Abstract
Screening and analysis of collections of DNA molecules is a standard aspect of many DNA computing approaches. We describe the use of three different polymerase chain reaction (PCR) detection methods to screen specific members of a 5-site, 2-variable DNA computing library previously created using parallel overlap assembly of unique sequences generated from the SynDCode program. The three PCR methods (conventional gel-based PCR, SYBR Green real-time PCR and TaqMan real-time PCR) could all successfully identify individual library members separately or in a mixture. The TaqMan approach was also able to identify members in the original library we had not yet sequenced, providing more evidence supporting our hypothesis that the DNA library we generated may be complete. We expect these three approaches will be useful in future screening of other DNA computing libraries and structures.
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Acknowledgments
The research was partially supported by an NSF grant DMS-UBM 0436298 for advancing undergraduate biomathematics which was awarded to Dr. Anthony Macula. The authors would also like to acknowledge the support of the Deutsche Akademische Austausch Dienst (DAAD) for funding Mr. Enke.
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Andam, C.P., Driscoll, J.R., DiCesare, J.A. et al. Comparison of different methods to analyze a DNA computing library using the polymerase chain reaction. Nat Comput 11, 339–349 (2012). https://doi.org/10.1007/s11047-011-9297-2
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DOI: https://doi.org/10.1007/s11047-011-9297-2