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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...
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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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: Jun 1, 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

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

Matti Annala1, Kirsti Laurila, Harri Lähdesmäki

  • 1Department of Signal Processing, Tampere University of Technology, Tampere, Finland. matti.annala@tut.fi

Plos One
|June 4, 2011
PubMed
Summary

Protein binding microarrays (PBMs) enable high-throughput DNA binding analysis. A new linear model predicts protein-DNA interactions by analyzing subsequence contributions, excelling in the DREAM5 challenge for motif recognition and transcription factor identification.

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Related Experiment Videos

Last Updated: Jun 1, 2026

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

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Published on: February 7, 2019

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Protein-DNA interactions are fundamental to cellular processes.
  • High-throughput methods are needed to characterize these interactions comprehensively.
  • Protein binding microarrays (PBMs) offer a powerful platform for studying DNA binding specificity.

Purpose of the Study:

  • To develop a predictive model for protein-DNA binding affinity using PBM data.
  • To identify DNA binding motifs from PBM data.
  • To develop a method for transcription factor (TF) identification based on PBM binding profiles.

Main Methods:

  • A linear model was developed to predict probe intensity as a sum of subsequence binding affinities.
  • The model characterizes DNA binding motifs.
  • An approach for TF identification was created using PBM binding profiles.

Main Results:

  • The developed linear model accurately predicted protein-DNA binding affinity.
  • The method achieved top performance in the DREAM5 transcription factor/DNA motif recognition challenge.
  • The TF identification approach also achieved best performance in the DREAM5 bonus challenge.

Conclusions:

  • Linear modeling of subsequence contributions provides an effective way to predict and interpret protein-DNA binding from PBM data.
  • This approach advances the understanding of DNA binding motifs and TF recognition.
  • The methods offer significant improvements for high-throughput analysis of protein-DNA interactions.