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Askari A, Kota S, Ferrell H, Swamy S, Goodman K, Okoro C, Spruell Crenshaw I, Hernandez D, Oliphant T, Badrayani A, Ellington A, Stovall G. UTexas Aptamer Database: the collection and long-term preservation of aptamer sequence information. Nucleic Acids Res 2024; 52:D351-D359. [PMID: 37904593 PMCID: PMC10767891 DOI: 10.1093/nar/gkad959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
A growing interest in aptamer research, as evidenced by the increase in aptamer publications over the years, has led to calls for a go-to site for aptamer information. A comprehensive, publicly available aptamer dataset, which may be a repository for aptamer data, standardize aptamer reporting, and generate opportunities to expand current research in the field, could meet such a demand. There have been several attempts to create aptamer databases; however, most have been abandoned or removed entirely from public view. Inspired by previous efforts, we have published the UTexas Aptamer Database, https://sites.utexas.edu/aptamerdatabase, which includes a publicly available aptamer dataset and a searchable database containing a subset of all aptamer data collected to date (1990-2022). The dataset contains aptamer sequences, binding and selection information. The information is regularly reviewed internally to ensure accuracy and consistency across all entries. To support the continued curation and review of aptamer sequence information, we have implemented sustaining mechanisms, including researcher training protocols, an aptamer submission form, data stored separately from the database platform, and a growing team of researchers committed to updating the database. Currently, the UTexas Aptamer Database is the largest in terms of the number of aptamer sequences with 1,443 internally reviewed aptamer records.
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Affiliation(s)
- Ali Askari
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Sumedha Kota
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Hailey Ferrell
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Shriya Swamy
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Kayla S Goodman
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Christine C Okoro
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | | | - Daniela K Hernandez
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Taylor E Oliphant
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Akshata A Badrayani
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
| | - Andrew D Ellington
- Institute for Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, The University of Texas, Austin, TX 78712, USA
| | - Gwendolyn M Stovall
- Freshman Research Initiative, The University of Texas, Austin, TX 78712, USA
- Institute for Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
- High School Research Initiative, The University of Texas, Austin, TX 78712, USA
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Kushner DB. Introducing SELEX via a semester-long course-based undergraduate research experience (CURE). BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:605-618. [PMID: 33914410 DOI: 10.1002/bmb.21519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 12/16/2020] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
With the growing importance of the field of RNA biology, undergraduates need to perform RNA-related research. Systematic evolution of ligands by exponential enrichment (SELEX) has become an important method in RNA biology. The principles of SELEX were applied to a semester-long course-based undergraduate research experience (CURE) in which two rounds of in vivo functional selection of regions of a viral RNA were performed. As the labwork had an unknown outcome, students indicated that they were excited by the work and became invested in the experience. By completing two rounds of SELEX, the students repeated molecular methods (e.g., RNA extraction, RT-PCR, agarose gel electrophoresis, DNA purification, cloning, and sequence analysis) and reported that repetition reinforced their learning and helped them build confidence in their lab abilities. Students also appreciated that they did not learn a "technique-per-week" without context, but rather they understood why certain methods were used for certain molecular tasks. Results from a 19-question multiple-choice assessment indicated increased comprehension of theory underlying methods performed. Details regarding experimental methods and timeline, and assessment and attitudinal results from three student cohorts, are described herein.
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Affiliation(s)
- David B Kushner
- Department of Biology, Dickinson College, Carlisle, Pennsylvania, USA
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