Journal
ACS COMBINATORIAL SCIENCE
Volume 20, Issue 10, Pages 585-593Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acscombsci.8b00048
Keywords
aptamers; CompELS; oligonucleotides; ligands; non-SELEX
Funding
- GT-AFOSR BIONIC Center of Excellence [FA9550-09-1-0162]
- DUMP grant from AFOSR [FA9550-10-1-0358]
- NSF Graduate Research Fellowship
- CD4 GAANN Fellowship
- NIH Training Grant (T32, NIBIB) [T32EB006343-02]
- Air Force Office of Scientific Research
- 3M Nontenured Faculty Award
- NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING [T32EB006343] Funding Source: NIH RePORTER
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Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N (K-d = 5.6 X 10(-)(10) M) compared to five other high affinity aptamer candidates (K-d = 10(-8)-10(-9) M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.
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