Quantitative evaluation of oligonucleotide surface concentrations using polymerization-based amplification

Quantitative evaluation of minimal polynucleotide concentrations has become a critical analysis among a myriad of applications found in molecular diagnostic technology. Development of high-throughput, nonenzymatic assays that are sensitive, quantitative and yet feasible for point-of-care testing are thus beneficial for routine implementation. Here, we develop a nonenzymatic method for quantifying surface concentrations of labeled DNA targets by coupling regulated amounts of polymer growth to complementary biomolecular binding on array-based biochips. Polymer film thickness measurements in the 20–220 nm range vary logarithmically with labeled DNA surface concentrations over two orders of magnitude with a lower limit of quantitation at 60 molecules/μm2 (∼106 target molecules). In an effort to develop this amplification method towards compatibility with fluorescence-based methods of characterization, incorporation of fluorescent nanoparticles into the polymer films is also evaluated. The resulting gains in fluorescent signal enable quantification using detection instrumentation amenable to point-of-care settings

Reaction engineering of radical-mediated polymerizations at surfaces and interfaces

Polymerization reactions initiated at a surface or interface constitute a class of problems in which the reaction rates are spatially inhomogeneous due to concentration gradients that inevitably arise, thereby requiring an understanding of the coupled reaction behavior and mass transport processes to be able to control the material properties. This thesis is focused on understanding radical-mediated interfacial polymerizations initiated by an enzyme-mediated redox system, which represents a unique design paradigm to form conformal polymeric coatings on 3D substrates. In particular, glucose oxidase catalyzes the reaction between Beta-D-glucose and oxygen, producing hydrogen peroxide, which in the presence of ferrous ions (Fe2+), generates hydroxyl radicals that are highly efficient for initiating (meth)acrylate polymerization. Interfacial coatings on hydrogel structures using this technique is realized by immersing a glucose-swollen hydrogel into an aqueous solution consisting of monomer, ferrous ion (Fe2+) and glucose-oxidase. The hydrogel serves as a template that spatially confines glucose prior to polymerization. Thus, the locus of the enzymatic reaction involving glucose is initially at the hydrogel boundary but is subsequently delocalized due to the rapid diffusion of glucose into the bulk media. This methodology represents the first instance of the use of interfacial radical polymerization with a non-stationary locus of the initiation reaction. Therefore, the establishment of design principles derived from understanding the reaction engineering aspects of this technique can immensely benefit the utilization of this technique as a material fabrication tool with a variety of monomers and initiating strategies. This thesis is focused on understanding the factors that influence the reaction delocalization to achieve desired properties of the interfacial film such as thickness, permeability and structure. The relationship between the interfacial film thickness and immersion time, influence of species concentration on coating thickness and the kinetics of enzyme encapsulation by the polymerization front were experimentally investigated to understand the interplay of reaction behavior and mass transport processes. A mathematical model describing the complex coupled reaction-diffusion process through the fundamental steps was developed. The model predictions of the variation of thickness as a function of time and the influence of species concentration on the interfacial film thickness agreed well with the experimental results. In addition, the model was able to characterize interfacial film properties that are difficult to investigate experimentally such as the evolution of polymer density gradients in the coating as well as the factors that can be used to manipulate them. Lastly, the glucose oxidase-mediated redox initiation was engineered to fabricate core-shell microparticles by interfacial polymerization. This investigation broadens the applicability of this technique besides providing a simple reaction engineering tool to tune the surface properties at the micrometer scale