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Related Concept Videos

Induced-fit Model01:13

Induced-fit Model

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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:

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Related Experiment Video

Updated: Jun 23, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

Exploring the relationship between aptamer binding thermodynamics, affinity, and specificity.

Obtin Alkhamis1, Caleb Byrd1, Juan Canoura1

  • 1Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695, United States.

Nucleic Acids Research
|March 29, 2025
PubMed
Summary
This summary is machine-generated.

Aptamer-ligand interactions are primarily driven by enthalpy, with high specificity linked to strong binding enthalpy and entropic penalties. This thermodynamic insight aids aptamer engineering for improved binding properties.

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Last Updated: Jun 23, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

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Determining the Thermodynamic and Kinetic Association of a DNA Aptamer and Tetracycline Using Isothermal Titration Calorimetry
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A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer
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A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer

Published on: September 13, 2022

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biotechnology

Background:

  • Aptamers are oligonucleotide bioreceptors with increasing use in diagnostics, bioimaging, and therapeutics.
  • Understanding aptamer-ligand interactions is crucial for engineering better aptamers.
  • Few studies comprehensively link aptamer binding properties to thermodynamics.

Purpose of the Study:

  • To systematically analyze thermodynamic binding data from DNA aptamers.
  • To explore the relationship between aptamer binding thermodynamics and specificity.
  • To identify patterns in aptamer-ligand interactions.

Main Methods:

  • Compiled isothermal titration calorimetry (ITC) data from 317 small-molecule-binding DNA aptamers.
  • Analyzed specificity profiles for approximately 6000 aptamer-ligand pairs.
  • Performed systematic analysis of the compiled thermodynamic and specificity datasets.

Main Results:

  • Ligand binding for most aptamers is predominantly driven by enthalpy.
  • Aptamers with higher binding enthalpy and greater entropic penalties exhibit higher specificity.
  • Identified distinct patterns and trends in aptamer-ligand binding thermodynamics.

Conclusions:

  • The study provides valuable thermodynamic insights into aptamer-ligand recognition.
  • Findings can guide sequence engineering for enhanced aptamer performance.
  • Further dataset expansion and analysis will deepen understanding of aptamer binding mechanisms.