Programmable low-cost DNA-based platform for viral RNA detection

Lifeng Zhou; Arun Richard Chandrasekaran; Jibin Abraham Punnoose; Gaston Bonenfant; Stephon Charles; Oksana Levchenko; Pheonah Badu; Cassandra Cavaliere; Cara T. Pager; Ken Halvorsen

The detection samples were run in 0.8% agarose gels unless otherwise noted, cast from molecular biology grade agarose (Fisher BioReagents) dissolved in 0.5× TBE buffer. Typical running conditions were 75 V for 45 to 70 minutes at room temperature or cold room. Samples were mixed with a Ficoll based blue loading dye prior to loading. Imaging was completed on a Bio-Rad Gel Doc XR+ imager with different exposure time based on the brightness of the detection bands. The detection efficiency was analyzed using included Image Lab software (Fig. 1F) . The profiles of detection bands were obtained in ImageJ 64 and then their integrated intensity were obtained by using the peak analysis function in Origin (OriginLab Corporation), such as the data presented in Fig. 1G, 3C and 4B . Detailed analysis procedure can be found in our previous publications 27 . For the E-gel related experiments, we used Invitrogen E-gel agarose system (Thermo Fisher Scientific) and its precast agarose gel (1.0%, SYBR stained). Ten µl of nanoswitch detection sample was loaded to each lane and the gel was run at 48 volts for 1 hour at room temperature. Since the E-gel system does not allow user control of the voltage, we used an external power supplier connected with the negative and positive electrodes of the precast agarose gel to supply 48 volts.