This project is aimed to modify a leucyl-tRNA synthetase (LeuRS) to incorporate fluorescent amino acids into proteins to produce fluorescent proteins in living cells. Fluorescent proteins are useful because they are easily analyzed and tracked in living organisms. In a small scale, we successfully prepared the library of LeuRS variants in which five amino acids are randomized in the leucine-binding site of a functional LeuRS without its editing domain. Currently, we are working on a large scale production of viable bacterial cells that cover the whole diversity of library (at least 34 million different LeuRS molecules). Initially, we attempted two-step process in which an N-terminal library fragment (for two randomized amino acids) is generated first and a C-terminal fragment (for three randomized amino acids) is added later. However, this two-step cloning process did not produce enough viable cells to cover all the possible variants. In a new approach, a complete library of LeuRS will be produced by overlapping extension PCR and introduced to E. coli in a single step to ensure highest possible transformation efficiency. Consequently, the library of LeuRS variants will be subject to a genetic selection experiment to obtain LeuRS variants that incorporate only fluorescent amino acids into proteins.

Diffusiophoresis is the migration of a relatively large particle (e.g., protein, polymer, nanoparticle) induced by a gradient of salt concentration. The salt-induced diffusiophoresis of lysozyme, a model protein, at pH 4.5 and 25 °C was examined as a function of salt concentration for three chloride salts: NaCl, KCl and MgCl2. Diffusiophoresis coefficients were theoretically extracted from experimental multicomponent diffusion data by applying irreversible thermodynamics. A selected mass-transfer process was theoretically examined to show that concentration gradients of MgCl2 produce significant lysozyme diffusiophoresis. The dependence of lysozyme diffusiophoresis on salt nature was theoretically examined and linked to protein charge. The effect of salt type on hydrogen-ion titration curves was experimentally characterized to understand the role of salt nature on protein charge. Our findings indicate that diffusiophoresis may be exploited for diffusion-based separation of proteins in the presence of salt concentration gradients and for the enhancement of protein adsorption onto solid surfaces relevant to biosensing applications.

The randomization of 11 bases in the theophylline-binding domain generated a library containing millions of different theophylline riboswitch variants. The dual genetic selection of this molecular library successfully led to the identification of a caffeine-specific synthetic riboswitch. When a chloramphenicol-resistance gene was expressed under control of this caffeine riboswitch, E. coli cells showed chloramphenicol resistance only in the presence of caffeine. For a colorimetric or fluorescence assay, the caffeine riboswitch gene was inserted upstream of the B-galactosidase (LacZ) or green fluorescence protein (GFP) gene, respectively. When tested with various concentrations of caffeine, the enzymatic activity of LacZ or the fluorescence intensity of GFP was proportional to the amount of caffeine, clearly indicating the caffeine-dependent gene regulation by the caffeine riboswitch. The caffeine synthetic riboswitch can be further developed as a biosensor to detect caffeine in complex biological samples such as urine and blood.

Abacavir or Ziagen, is an antiretroviral medicine that is used in conjunction with other
medicines to treat HIV. Although it is not a cure, it has been clinically proven to be
effective in diminishing the rate of HIV replication. The synthetic process of creating
Abacavir is both timely and costly, so therefore a new synthetic process has been
created to generate a chemical analog (specifically a triazine derivative) that is cheaper
to produce that can be if not potentially more chemically effective than Abacavir. Once
the analog is produced, a series of analytical tests will be done on a micro organismic
level to determine if the analog is both effective and safe enough to be used in human
clinical studies further down the road.

The pyrrolophenanthridone alkaloid pratosine is a natural product related to hippadine, which is known to be a powerful but reversible inhibitor of spermatogenesis in rats. Hippadine has also shown cardiovascular as well as anticancer activity. Given the structural similarities between the two molecules, it is expected that pratosine and hippadine will demonstrate similar biological effects. Our work toward a laboratory synthesis of pratosine will facilitate large-scale production thus affording sufficient quantities of the material for a complete pharmacological study of its properties. Although we have a synthetic plan for preparing pratosine, several reactions have failed due to solubility problems. This research focuses on solving these problems by using an alternate starting material. The commercially available compound vanillin, which is extracted from vanilla beans, is a simple and inexpensive aldehyde with an appropriate structure for attaching other groups that should improve the solubility properties of several of the synthetic intermediates. Our goal is to find a specific substituent that will provide the required characteristics but which can also be removed later to generate the final product.