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The research theme of the Center for BioOptical Nanotechnology (BON) focuses on uncovering the functional nanostructures of biology and creating new function by exploring chemical space. Some of these approaches take advantage of a set of very sophisticated optical instruments involved both in the analysis of natural samples and the synthesis and analysis of chemically diverse libraries from which new molecular functionality can be selected or evolved. A hallmark of the center’s competency in general is the ability to create and explore chemical diversity.

With this as a foundation, we are directly embedded in three of the major Biodesign Institute-wide projects currently underway:

Creation of a table-top diagnostic platform for monitoring of a broad spectrum of health indicators (Doc-In-a-Box): If we are to revolutionize medicine, both functionally and economically, we must start by treating disease in its earliest stages. This will require new diagnostic platforms that sense the bodies response to infection or disease states long before classical symptoms are present. Our role is in the development of sensitive and specific molecular recognition elements or systems through the exploration of chemically diverse libraries.

Development of Sustainable Energy Sources: Our current dependence on fossil fuels has political, economic and environmental consequences that are not sustainable. We are exploring chemical space for the development of catalysts that convert carbon-neutral sources of energy into chemical fuels.

Synthetic Biology: We have a major effort in the creation and generation of new molecular recognition elements, structural elements (protein folds) and catalytic elements that could be readily incorporated into synthetic biological systems. Here we interface with other groups that are developing the host organisms and creating the synthetic genes.

Chemical Diversity:
A major competency of BON is in the creation, generation and searching of chemical space. We have multiple methods for accomplishing this. We are currently using the technique of mRNA display to search libraries of peptides and proteins as large as 10^13-14 and select those with the desired traits. We have also developed the capability to synthetically create libraries on the order of 10⁶ peptides or other synthetic chemical structures using the kind of light directed synthesis that is used in the generation of DNA chips. We have generalized the chemistry to be used for other kinds of compounds that can be constructed from building block components.

Ultrafast Laser Spectroscopy and Microscopy:
BON members manage ASU’s ultrafast laser spectroscopy and microscopy facility, and this represents another of our key competencies. The facility is well equipped with state-of-arts ultrafast lasers and detection systems, including 2 transient absorption spectrometers, a kilohertz femtosecond up-conversion apparatus, a single photon counting system, a streak camera fluorescence FLIM spectrometer, 2 microscope systems for single molecule spectroscopy. Here it is possible to perform femtosecond timescale spectroscopy in many different forms (absorbance, fluorescence, etc.) both in solution, on surfaces, in living cells or tissues and at the single molecule level.

Synthetic Antibodies (Synbodies):
We are collaborating with the Biodesign Institute's Center for Innovations in Medicine to apply our chemical diversity capability to the production of synthetic antibodies. Here, we use various methods to search chemical space for weak binders and then orient them to create systems with high affinity and specificity, mimicking antibody function.

Generation of de novo Catalysts using mRNA Display:
mRNA display technologies are also being used to evolve new protein folds and functions in vitro. Recently, an entirely de novo protein that catalyzes the synthesis of adenosine 5’-pentaphosphate from ATP has been created generated in Prof. Chaput’s lab. They are continuing to optimize this approach and develop other, novel artificial enzymes.

Creation Generation of Catalysts for Energy Conversion using Patterned Synthesis:
We have utilized our directed synthetic chemical diversity platform (described above) to create tens of thousands of potential electro-catalysts directly on electrodes. We are synthesizing libraries of metal binding peptides to search for new water splitting catalysts that mimic the activity of the oxygen evolving complex of photosystem II in collaboration with ASU professors James Allen and JoAnn Williams of the chemistry and biochemistry department and Trevor Thornton of the electrical engineering department. In collaboration with Combimatrix, we are also developing high throughput electrosynthesis methodologies as a potential platform for library generation.

Optically Directed Cellular Evolution:
We are also extending our optical patterning of chemistry to cells. We have developed a means of patterning cell growth on a surface using the photolyase repair system to affect light activated rescue from cell death. This makes it possible to observe a large number of cells on a surface and then select a subset to allow to grow while killing the remainder.

The Role of Protein Dynamics in Photosynthetic Electron Transfer:
We have a fundamental program in the study of the ultrafast electron transfer reactions of bacterial photosynthetic reaction centers. This work utilizes ASU’s ultrafast laser facility to follow these electron transfer reactions on the femtosecond to picosecond timescale. Recently, we have discovered that the kinetics of electron transfer in this system is directly limited by protein motion and we are continuing to explore how this complex protein dance serves to mediate biochemical reaction.

Discovering and Characterizing Novel, Non-natural Protein Folds:
Another area of fundamental study in BON is exploring the realm of non-natural protein folds. Just how well has nature explored the possible structural elements that make up proteins? Has it found all the useful ones, most of them, or very few of them? Using mRNA display and novel selection methodologies, John Chaput’s lab has uncovered entirely new folds never seen in nature and has shown they can function in catalysis.

Analyzing the Structure and Dynamics of Chromatin:
The critical role of chromatin structure in controlling gene expression is becoming more and more evident. Of particular interest to us is the dynamics of the DNA/protein interaction in the nucleosome, the most elemental chromatin structural component. We are using single molecule spectroscopy and AFM to explore the structure and dynamics of these particles as a function of DNA sequence and under the influence of transcription factors that affect gene expression. This work is done in collaboration with the Biodesign Institute's Center for Single Molecule Biophysics (Stuart Lindsay) and with Dennis Lohr in ASU's chemistry and biochemistry department.

Directed Molecular Assembly of Nanoscale:
John Chaput’s laboratory is collaborating with Hao Yan in the Center for Single Molecule Biophysics to functionalize self-assembled nanostructures with peptides and proteins. Together, they have developed a new technology called Nanodisplay that allows them to position polypeptides at specific locations on synthetic DNA nanostructures. These polypeptides can then be used to study different protein-protein interactions or template the synthesis of additional molecules, such as inorganic nanocrystals that could be used to develop new electronic materials.