Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS

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 though...

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Bibliographic Details
Published in:Molecules (Basel, Switzerland) Switzerland), 2019-04, Vol.24 (8), p.1572
Main Authors: Sullivan, Richard, Adams, Mary Catherine, Naik, Rajesh R, Milam, Valeria T
Format: Article
Language:English
Subjects:
Activity recognition
Aptamers
Classification schemes
DNA sequencing
DNA structure
Next-generation sequencing
nucleic acid ligands
Nucleic acids
Nucleotide sequence
Protein structure
Secondary structure
Single-stranded DNA
Spectrum analysis
Structural analysis
Structural members
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Summary: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.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules24081572