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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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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...
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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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.
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Related Experiment Video

Updated: Feb 2, 2026

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors
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Strain-specific effect on biphasic DNA binding by HIV-1 integrase.

Kyle J Hill1,2,3, Leonard C Rogers1,3,4, Duncan T Njenda5

  • 1Department of Molecular Microbiology and Immunology.

AIDS (London, England)
|November 27, 2018
PubMed
Summary

HIV-1 integrase binds DNA in two distinct modes: high-affinity and low-affinity. Genetic variations in integrase can alter these binding affinities, potentially impacting antiviral drug effectiveness.

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Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • The precise mechanism of human immunodeficiency virus type 1 (HIV-1) integrase oligomerization on DNA remains incompletely elucidated.
  • Understanding this process is crucial for developing effective antiviral therapies targeting HIV-1 replication.

Purpose of the Study:

  • To investigate the binding kinetics of HIV-1 integrase to DNA.
  • To determine if DNA binding occurs in distinct affinity modes.
  • To assess the impact of naturally occurring polymorphisms on integrase-DNA binding.

Main Methods:

  • The study employed biophysical techniques to measure the binding affinity of HIV-1 integrase to DNA.
  • Dissociation constants (Kd) were determined for high- and low-affinity binding modes.
  • Patient-derived integrase variants with subtype-specific polymorphisms were analyzed.

Main Results:

  • HIV-1 integrase exhibits biphasic DNA binding, characterized by high- and low-affinity modes.
  • For HIV-1 subtype B, the high-affinity binding is approximately 100-fold stronger than low-affinity binding (Kd values of 37 nmol/L and 3400 nmol/L, respectively).
  • Subtype-specific polymorphisms in patient-derived integrases resulted in two- to four-fold changes in Kd.DNA values.

Conclusions:

  • HIV-1 integrase demonstrates a biphasic DNA binding mechanism.
  • Naturally occurring polymorphisms in HIV-1 integrase can modulate its DNA binding affinity.
  • These alterations in binding affinity may influence the efficacy of integrase inhibitors, which target the integrase-DNA complex.