Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS
Abstract
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Apr 21, 2019
- Source ID
- 10.3390/molecules24081572
Entities
People
- Mary Catherine Adams
- Rajesh R Naik
- Richard Sullivan
- Valeria T Milam
Organizations
- Air Force Office of Scientific Research
- Georgia Tech
- National Science Foundation