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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level.

Yulin Du1, Yifan Lyu1,2,3, Shiquan Li1

  • 1Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.

Angewandte Chemie (International Ed. in English)
|December 8, 2022
PubMed
Summary

We developed ligand dilution analysis (LDA) to quantify cell surface receptor density using aptamers. This method enables precise analysis of aptamer-receptor interactions and receptor dynamics in live cells.

Keywords:
AptamersBinding SiteDilutionFluorescent ProbesMotion Analysis

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Background:

  • Cell-specific aptamers are crucial for studying membrane receptors at the single-molecule level.
  • Analyzing highly expressed cell surface receptors in situ is challenging due to their dense distribution and rapid movement.

Purpose of the Study:

  • To introduce a novel aptamer-based receptor study strategy, ligand dilution analysis (LDA).
  • To enable accurate quantification of cell surface receptor density and detailed analysis of aptamer-receptor binding modes.

Main Methods:

  • Development of a random sampling-based analysis strategy (LDA).
  • Utilizing a synergistic ligand dilution design for aptamer and monoclonal antibody (mAb) binding differentiation.
  • Employing molecular docking and molecular dynamics simulations to determine binding sites and modes.

Main Results:

  • LDA allows for the calculation of receptor density on the cell surface via a regression model.
  • The synergistic ligand dilution design facilitates colocalization and differentiation of aptamer and mAb binding on single receptors.
  • Precise binding sites and aptamer-receptor binding modes can be determined.

Conclusions:

  • LDA provides an easily implemented method for aptamer-based receptor studies.
  • This strategy enables detailed analysis of aptamer-receptor interactions and receptor dynamics on live cell membranes.