Research

Our ongoing research is focused primarily on techologies for identification of clinical pathogens and biothreat agents in point of care settings, through rapid isothermal DNA amplification coupled with visual or electronic detection. We are further developing methods for bottom-up fabrication of nanostructured surfaces based on self-assembly and biomolecular recognition.

Isothermal DNA Amplification with Colorimetric Detection

To enable the simple and rapid identification of specific DNA sequences, we have combined a novel isothermal amplification method for short oligonucleotides (EXPAR) with colorimetric detection through aggregation of DNA-functionalized gold nanospheres. The overall assay is sequence-specific, and permits detection of 100 fM trigger or less in under 10 minutes with minimal requirement for instrumentation. We have coupled this assay with the generation of short oligonucleotides called triggers from genomic DNA sequences of Herpes Simplex Virus. Due to its simplicity, versatility and speed, this assays hold great potential for point-of-care applications.

Impedance-based Electronic DNA Detection on Silicon

We have developed biosensors for label-free electronic DNA detection, suitable for direct interfacing with microelectronic devices. DNA hybridization to probe DNA-functionalized silicon biosensor electrodes leads to a change in surface charge density, which in turn causes a shift in the semiconductor’s impedance response through the field effect. To increase the sensitivity of detection, we have combined electronic DNA detection with isothermal DNA amplification through the EXPAR reaction. To enable miniaturized multiplexed detection, we have fabricated an array of individually addressable microsensor electrodes. We are further investigating how co-immobilizing DNA functionalized gold nanospheres affects the observed shift in impedance response. These sensors are expected to facilitate rapid, specific, and sensitive detection of clinical pathogens and biothreat agents in point of care settings.

DNA Nanoarrays

We have developed a method for depositing DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin PS-PMMA diblock copolymer films on silicon. The deposition occurs spontaneously from solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. Deposition of biofunctionalized nanoparticles into nanostructured surfaces based on of intrinsic molecular interactions, in particular of bio-inspired, specific self-assembly, is expected to facilitate the fabrication of complex surface structures, and enable the development of biosensor surfaces.

Functional enzyme immobilization in hydrogel microarrays

We are developing a microarray-based technology platform to enable experimental investigation of enzymatic activities in a high throughput format. Our focus is on protein phosphatases, which play an important role in regulatory networks. Functional microarrays are obtained through a combination of affinity capture and copolymerization of proteins within hydrogel pad microarrays on glass slides. Quantification of enzymatic activities involves the correlation of experimental data obtained from fluorogenic assays with simulations of the reaction-diffusion system.