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Center of Excellence

Synthesis and characterization of "safe" fluorescent stains for DNA

For decades, the stain used to visualize DNA bands after gel electrophoresis has been ethidium bromide. However, the use of this stain is not without serious drawbacks: 1) the compound itself is not mutagenic, but there is good evidence that its metabolites are; and 2) in many states, ethidium bromide solution is regulated as hazardous waste, which highlights another problem with this stain. We are disigning fluorescent compounds that can be used as safe replacements for ethidium bromide. These stains will be based on the 4-amino-1,8-naphthalimide fluorophore, which is known to be non-mutagenic, and that we have found to be stable to storage for over a decade (two of our patented dyes have passed this mark). We are now designing a dye that should bind to the minor groove of the DNA, like the antimicrobial agent, netrospin, or to the major groove, like the nucleic acid stain, methyl green.

 The goal of this chemical education/scholarship of teaching and learning project is to investigate whether substituting a single inquiry-based experiment for a traditional experiment in first semester general chemistry at UWEC leads to a measureable improvement in student performance. 

Undergraduate student researchers are an integral part of this research project by processing participant responses to pre- and post-treatment surveys and academic assessments as well as analyzing quantitative data using IBM SPSS software. Students can also assist in writing and revising manuscripts and proposals. Students working on this project benefit from an interdisciplinary research experience combining chemistry, education and statistical methods for data analysis.

Both projects are geared towards undergraduate students (freshman through senior), will provide opportunities for students to present their results at local and national conferences, and will enable students to be co-authors in peer-reviewed publications. To ensure a positive research experience over the academic year, I meet individually with students on a weekly basis to discuss current results and troubleshoot experiments. All research students and I will have biweekly group meetings to discuss and decode relevant research articles to get students to be able to read scholarly articles and increase critical thinking skills. Students will present their research results to each other and to other research groups in the chemistry department to gain presentation skills and to promote a community of scientists at UW-EC.

Our research is concerned with the structural and energetic properties in “molecular complexes”; associations (strong weak or intermediate) between two otherwise stable molecules. Over the long term, we have sought to identify and characterize systems that undergo major structural changes in response to condensed-phase environments (e.g., gas-phase to solid or solution), and the primary effect is a dramatic shortening of the donor-acceptor bond. This is depicted at the right for two nitrile - BF3 complexes, in which the B-N distances contract from 2.01 or 2.47 Å to about 1.65 Å while transitioning from the gas phase to the solid state. Our work has been primarily concerned with the effects of bulk condensed-phase media (e.g., solvents, and so-called “noble gas matrices” – cryogenic samples of solid neon, argon, or neon), and we have obtained insight into structural changes via shifts in vibrational frequencies measured by infrared spectroscopy. In addition, we gain key insight from quantum-chemical computations (computer simulations of the bonding). From these we obtain structures and frequencies for the gas-phase complexes, and most importantly, energy profiles along the donor acceptor bond (for both the gas-phase complex and in hypothetical solvents). These data have enabled us to propose a generalized mechanism for medium-induced structural change.

Going forward, we will pursue new directions by following one specific avenue motivated by a practical consideration, and also engage in an overall broadening our scope in an effort to identify new types of systems peculiar with structural and energetic properties like those described above. Just recently, we have been investigating nitrile (-CN) complexes of Group IV (M=Si, Ge, Ti) acceptors (e.g., CH3CN–SiF4) and we have demonstrated that we can modulate the strength of the donor-acceptor interaction and enhance the extent of condensed-phase structural change by altering the atom(s) on the end of the CH3CN subunit (e.g., FCH2CN–GeF4). Now, we will turn to derivatives the of the MX4 acceptors (M=Ge, Si; X=F, Cl) in which we will replace one of the X atoms with an organic group (R=CH3-, or C6H5-). If we can similarly optimize the condensed-phase response in these systems, we may have identified a route to a new class of molecular machines. Because both the nitrile (-CN) and MX4 (or MX3R) subunits have bonds that point directly opposite the donor-acceptor linkage, this could enable one to embed this structural motif into a larger structure of some type (e.g., a liquid crystal, or molecular wire). This process is depicted at the right. The general idea is that these structures could be exploited to exert a force along the length of that structure, which would open up this chemistry to a variety of electro-mechanical applications.

Our understanding of distribution of atmospheric pollutants is constrained by the kinds of platforms available for monitoring small quantities of trace gases. Studies on the air quality around Lake Michigan have shown steep gradients across the meso-scale meteorological process of the lake breeze front which passes over land on a daily basis. Our understanding of high ozone near Lake Michigan can be better understood by determining vertical mixing of ozone which requires sending sensors aloft. The advancements of both small Unmanned Aerial Vehicles (UAV) and smaller ozone monitors has paved the way for designing and implementing a sensor package on a remotely piloted vehicle.

Students in my research group have been working on integrating a sensor package that can measure temperature, humidity, wind vectors and ozone from a UAV.This project requires students to calibrate sensors, program and assemble microcomputers that serve as small datalogging systems, develop a working knowledge of UAV control systems and remote data streaming so as to design a platform that will be robust. We work on this project with Dr. Joe Hupy from the Geography department for prototyping and testing.

 

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