Programmable DNA Nanoswitches for Detection of Nucleic Acid Sequences

Detection of nucleic acid sequences is important for applications such as medicine and forensics, but many detection strategies involve multiple time-consuming steps or require expensive lab equipment. Here we report a programmable DNA nanoswitch that undergoes a predefined conformational change upon binding a target sequence, flipping the switch from a linear “off” state to a looped “on” state. The presence of the target sequence is determined without amplification using standard gel electrophoresis to separate the on and off states. We characterized the nanoswitch on a variety of DNA sequences and fragment lengths, showing detection of fragments as short as 20-nt, and sensitivity into the low picomolar range. Specificity and robustness were demonstrated by detection of a single target sequence from both a randomized pool of high concentration oligonucleotides and from a solution of fetal bovine serum (FBS), with no false positive detection in either case. Furthermore, we optimized the process to take less than 30 minutes from sample mixture to readout. By leveraging the already ubiquitous technique of gel electrophoresis, our low cost approach will be especially accessible to researchers in the biomedical sciences.