Highly sensitive and specific nanomechanical detection of DNA /RNA hybridization through intrinsic elasticity

Keywords:
DNA, RNA, Hybridization, Biosensing, AFM, Torsional harmonic cantilever

Abstract:
Recently developed torsional harmonic cantilevers were used to detect a label free and specific hybridization of DNA/RNA molecules on an assay similar to current microarray platform. A new, fast, approach was used for the squeezing (gentle tapping in submicrosecond) of hybridized and unhybridized DNAs and thus their intrinsic properties were extracted in terms of quantitative stiffness ( QS ) map at single molecule level over nanometer scale spatial resolution. First time, we report that short DNA molecules hybridized on the surface and measured in ambient conditions are very rigid, stable and can be repeatedly scanned in AFM with no change in their intrinsic properties. QS maps were used to 1. discriminate (specifically) the hybridized dsDNA and unhybridized ssDNA molecules from the contaminates e.g. junk, salt and 2. give the precise number of hybridized DNA molecules on the surface. A wide dynamic range of cDNA detection was observed for concentrations nM to aM depending on immobilization area and volume of reaction. Furthermore, hybridization of RNA molecules was detected respective to their pre-immobilized target ssDNA. Taken all together, this potentially specific label free approach is capable of detecting high (nM) to very low concentration of cDNA (aM) with high spatial resolution can be exploited in new ‘DNA Nanoarray’ technologies to monitor the expression of thousands of genes simultaneously on nano array platform.

Nanotech 2008 Conference Program Abstract