Sagnik Basuray

Shear and AC Field Enhanced Carbon Nanotube Impedance Assay for Rapid, Sensitive, and Mismatch-Discriminating DNA Hybridization.

Other than concentrating the target molecules at the sensor location, we demonstrate two distinct new advantages of an open-flow impedance-sensing platform for DNA hybridization on carbon nanotube (CNT) surface in the presence of a high-frequency AC electric field. The shear-enhanced DNA and ion transport rate to the CNT surface decouples the parasitic double-layer AC impedance signal from the charge-transfer signal due to DNA hybridization. The flow field at high AC frequency also amplifies the charge-transfer rate across the hybridized CNT and provides shear-enhanced discrimination between DNA from targeted species and a closely related congeneric species with three nucleotide mismatches out of 26 bases in a targeted attachment region. This allows sensitive detection of hybridization events in less than 20 min with picomolar target DNA concentrations in a label-free CNT-based microfluidic detection platform.

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

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.

Designing a sensitive and quantifiable nanocolloid assay with dielectrophoretic crossover frequencies

Dielectrophoretic nanocolloid assay is a promising technique for sensitive molecular detection and identification, as target molecule hybridization onto the probe-functionalized nanocolloids can change their surface conductance and consequently their dielectrophoretic crossover frequencies. Thus, instead of relying on surface charge density increase after hybridization, as in many capacitive and field effect transistor impedance sensing techniques, the current assay utilizes the much larger surface conductance (and dielectrophoresis crossover frequency) changes to effect sensitive detection. Herein, we present a Poisson-Boltzmann theory for surfaces with finite-size molecular probes that include the surface probe conformation, their contribution to surface charge with a proper delineation of the slip and Stern planes. The theory shows that the most sensitive nanocolloid molecular sensor corresponds to a minimum in the dielectrophoretic crossover frequency with respect to the bulk concentration of the molecular probes (oligonucleotides in our case) during nanocolloid functionalization. This minimum yields the lowest number of functionalized probes that are also fully stretched because of surface probe-probe interaction. Our theory provides the surface-bulk oligonucleotide concentration isotherm and a folding number for the surface oligonucleotide conformation from the crossover frequency, the zeta potential, and the hydrodynamic radius data.

A Versatile Self-Assembly Approach toward High Performance Nanoenergetic Composite Using Functionalized Graphene

Exploiting the functionalization chemistry of graphene, long-range electrostatic and short-range covalent interactions were harnessed to produce multifunctional energetic materials through hierarchical self-assembly of nanoscale oxidizer and fuel into highly reactive macrostructures. Specifically, we report a methodology for directing the self-assembly of Al and Bi2O3 nanoparticles on functionalized graphene sheets (FGS) leading to the formation of nanocomposite structures in a colloidal suspension phase that ultimately condense into ultradense macrostructures. The mechanisms driving self-assembly were studied using a host of characterization techniques including zeta potential measurements, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), particle size analysis, micro-Raman spectroscopy, and electron microscopy. A remarkable enhancement in energy release from 739 ± 18 to 1421 ± 12 J/g was experimentally measured for the FGS self-assembled nanocomposites.

A Nanomembrane-Based Nucleic Acid Sensing Platform for Portable Diagnostics

In this perspective article, we introduce a potentially transformative DNA/RNA detection technology that promises to replace DNA microarray and real-time PCR for field applications. It represents a new microfluidic technology that fully exploits the small spatial dimensions of a biochip and some new phenomena unique to the micro- and nanoscales. More specifically, it satisfies all the requisites for portable on-field applications: fast, small, sensitive, selective, robust, label- and reagent-free, economical to produce, and possibly PCR-free. We discuss the mechanisms behind the technology and introduce some preliminary designs, test results, and prototypes.

Dynamic double layer effects on ac-induced dipoles of dielectric nanocolloids

Normal and tangential surface ionic currents around low-permittivity nanocolloids with surface charges are shown to produce three different conductive mechanisms for ac-induced dipoles, all involving dynamic space charge accumulation at the double layerbulk interface with a conductivity jump. However, the distinct capacitor dimensions and diffusive contributions produce three disparate crossover frequencies at which the induced dipole reverses direction relative to the bulk field. A highly conducting collapsed diffuse layer, with bulk ion mobility, renders the particle conductive and produces an ionic strength independent crossover frequency for weak electrolytes. A precipitous drop in crossover frequency occurs at high ionic strengths when charging occurs only at the poles through field focusing around the insulated colloid. A peculiar maximum in crossover frequency exists between these two asymptotes for colloids smaller than a critical size when normal charging of the diffuse layer occurs over the entire surface. The crossover frequency data for latex nanocolloids of various sizes in different electrolytes of wide ranging ionic strengths are collapsed by explicit theoretical predictions without empirical parameters.

