M13 filamentous bacteriophage has been used as a biotemplate for the nucle- ation of materials. Phage is an ideal and diverse scaffold with its large aspect ratio and ability to display biomolecules to bind a range of targets. To form more complex patterned materials, interactions between the phage must be specific and reliable. We develop a phage labeling method using sortase enzymes to create multi-phage nanostructures. We exploit two sortases and functionalize the N-termini of the pIII, pIX, and pVIII proteins with small and large moieties. For the pVIII, we show a 100 fold improvement in display of GFP molecules on the phage surface. Taking advantage of orthogonal sortases, we simultaneously label two capsid proteins on a single phage particle. Using these N-terminal labeling techniques, we demonstrate fluorescent staining of cells and construct a lampbrush phage structure linking the pIII of one phage to the pVIII of another using a biotin-streptavidin linkage. To further expand our labeling repertoire, C-terminal sortase labeling of phage was pursued. To achieve this goal, we transfer a loop structure from cholera toxin to pIII and label it with a fluorophore and a multi-domain protein. With this archi- tecture, we form end-to-end dimers using sortase to conjugate the loop structure to phage containing the nucleophile motif. Lastly, we investigate DNA hybridization as a method for crosslinking phage. Using sortase, we label the pVIII on two sets of phage: one with ssDNA and the other with a complementary DNA oligonucleotide. We anneal these phages together and observe phage networks that are dispersed by heat and reform upon cooling.

The successful fabrication and characterization of two chemiresistive platforms for biomolecule detection was demonstrated by this work. The Si/Silica based single walled nanotube thin film (SWNTTF) platform was developed to understand the effect of device geometry on pH and M13 bacteriophage sensing capabilities as well as the underlying mechanisms governing SWNTTF chemiresistive biosensors. The dominant mechanism of sensing switched from direct chemical doping to electrostatic gating when the target analyte changed from H+/OH- ions in pH testing to whole viruses. The experimental limit of detection for M13 for this platform was 0.5pM and an increased sensitivity as well as variability was observed in devices with smaller channel widths. Preliminary device calibration was completed in order to correlate a resistance response to a bulk M13 concentration. The polyethylene terephthalate (PET) based SWNTTF platform was developed to demonstrate the commercial potential of SWNTTF chemiresistive biosensors by detecting relevant concentrations of brain natriuretic peptide (BNP) on economically viable substrates. The pH response of these chemiresistors confirmed that chemical doping was the cause for resistance change in the SWNTTFs. The preliminary results demonstrated successful BNP detection at 50pg/mL using both aptamers and antibodies as recognition elements. Using SWNTTFs as the transducing element of chemiresistors allowed for further understanding of electrical mechanisms of sensing as well as achieving sensitive, real-time and reproducible electrical virus and biomolecule detection. Although these platforms do not achieve ultrasensitive limits of detection, they demonstrate the commercial potential of platforms using SWNTTFs as the transducing element of electrical biomolecule sensors.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Richard 'Dick' Hesse / Carol Wyatt / Over the last two decades molecular laboratory techniques have enabled researchers to investigate the infection, replication and pathogenesis of viral disease. In the early eighties, Dr. George Smith developed a unique system of molecular selection. He showed that the fd bacteriophage genome could be manipulated to carry a sequence of DNA coding for a protein not contained in the phage genome. Infection of the recombinant bacteriophage or phagemid into a specific strain of the bacterium, Escherichia coli, produced progeny phage with the coded protein displayed as a fusion with the phage's coat protein. Antibody phage display utilizes the same technology with the DNA encoding an antibody fragment. The DNA insert can carry the information to produce either a single chain variable fragment (scFv) producing the heavy chain variable and light chain variable (VH-VL) portion or a Fab fragment which also contains the heavy chain constant 1 with the light chain constant (CH and CL) portion of an antibody. Screening an antibody phage display library has the possibility of producing an antibody not produced in the normal course of immune selection. This decade also saw the emergence of a viral disease affecting the porcine population. The Porcine Reproductive and Respiratory Syndrome virus (PRRSV) has been one of the most costly diseases affecting the pig producer. Molecular investigations found that PRRSV is a single, positive-stranded RNA virus which codes for five structural and 12-13 nonstructural proteins producing an enveloped, icosahedral virus. An interesting characteristic of PRRSV is the ability to produce infective progeny with genomic deletions, insertions and mutations within the nonstructural protein 2 (nsp2). With this knowledge, many researchers have produced marker vaccines containing fluorescent tags with the hope of developing a DIVA (Differentiate Infected from Vaccinated Animals) vaccine. In my Master‟s studies, I studied the techniques of antibody phage display technology and how to apply these methods to producing scFvs which recognize a recombinant PRRSV nsp2 fragment protein and the native protein during infection of MARC-145 cells.