Competition-Enhanced Ligand Selection to Identify DNA Aptamers

Area of Science:

• Biotechnology
• Molecular Biology
• Materials Science

Background:

• Traditional aptamer screening methods like SELEX (systematic evolution of ligands by exponential enrichment) are time-consuming and involve iterative steps.
• Identifying high-affinity aptamers for nonbiological targets requires efficient and reliable screening platforms.
• Aptamers are single-stranded DNA or RNA molecules that can bind to specific targets with high affinity and specificity.

Purpose of the Study:

• To introduce and validate a novel aptamer screening approach, Competition-enhanced ligand screening (CompELS).
• To identify and characterize aptamers that bind to a gold surface using CompELS.
• To establish a classification scheme for aptamers based on structure and binding affinity.

Main Methods:

• CompELS was used to screen large DNA libraries against a gold surface, involving repeated introduction of unenriched random sequences.
• The screening process bypassed iterative elution and polymerase chain reaction (PCR) amplification steps.
• Identified aptamers were evaluated for binding affinity and structural patterns, culminating in a competition experiment.

Main Results:

• Twenty-five aptamers were identified against the gold surface using CompELS.
• One aptamer, designated 1N, demonstrated the highest binding affinity (Kd = 5.6 × 10^-10 M) for the gold substrate.
• Aptamer 1N exhibited at least an order of magnitude higher binding affinity compared to other candidates from similar structural families.

Conclusions:

• CompELS provides a rapid, reliable, and efficient platform for aptamer screening and characterization.
• The study successfully identified a high-affinity aptamer for a nonbiological target (gold surface).
• The developed classification scheme aids in understanding aptamer structure-function relationships for both biological and nonbiological applications.