Loop-Ligation of DNA Nanoswitch for Sensitivity Increase

Lecture Centre Concourse

DNA nanoswitches are tools to detect nucleic acids such as microRNAs and viral RNAs. The DNA nanoswitch is a linear duplex structure created from single-stranded circular viral M13 DNA using a DNA origami approach. Each nanoswitch can be designed to have explicit detector strands that bind to a specific DNA sequence. In the presence of a particular target sequence, the DNA nanoswitch will undergo a conformational change in which it switches from a linear “off” state to a looped “on” state. The shape of the DNA nanoswitch can then be detected using standard gel electrophoresis, a cheap and simple test. In this project, we aim to improve the sensitivity of the DNA nanoswitches in detecting target strands using DNA loop-ligation. This strategy will allow the target strand to be “recycled” in solution after a more permanent looped nanoswitch is formed and continue to convert more linear nanoswitches into looped nanoswitches through target recycling. We were able to confirm permanently looped nanoswitches after ligation using T4 DNA Ligase enzyme. We will optimize the reaction conditions to show stability and signal amplification of the nanoswitch. Ultimately, we hope to amplify detection signal at least 10-100 fold using this approach, bringing our sensitivity to the aM (10^-18M) range.