Comparison of different methods to analyze a DNA computing library using the polymerase chain reaction

  • Authors:

  • Cheryl P. Andam;Jonathan R. Driscoll;Jaime A. Dicesare;Tim N. Enke;Anthony J. Macula;Susannah Gal

  • Affiliations:

  • Department of Biological Sciences, Binghamton University, Binghamton, USA 13902 and Department of Crop and Soil Science, Cornell University, Ithaca, USA 14850;Department of Biological Sciences, Binghamton University, Binghamton, USA 13902;Department of Biological Sciences, Binghamton University, Binghamton, USA 13902;Department of Biological Sciences, Binghamton University, Binghamton, USA 13902;Biomathematics Group, SUNY-Geneseo, Geneseo, USA 14454;Department of Biological Sciences, Binghamton University, Binghamton, USA 13902

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2012

Quantified Score

Hi-index 0.00

Visualization

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.