In the vast landscape of molecular biology, aptamers have emerged as versatile tools with great potential for various applications. These single-stranded nucleic acid molecules can bind to specific target molecules with high affinity and specificity, rivaling the capabilities of antibodies. Aptamers offer numerous advantages such as their stability, ease of synthesis, and the ability to target a wide range of molecules, including ions, small molecules, peptides, DNA, RNA, proteins, and synthetic particles. However, to fully exploit the potential of aptamers, it is crucial to understand and characterize their interactions with target molecules.
Aptamer characterization involves a set of techniques and assays aimed at elucidating the binding properties, kinetics, thermodynamics, and functional aspects of aptamer-target interactions. By thoroughly understanding the characteristics of aptamers and their target molecules, researchers can optimize aptamer design, improve binding affinity, and develop aptamer-based applications tailored to specific needs.
Application areas of aptamers (Li, 2020).
Creative Proteomics performs steady-state binding assays using a variety of advanced technologies, including microscale thermophoresis (MST), bio-layer interferometry (BLI), and isothermal titration calorimetry (ITC). You are able to determine the affinity (KD) of an aptamer for its natural target or any other desired target molecule. The high sensitivity and precision of these techniques allow for accurate measurement of binding affinity for a variety of molecular targets.
The kinetic behavior of aptamer-target interactions can be studied using Creative Proteomics' BLI platform. This analysis allows you to study the aptamer open-break rate (kon and koff), providing valuable kinetic information for applications requiring specific binding kinetics that can influence aptamer design and selection.
Creative Proteomics utilizes MST technology for high-throughput screening of small molecule compounds or molecular fragments for binding to protein targets. The method is capable of analyzing tens of thousands of compounds with minimal sample consumption and high accuracy. You can efficiently identify potential hapten binders.
Thermodynamic analysis of aptamer-target interactions contributes to the understanding of the underlying driving forces and energetics of the binding process. Creative Proteomics uses isothermal titration calorimetry (ITC) to characterize the thermodynamic parameters of aptamer-target interactions, including enthalpy (ΔH), free enthalpy of binding (ΔG), entropy (ΔS), and stoichiometry, to help optimize and design inducers with the desired binding properties.
To ensure the biological relevance of aptamer-target interactions, Creative Proteomics offers aptamer characterization services in relevant biological fluids such as serum, plasma, cell lysate, urine, mucose, or environmental matrices. By performing aptamer-target interaction studies in complex biological matrices, unwanted side-interactions can be excluded, providing a more accurate representation of the aptamer's behavior in physiological conditions.
We have specifically developed an aptamer-based sandwich assay using MST and BLI techniques. Sandwich assays involve the selection of two inducers that bind to different epitopes on the same target molecule. By utilizing MST and BLI technologies, Creative Proteomics ensures the specificity and sensitivity of the aptamer-based sandwich assay, enabling accurate detection and quantification of target molecules.
Creative Proteomics offers competition assays using both MST and BLI technologies. These assays assess the ability of an inducer to disrupt a target-ligand complex or affect target-ligand interactions. By studying the competitive behavior of aptamers, you can gain insight into their efficacy to interfere with specific interactions. Competition assays can help design inducers to disrupt harmful protein-protein interactions or inhibit the binding of disease-associated molecules.