Ionic conductivity enhancement of sputtered gold nanoparticle-in-ionic liquid electrolytes

Ionic liquids (ILs) are being widely investigated as advanced electrolytes within electric double-layer capacitors (EDLCs) due to their inherent ionic conductivity, wide electrochemical windows, essentially zero volatility, and high temperature stability. Despite being composed entirely of ions, the ionic conductivity of a typical IL is significantly hindered by its high viscosity, rendering it akin to normal electrolytes. In this light, in order to increase the applicability of IL electrolytes, it is of the utmost priority to discover approaches for improving the electrochemical properties of ILs without adversely affecting their other beneficial attributes. In this work, we make important strides toward this goal by employing low energy sputtering to generate novel electrolytes comprising gold nanoparticle dispersions within the prototypical IL 1-ethyl-3-methylimidazolium ethyl sulfate, [emim][EtSO4]. This study also afforded the unique opportunity to investigate nanoscale growth mechanisms occurring within the IL. Cyclic voltammetry and electrochemical impedance spectroscopy analyses revealed that when the IL contained a substantial fraction of sub-nanometer-sized particles, the double-layer capacitance was increased by ∼190%, concomitant with a bulk electrolyte resistance decrease of ∼70% with respect to a gold-free control. An exponential rise in resistance accompanied by a proportional decrease in capacitance accompanies nanoparticle growth until a critical size is reached—typically within 10 h at room temperature—beyond which the final capacitance is typically ∼60% higher than the control with an electrolyte resistance similar to the control. Overall, our results reveal an anomalous capacitance increase and low internal resistance for nanoparticle-in-IL dispersions, suggesting intriguing potential as electrolytes for next-generation EDLCs, fuel cells, and sensors.

Identification and separation of DNA-hybridized nanocolloids by Taylor cone harmonics

A rapid (minutes) electrospray bead‐based DNA hybridization detection technique is developed by spraying a mixture of hybridized and unhybridized silica nanocolloids. With proper far‐field control by external electrodes, the trajectory of the ejected nanobeads from the electrospray is governed by specific harmonics of the Laplace equation, which select discrete polar angles along well‐separated field maxima near the conducting Taylor cone. Due to Rayleigh fission and evaporation, beads of different size acquire different total charge after ejection and suffer different normal electrophoretic displacement such that they are ejected along well‐separated field maxima and are deposited in distinct rings on an intersecting plane. As the hybridized DNA is of the same dimension as that of the nanocolloid, the nanocolloids are hence easily differentiated from the unhybridized ones. This technique is highly specific as the high shear stress in the microjet shears away any non‐specifically bound DNA from the nanocolloid surface.

Enhanced fluorescence through the incorporation of nanocones/gaps into a plasmonic gratings sensor platform

In this article, a novel plasmonic grating sensor platform was developed and tested for feasibility in sensor applications using a “lights-on” fluorescence based DNA sensor. The sensor platform combined the fluorescence enhancement of a grating-based plasmonic platform with the electric field intensifying effects of nano-scale cones and cavities. The gratings were made through a microcontact printing process that replicated HD-DVD discs in polymethylsilsesquioxane (PMSSQ) and coated in a thin gold film. Nanocavities were incorporated into the sensor platform during the printing process and nanocones were incorporated during the 100 nm gold deposition process. Fluorescently-tagged single-strand (SS) DNA molecules were immobilized onto the surface and were designed such that the molecules would fluoresce when bound to a complementary sequence. Sensor substrates were imaged after exposure to a mismatched and matched oligomer to quantify the fluorescence enhancement of the sensor. Much higher fluorescence intensity was observed on all of the plasmonic structures as compared to flat gold.

Single Molecule Oscillations of an RNA/DNA Duplex in a Plasmonic Nanocavity

We report the visualization of single molecule dynamics in epifluorescence mode through extraordinary plasmonic enhancement provided by silver grating with embedded nanocavities. Cy3/Cy5-labeled DNA/RNA hybrid duplexes were affixed to SiO 2-capped silver gratings produced by soft lithography process. Tracking single-molecule fluorescence revealed damped sub-1 Hz periodic Cy3 intensity fluctuations with strong dependence on the bulk MgCl 2 concentration. Extreme concentration of electric field at the nanocavity edge induces plasmonic heating, which sets up convection deep within the nanocavity. Local fluctuations in Mg 2+ ion concentration promote a bent or unbent duplex conformational state, respectively, by varying degrees of negative charge screening along the duplex backbone. These oscillations continue until the duplex conformational state stabilizes or the dyes bleach. This unique molecular behavior in the nanocavity could be used to study duplex complementarity, structural polymorphisms, and protein-nucleic acid interactions at the single molecule level.