A thermodynamic approach to designing structure-free combinatorial DNA word sets
| Autor: | DongGee Hong, Seo Bong Chang, Anne Condon, Michael R. Shortreed, Maggie Phillips, Mirela Andronescu, Dan Tulpan, Bridget Campion, Lloyd M. Smith, Holger H. Hoos |
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| Rok vydání: | 2005 |
| Předmět: |
Guanine
Biology Nucleic Acid Denaturation 010402 general chemistry 01 natural sciences Article DNA sequencing Cytosine 03 medical and health sciences Nucleic acid thermodynamics chemistry.chemical_compound Genetics A-DNA Base sequence 030304 developmental biology 0303 health sciences Base Sequence Tandem Nucleic Acid Heteroduplexes Temperature Computational Biology Nucleic Acid Hybridization DNA Sequence Analysis DNA Experimental validation 0104 chemical sciences chemistry Nucleic Acid Conformation Thermodynamics Algorithm Algorithms |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gki812 |
| Popis: | An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA 'word' structure is employed in which individual DNA 'words' of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This approach, where multiple word variants are used at each tandem word position, allows very large sets of non-interacting DNA strands to be assembled from combinations of the individual words. Word sets were generated and their figures of merit are compared to sets as described previously in the literature (e.g. 4, 8, 12, 15 and 16mer). The predicted hybridization behavior was experimentally verified on selected members of the sets using standard UV hyperchromism measurements of duplex melting temperatures (T(m)s). Additional experimental validation was obtained by using the sequences in formulating and solving a small example of a DNA computing problem. |
| Databáze: | OpenAIRE |
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