B Lukatsky

  • 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Biophysical Journal
|July 5, 2011
PubMed
Summary
This summary is machine-generated.

Transcription factors (TFs) bind DNA to regulate gene expression. Enhanced DNA sequence correlations, like poly(dA:dT) tracts, increase nonspecific TF-DNA binding, aiding the search for specific sites.

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Related Experiment Videos

Last Updated: May 31, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Area of Science:

  • Genetics
  • Molecular Biology
  • Biophysics

Background:

  • Transcription factors (TFs) are proteins that regulate gene expression by binding to specific DNA sequences.
  • Nonspecific binding of TFs to DNA is a crucial factor in the efficiency of gene regulation.
  • Understanding the factors influencing TF-DNA interactions is key to deciphering gene regulatory networks.

Purpose of the Study:

  • To analytically predict how homooligonucleotide sequence correlations affect TF-DNA binding affinity.
  • To investigate the role of sequence correlations in facilitating the search for specific TF binding sites.
  • To determine if enhanced sequence correlations correlate with TF occupancy in the yeast genome.

Main Methods:

  • Analytical modeling of TF-DNA interactions.
  • Statistical analysis of sequence correlations in DNA.
  • Correlation analysis of TF binding sites in the yeast genome.

Main Results:

  • Enhanced homooligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance nonspecific TF-DNA binding affinity.
  • Nonspecific TF binding affinity is universally controlled by the strength and symmetry of DNA sequence correlations.
  • Yeast genomic regions with high TF occupancy exhibit stronger homooligonucleotide sequence correlations.

Conclusions:

  • Enhanced DNA sequence correlations increase nonspecific TF binding, acting as an effective potential to enhance TF diffusion along DNA.
  • This mechanism speeds up the stochastic search for specific TF binding sites.
  • The effect of sequence correlations may impose an upper limit on the size of TF-DNA binding motifs.