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In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

Quantitative selection and parallel characterization of aptamers.

Minseon Cho¹, Seung Soo Oh, Jeff Nie

¹Departments of Mechanical Engineering, Molecular, Cellular, and Developmental Biology, Chemistry, and Materials Department, University of California, Santa Barbara, CA 93106.

Proceedings of the National Academy of Sciences of the United States of America

|October 30, 2013

Summary

This summary is machine-generated.

We developed Quantitative Parallel Aptamer Selection System (QPASS) to accelerate aptamer discovery. QPASS enables parallel measurement of affinity and specificity for thousands of aptamers, identifying high-affinity aptamers for cancer biomarker Angiopoietin-2.

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Area of Science:

Biotechnology
Molecular Biology
Biochemistry

Background:

Aptamers are synthetic affinity reagents with potential for high-throughput discovery.
Current aptamer generation is laborious and low-throughput due to serial binding characterization.
Characterizing affinity and specificity of individual aptamers is a critical bottleneck.

Purpose of the Study:

To develop a high-throughput method for aptamer discovery and characterization.
To accelerate the identification of high-affinity aptamers for specific biomarkers.
To enable parallel measurement of aptamer affinity and specificity.

Main Methods:

Quantitative Parallel Aptamer Selection System (QPASS) integrating microfluidic selection and next-generation sequencing.
In situ synthesis of aptamer arrays for parallel measurements.
Parallel quantification of aptamer affinity (Kd) and specificity using labeled proteins and complex samples like serum.

Main Results:

QPASS successfully selected high-affinity aptamers for human cancer biomarker Angiopoietin-2 (Ang2), with Kd as low as 20.5 ± 7.3 nM.
Parallel measurement of specificity was achieved by comparing binding to target and non-target proteins.
Aptamer binding in undiluted serum was quantified, demonstrating applicability in complex biological samples.
Structure-function relationships were explored by linking sequencing data with affinity measurements.

Conclusions:

QPASS significantly accelerates aptamer discovery and characterization by enabling parallel analysis of thousands of aptamers.
The system allows for rapid identification of high-affinity and specific aptamers for biomarkers.
QPASS provides a powerful platform for exploring aptamer structure-function relationships.