Swati Goyal

Electrical detection of single-base DNA mutation using functionalized nanoparticles

We report an electrical scheme to detect specific DNA. Engineered hairpin probe DNA are immobilized on a silicon chip between gold nanoelectrodes. Hybridization of target DNA to the hairpin melts the stem nucleotides. Gold nanoparticle-conjugated universal reporter sequence detects the open hairpins by annealing to the exposed stem nucleotides. The gold nanoparticles increase charge conduction between the electrodes. Specifically, we report on a hairpin probe designed to detect a medically relevant mutant form of the K-ras oncogene. Direct current measurements show three orders of magnitude increase in conductivity for as low as 2fmol of target molecules.

Isothermal amplification method for next-generation sequencing

Significance We have developed a cost-effective in situ isothermal amplification method for next-generation sequencing (NGS) that can generate billions of monoclonal colonies in less than 30 minutes. This method can be used on NGS platforms to make the

Vapor-Phase Facile Coatings of Nanotextured Organic Biocompatible Films on Solid-State Substrates

1,000 genome possible and simplify the workflow for clinical genomic applications. We report an approach for generating immobilized monoclonal templates for next- generation sequencing applications. Our isothermal amplification method is based on a template walking mechanism using a pair of low-melting temperature (Tm) solid-surface homopolymer primers and a low-Tm solution phase primer. The method can generate more than one billion submicrometer-sized colonies in a single lane of a next-generation sequencing flowchip. An alternative paired-end sequencing method using interstrand DNA photo cross-linking to covalently link the complementary strands of the original templates to the solid surface is also demonstrated.

Effect of fluorescent tags on translocation through nanochannels

Fluorinated coatings of solid surfaces are important for many applications ranging from corrosion resistance to low surface energy biological interfaces. We present a facile approach to coat solid-state surfaces directly from vapor phase without harsh chemical or plasma treatments. The coatings show nanostructures with high surface area, which is important for variety of surface functionalizations, for example, in molecule attachment and cell growth. The novel polymeric nanoporous film is achieved from the reaction and deposition of two molecules. The surface morphology and pore sizes of the coating on solid-state surfaces can be tuned with change in concentration of monomers in a simple reaction chamber. The X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy analyses show organic nature of the coating. Cell growth studies are done to gauge biocompatibility and adsorption of proteins and cells. The approach can be used to coat, functionalize, and treat nano- and microstructures for a variety of applications with minimal chemical footprint.

Nano-scale biosensors

The fluorescent tagging of biomolecules can have substantial effects on the charge distribution and translocation of the molecules through nanochannels. We show that the diffusion and calculated flux of translocating protein molecules through nanochannels are strong functions of the tags used. The size of the nanopore channels of a membrane also affect whether the channels provide facilitated transport or act just like affinity chromatography. These findings have important implications on micro/nanofluidic based biophysical studies that greatly discount the effects of tagged dyes on molecular transport and their mechanics.