Ultrafast DNA Sensors with DNA Framework-Bridged Hybridization Reactions

Abstract

Intracellular DNA-based hybridization reactions generally undergo under tension rather than in free states, which are spa-tiotemporally controlled in physiological conditions. However, how nanomechanical forces affect DNA hybridization effi-ciencies in in-vitro DNA assays, e.g. biosensors or biochips, remains largely elusive. Here we design DNA framework-based nanomechanical handles that can control the stretching states of DNA molecules. Using a pair of tetrahedral DNA frame-work (TDF) nanostructured handles, we develop bridge DNA sensors that can capture target DNA with ultrafast speed and high efficiency. We find that the rigid TDF handles binds two ends of a single-stranded DNA (ssDNA) and holds it at a stretched state, with apparent stretching length comparing to its counterpart of double-stranded DNA (dsDNA) via atom-ic force microscopy (AFM) measurement. The DNA stretching effect of ssDNA is then monitored using single molecular fluorescence energy transfer (FRET), resulting in decreased FRET efficiency in the stretched ssDNA. By controlling the stretching state of ssDNA, we obtained significantly improved hybridization kinetics (within 1 min) and hybridization effi-ciency (~ 98%) under the target concentration of 500 nM. The bridge DNA sensors demonstrated high sensitivity (1 fM), high specificity (single mismatch mutation discrimination) and high selectivity (suitable for the detection in serum and blood) under the target concentration of 10 nM. The controlling of stretching state of ssDNA show great potential in the applications of biosensors, bioimaging and biochips.