The study of biology has undergone a fundamental change due to advancements in genetic engineering, DNA synthesis and DNA sequencing technologies. As opposed to the traditional dissective mentality of discovering genes via genetics, describing genetic behaviors through biochemistry, and then drawing diagrams of functional networks, researchers now have the potential (albeit limited) to construct novel biological molecules, networks, and even whole organisms with user-defined specifications. We have engineered novel catalytic DNAs (deoxyribozymes) with the ability to 'read' an input DNA sequence and then 'write' (by ligation) a separate DNA sequence which can in turn be detected sensitively. In addition, the deoxyribozymes can read unnatural (synthetic) nucleotides and write natural sequence information. Such simple nanomachines could find use in a variety of applications, including the detection of single nucleotide polymorphisms in genomic DNA or the identification of difficult to detect (short) nucleic acids such as microRNAs. As an extension of in vitro biological engineering efforts, we aimed to construct novel signal transduction systems in vivo. To this end, we used directed evolution to generate a catalytic RNA (ribozyme) capable of creating genetic memory in E. coli. In the end we evolved an RNA which satisfied the conditions of our genetic screen. Rather than maintaining genetic memory, however, the RNA increased relative cellular gene expression by minimizing the translational burden it imposed on the host cell. Interestingly, detailed mutational analysis of the evolved RNA led us to new studies on the relationship between ribosome availability and stochasticity in cellular gene expression, an effect that had frequently been alluded to in the literature, yet never examined. We have also taken a more canonical approach to the forward engineering of biological systems with unnatural behaviors. To this end, we designed a protein-based synthetic genetic circuit that allows a community of E. coli to function as biological film, capable of capturing and recapitulating a projected light pattern at high resolution (theoretically 100 mexapixels). The ability to control bacterial gene expression at high resolution could be used to ‘print’ complex bio-materials or deconvolute signaling pathways through precise spatial and temporal control of regulatory states. / text

Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, alpha-Synuclein can be found localized at synaptic terminals where it is hypothesized to be involved in vesicle trafficking and recycling. However, its biochemical profile reveals a hydrophobic region that, once subjected to insult, initiates an aggregation cascade. Oligomeric species—products of the aggregation cascade—demonstrate marked neurotoxicity in dopaminergic neurons and illustrate migratory potential to neighboring healthy neurons, thereby contributing to progressive neurodegeneration. The current golden standard for PD diagnostics is a highly qualitative system involving a process-by-elimination with accuracy that is contingent upon physician experience. This, and a lack of standardized clinical testing procedures, lends to a 25% misdiagnosis rate. Even under circumstances of an accurate PD diagnosis, the only treatment options are pharmacologics that have a wide range of adverse side effects and ultimately contribute to systemic metabolic dysfunction. Thus, the research presented in this thesis seeks to overcome these current challenges by providing (1) a quantitative diagnostic platform and (2) a biomolecular therapeutic, towards oligomeric alpha-Synuclein. Aim 1: serves as a proof-of-concept for the use of catalytic nucleic acid moieties, deoxyribozymes and aptamers, to quantify alpha-Synuclein in a novel manner and explore the ability to detect oligomeric cytotoxic species. The cost-effective nature of these sensors allows for continued optimization. Aim 2: serves to establish a potential therapy that can abrogate alpha-synuclein oligomerization and toxicity through use of a modified Protein Disulfide Isomerase (PDI) peptide when introduced to live cells treated to simulate pre-parkinsonian pathology.