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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-04-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/24/8/1572 |
| _version_ | 1811270628481695744 |
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| author | Richard Sullivan Mary Catherine Adams Rajesh R. Naik Valeria T. Milam |
| author_facet | Richard Sullivan Mary Catherine Adams Rajesh R. Naik Valeria T. Milam |
| author_sort | Richard Sullivan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T22:05:38Z |
| format | Article |
| id | doaj.art-a98c02dfcbf14ca5980366f6978c0fce |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-04-12T22:05:38Z |
| publishDate | 2019-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-a98c02dfcbf14ca5980366f6978c0fce2022-12-22T03:14:57ZengMDPI AGMolecules1420-30492019-04-01248157210.3390/molecules24081572molecules24081572Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELSRichard Sullivan0Mary Catherine Adams1Rajesh R. Naik2Valeria T. Milam3School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USASchool of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson AFB, OH 45433, USASchool of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USAIn 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.https://www.mdpi.com/1420-3049/24/8/1572aptamerssingle-stranded DNAnucleic acid ligandssecondary structure |
| spellingShingle | Richard Sullivan Mary Catherine Adams Rajesh R. Naik Valeria T. Milam Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS Molecules aptamers single-stranded DNA nucleic acid ligands secondary structure |
| title | Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS |
| title_full | Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS |
| title_fullStr | Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS |
| title_full_unstemmed | Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS |
| title_short | Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS |
| title_sort | analyzing secondary structure patterns in dna aptamers identified via compels |
| topic | aptamers single-stranded DNA nucleic acid ligands secondary structure |
| url | https://www.mdpi.com/1420-3049/24/8/1572 |
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