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Related Concept Videos

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...
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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

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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...
Nucleosome Remodeling02:54

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Related Experiment Video

Updated: May 9, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

DNA binding and bending by Sac7d is stepwise.

Justin Spiriti1, Arjan van der Vaart

  • 1Department of Chemistry, University of South Florida, 4202 E. Fowler Ave. CHE 205, Tampa, FL 33620, USA.

Chembiochem : a European Journal of Chemical Biology
|July 16, 2013
PubMed
Summary
This summary is machine-generated.

The protein Sac7d binds to DNA before the DNA bends, suggesting a specific binding mechanism. This finding challenges the idea that the protein and DNA change shape simultaneously during binding.

Keywords:
DNADNA recognitionconformational selectionintercalationmolecular dynamics

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • The interaction between proteins and DNA is fundamental to cellular processes.
  • Understanding the sequence of events in protein-DNA binding, such as DNA bending and protein association, is crucial for deciphering molecular mechanisms.
  • The protein Sac7d from Sulfolobus acidocaldarius is known to interact with DNA.

Purpose of the Study:

  • To determine the temporal order of events during the binding of Sac7d to DNA.
  • To investigate whether DNA bending precedes or follows Sac7d binding.
  • To assess the likelihood of a conformational selection mechanism in Sac7d-DNA interactions.

Main Methods:

  • Utilized thermodynamic cycles derived from experimental measurements of binding free energy.
  • Employed free energy simulations to model the binding process.
  • Analyzed the kinetics and thermodynamics of Sac7d-DNA complex formation.

Main Results:

  • Demonstrated that the binding of Sac7d to DNA occurs prior to DNA bending.
  • Experimental and simulation data indicate a specific sequence of molecular events.
  • The results provide quantitative insights into the Sac7d-DNA interaction dynamics.

Conclusions:

  • The binding of Sac7d to DNA precedes DNA bending.
  • A conformational selection mechanism is unlikely to be the primary mode of interaction for Sac7d binding to DNA.
  • This study elucidates a key aspect of DNA-protein recognition in archaea.