Selection of structure-induced aptamer targeting small molecule based on capillary sieving electrophoresis

Area of Science:

• Biotechnology and Molecular Biology
• Analytical Chemistry
• Nucleic Acid Aptamer Technology

Background:

• Aptamers are nucleic acid-based molecules that can bind to specific targets, including small molecules.
• Traditional aptamer selection methods often struggle with targeting small molecules due to their low molecular weight and lack of complex structures.
• The structural conformation of aptamers plays a crucial role in their binding affinity and specificity.

Purpose of the Study:

• To develop and validate a novel method for selecting structure-induced aptamers targeting small molecules.
• To utilize capillary sieving electrophoresis (CSE) for both pre-organizing aptamer structures and selecting target-specific aptamers.
• To identify aptamers with high binding affinity and selectivity for L-tyrosinamide.

Main Methods:

• Capillary sieving electrophoresis (CSE) was employed with hydroxypropyl cellulose as a sieving matrix.
• A DNA sub-library with pre-organized, straight-chain-like structures was created using CSE.
• Structure-induced aptamers targeting L-tyrosinamide were selected from this pre-organized sub-library.

Main Results:

• Six aptamer candidates targeting L-tyrosinamide were successfully selected.
• One selected aptamer demonstrated binding ability comparable to previously reported L-tyrosinamide aptamers.
• The selected aptamer exhibited significant selectivity towards L-tyrosinamide analogs.

Conclusions:

• The proposed CSE-based method is effective for selecting structure-induced aptamers against small molecules.
• This approach enhances the selection of aptamers by controlling their structural pre-organization.
• The identified aptamers show potential for applications in diagnostics and therapeutics involving small molecule detection.