A rapid field-use assay for mismatch number and location of hybridized DNAs

Abstract

Molecular dielectrophoresis (DEP) is employed to rapidly (<ms) trap ssDNA molecules in a flowing solution to a cusp-shaped nanocolloid assembly on a chip with a locally amplified AC electric field gradient. By tuning AC field frequency and DNA DEP mobility relative to its electrophoretic mobility due to electrostatic repulsion from like-charged nanocolloids, mismatch-specific binding of DNA molecules at the cusp is achieved by the converging flow, with a concentration factor about 6 orders of magnitude higher than the bulk, thus allowing fluorescent quantification of concentrated DNAs at the singularity in a generic buffer, at room temperature within a minute. Optimum flow rate and the corresponding hybridization rate change by nearly a factor of 2 with a single mismatch in the 26 base docking sequence and are also sensitive to the mismatch location. This dielectrophoresis and shear enhanced pico-molar sensitivity and SNP selectivity can hence be used for field-use DNA detection/identification.

Floating-electrode enhanced constriction dielectrophoresis for biomolecular trapping in physiological media of high conductivity

“…21,22 The resulting temperature gradients cause bulk electrothermal flow, which can dissipate the DEP trapping. Strategies for enhancing the net trapping force on nanoscale biomolecules over dissipative fluid flow due to Joule heating include the application of DEP to DNA immobilized on nanoparticles 23,24 or applying DEP towards the direct manipulation of DNA within devices containing sharp insulating tips or constrictions to enhance field gradients (E.dE/dx or rE 2 ). In our recent work, 25 we have extended this latter approach by coupling the dielectric constriction to an electrically floating electrode with immobilized DNA capture probes to enable low frequency ($1 KHz) DEP trapping of ss-DNA target ($150 bases) in high conductivity saline media (r m $ 1 S/m), without electrolysis.…”

Selective dynamic concentration of peptides at poles of cation-selective nanoporous granules

“…Fundamental improvements in analytical science must be implemented before such biomarker detection is feasible. The dielectrophoretic concentration method does not apply to small molecules, such as peptides, because of the small intensities of their induced dipoles, 4 unless this method is conducted in laboriously fabricated nanochannels. 6 Other analyte concentration techniques based on electrokinetic mechanisms have been suggested.…”

Plasmonic hotspots of dynamically assembled nanoparticles in nanocapillaries: Towards a micro ribonucleic acid profiling platform

“…Induced DC and AC NP dipoles (related to dielectrophoresis) have been used to assemble NP crystals by embedded micro-electrodes to provide the requisite high field. 20,21 The resulting NP crystals are ideal for plasmonic hot spots, since the spacing of the regimented NP crystal can be controlled by the applied voltage. Conic nanocapillaries 22,23 will be used here for such field-induced NP assembly because the submicron-tip can focus the electric field into sufficient high intensity for NP assembly without embedded-electrodes.…”

“…Strong shear during electrophoretic packing has probably endowed this high selectivity. 20 Using the protocol above, the LOD and dynamic range of the target was determined (Fig. 2(e)).…”