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Related Concept Videos

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...
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...
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...
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: Jul 7, 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

Using DNA duplex stability information for transcription factor binding site discovery.

Raluca Gordân1, Alexander J Hartemink

  • 1Duke University, Dept. of Computer Science, Box 90129, Durham, NC 27708, USA. raluca@cs.duke.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|January 31, 2008
PubMed
Summary
This summary is machine-generated.

Discovering transcription factor (TF) binding sites is crucial for understanding gene regulation. This study enhances TF motif discovery by incorporating DNA double-helical stability, significantly improving accuracy in yeast ChIP-chip data analysis.

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Last Updated: Jul 7, 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

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transcription factor (TF) binding site discovery is essential for understanding transcriptional regulation.
  • Current computational tools for TF motif detection have limited accuracy, often neglecting TF-DNA structural interactions.
  • Previous work highlighted the utility of TF structural class and nucleosome occupancy for improving motif discovery.

Purpose of the Study:

  • To demonstrate the benefits of integrating DNA double-helical stability information into TF motif discovery algorithms.
  • To develop and apply informative positional priors based on DNA energetic stability.
  • To enhance the accuracy of TF binding site prediction.

Main Methods:

  • Investigated the relationship between DNA double-helical stability and TF binding sites.
  • Observed that TF binding sites generally require more energy to destabilize the DNA helix compared to random DNA sites.
  • Derived informative positional priors from DNA energetic stability data.
  • Incorporated these priors into a motif finding algorithm.
  • Applied the enhanced algorithm to yeast ChIP-chip data.

Main Results:

  • TF binding sites exhibit higher DNA double-helical stability compared to random DNA sequences.
  • The novel informative priors derived from DNA stability significantly improved motif finder performance.
  • The enhanced motif discovery method showed significant performance gains on yeast ChIP-chip data.
  • Outperformed motif finding algorithms using priors that do not incorporate energetic stability information.

Conclusions:

  • DNA double-helical stability is a valuable feature for improving transcription factor motif discovery.
  • Incorporating energetic stability into motif finding algorithms offers a significant performance advantage.
  • This approach enhances the accuracy of identifying TF binding sites, advancing the understanding of transcriptional regulation.