In-silico Design of DNA Oligonucleotides: Challenges and Approaches
DNA oligonucleotides are essential components of a high number of technologies in molecular biology. The key event of each oligonucleotide-based assay is the specific binding between oligonucleotides and their target DNA. However, single-stranded DNA molecules also tend to bind to unintended targets...
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| Format: | Article |
| Language: | English |
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Elsevier
2019-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037019300844 |
| _version_ | 1811318906729529344 |
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| author | Michaela Hendling Ivan Barišić |
| author_facet | Michaela Hendling Ivan Barišić |
| author_sort | Michaela Hendling |
| collection | DOAJ |
| description | DNA oligonucleotides are essential components of a high number of technologies in molecular biology. The key event of each oligonucleotide-based assay is the specific binding between oligonucleotides and their target DNA. However, single-stranded DNA molecules also tend to bind to unintended targets or themselves. The probability of such unspecific binding increases with the complexity of an assay. Therefore, accurate data management and design workflows are necessary to optimize the in-silico design of primers and probes. Important considerations concerning computational infrastructure and run time need to be made for both data management and the design process. Data retrieval, data updates, storage, filtering and analysis are the main parts of a sequence data management system. Each part needs to be well-implemented as the resulting sequences form the basis for the oligonucleotide design. Important key features, such as the oligonucleotide length, melting temperature, secondary structures and primer dimer formation, as well as the specificity, should be considered for the in-silico selection of oligonucleotides. The development of an efficient oligonucleotide design workflow demands the right balance between the precision of the applied computer models, the general expenditure of time, and computational workload.This paper gives an overview of important parameters during the design process, starting from the data retrieval, up to the design parameters for optimized oligonucleotide design. Keywords: Oligonucleotide design, Sequence database, Alignment, Oligonucleotide secondary structures |
| first_indexed | 2024-04-13T12:33:23Z |
| format | Article |
| id | doaj.art-32c02392d3234221acf05d4e476b223b |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-13T12:33:23Z |
| publishDate | 2019-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-32c02392d3234221acf05d4e476b223b2022-12-22T02:46:44ZengElsevierComputational and Structural Biotechnology Journal2001-03702019-01-011710561065In-silico Design of DNA Oligonucleotides: Challenges and ApproachesMichaela Hendling0Ivan Barišić1Corresponding author.; Austrian Institute of Technology GmbH, Center for Health & Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210 Vienna, AustriaAustrian Institute of Technology GmbH, Center for Health & Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210 Vienna, AustriaDNA oligonucleotides are essential components of a high number of technologies in molecular biology. The key event of each oligonucleotide-based assay is the specific binding between oligonucleotides and their target DNA. However, single-stranded DNA molecules also tend to bind to unintended targets or themselves. The probability of such unspecific binding increases with the complexity of an assay. Therefore, accurate data management and design workflows are necessary to optimize the in-silico design of primers and probes. Important considerations concerning computational infrastructure and run time need to be made for both data management and the design process. Data retrieval, data updates, storage, filtering and analysis are the main parts of a sequence data management system. Each part needs to be well-implemented as the resulting sequences form the basis for the oligonucleotide design. Important key features, such as the oligonucleotide length, melting temperature, secondary structures and primer dimer formation, as well as the specificity, should be considered for the in-silico selection of oligonucleotides. The development of an efficient oligonucleotide design workflow demands the right balance between the precision of the applied computer models, the general expenditure of time, and computational workload.This paper gives an overview of important parameters during the design process, starting from the data retrieval, up to the design parameters for optimized oligonucleotide design. Keywords: Oligonucleotide design, Sequence database, Alignment, Oligonucleotide secondary structureshttp://www.sciencedirect.com/science/article/pii/S2001037019300844 |
| spellingShingle | Michaela Hendling Ivan Barišić In-silico Design of DNA Oligonucleotides: Challenges and Approaches Computational and Structural Biotechnology Journal |
| title | In-silico Design of DNA Oligonucleotides: Challenges and Approaches |
| title_full | In-silico Design of DNA Oligonucleotides: Challenges and Approaches |
| title_fullStr | In-silico Design of DNA Oligonucleotides: Challenges and Approaches |
| title_full_unstemmed | In-silico Design of DNA Oligonucleotides: Challenges and Approaches |
| title_short | In-silico Design of DNA Oligonucleotides: Challenges and Approaches |
| title_sort | in silico design of dna oligonucleotides challenges and approaches |
| url | http://www.sciencedirect.com/science/article/pii/S2001037019300844 |
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