Journal
MOLECULES
Volume 24, Issue 8, Pages -Publisher
MDPI
DOI: 10.3390/molecules24081572
Keywords
aptamers; single-stranded DNA; nucleic acid ligands; secondary structure
Funding
- GT-AFOSR BIONIC Center of Excellence [FA9550-09-1-0162]
- DURIP grant funding from AFOSR [FA9550-10-1-0358]
- CRASI (Community for Research on Active Surfaces and Interfaces) at Georgia Tech
- Center for Pediatric Nanomedicine at Georgia Tech
- Integrated Cancer Research Center at Georgia Tech
- School of Materials Science & Engineering at Georgia Tech
- NSF IGERT [1258425]
- Air Force Office of Scientific Research
- Children's Healthcare of Atlanta
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In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.
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