Flow-Cell-Based Technology for Massively Parallel Characterization of Base-Modified DNA Aptamers.

Area of Science:

• Biotechnology
• Molecular Biology
• Chemical Biology

Background:

• Aptamers with chemically modified bases show improved affinity and specificity over natural aptamers.
• Characterizing these modified aptamers is typically a slow, low-throughput process.

Purpose of the Study:

• To develop a high-throughput method for generating and characterizing base-modified DNA aptamers.
• To identify optimal chemical modifications for enhanced aptamer performance.
• To create aptamers with high specificity and affinity in complex biological samples.

Main Methods:

• The non-natural aptamer array (N2A2) system was developed using a minimally modified Illumina MiSeq instrument.
• N2A2 facilitates high-throughput screening of base-modified DNA aptamer libraries.
• The system assesses both target binding and specificity for aptamer selection.

Main Results:

• N2A2 successfully screened multiple base modifications to find optimal chemistries for high-affinity binding.
• Aptamers generated using N2A2 demonstrated excellent specificity in complex samples, including diluted human serum.
• The selected aptamers maintained strong target affinity in both buffer and serum conditions.

Conclusions:

• The N2A2 system provides a broadly accessible tool for high-quality affinity reagent generation.
• Minor modifications to the Illumina MiSeq enable high-throughput aptamer characterization.
• This technology supports diverse applications requiring specific and high-affinity aptamers.