Due to the considerable challenges for reliable and expedient detection of virulent vegetative bacterial, bacterial endospores and other hazardous biological agents, accidental exposure is a principal cause of fatality due to wound infection or slow diagnosis. Staining techniques, due to their simplicity, form a set of important tools for pathogen monitoring and control. The staining assays, such as immunoassays, however, provide only Boolean information: i.e., stain vs. does not stain. As a result, only the species being sought may have a chance to be identified, leaving key determining factors for the diagnosis quite susceptible to human error.

Our principle motivation for this project is to expand the current analytical techniques beyond their Boolean nature, and to address the apparent need for simple, expedient and inexpensive assays. We describe the development of an assay system based on the dynamics of fluorophore uptake that will serve as a robust platform for detection of both vegetative and endospore bacterial contaminants. The kinetics of fluorescence staining depends on the coatings and protein content, which reflect the species phenotype. Hence, such kinetic measurements gain access to genetic information, in less than a minute, without conducting amplification procedures such as PCR.

We have demonstrated for the first time that the kinetics of emission enhancement, caused by cell uptake of fluorophores, provides statistically significant discernibility between different and closely related vegetative bacteria and bacterial endospore species respectively. We observed that the time course of the fluorescence signal provides a unique species-specific signature that can prove indispensible for the identification of dangerous and life-threatening spores.

Visualizing the dynamics of nanometer-sized macromolecules presents considerable challenges that stem from non-specific interfacial interactions between the micrometer-sized probes used in those visualizations; as a result, advances in single-molecule protein interaction studies have not been extensively explored. The first part of my doctoral research sought to address this limitation by determining the capability of different surface coatings of polyethylene glycol to suppress non-specific interfacial interactions. Concurrently, we developed a magnetic puller setup capable of attaining forces between hundreds of femto-newtons and approximately one hundred pico-newtons. Magnetic pullers allow for probing thousands of single-molecule events simultaneously, providing considerable advantages over traditional magnetic tweezers. The design and application of thermally-regulated electromagnetic pullers, capable of attaining forces in the fN-to-nN dynamic range, is essential for single-molecule proteomic studies.

By applying relatively weak pulling forces (e.g., ~1.2 pN), we examined the efficacy of removing polystyrene microbeads from glass surfaces. When either the glass or the beads were not PEGylated, the adhesion between them was substantial. Furthermore, when the PEG polymers were too short or too long, we still observed substantial adhesion of the beads to the glass surfaces. Coatings of PEG with molecular weights ranging between 3 and 10 kDa proved critical for suppressing the adhesion.

My research also focused on investigating anthranilamide derivatives, as bioinspired electrets, for improving the efficiency of interfacial charge transfers that are essential for solar-energy applications. A substantial portion of these studies were directed toward understanding the fundamental electrostatic properties of amides, with a focus on carboxyamides. Carboxyamides are small polar groups that, as peptide bonds, constitute the principle structural components of proteins. The electric fields from the amide dipoles govern the electrostatic properties and activity of proteins. Therefore, we undertook a detailed study of the medium dependence of the molar polarization and of the permanent dipole moments of amides with different states of alkylation. The experimentally-measured and theoretically-calculated dipole moments of the solvated amides both manifested a dependence on the media polarity. Specifically, an increase in solvent polarity led to a subsequent increase in both the measured and calculated permanent dipole moments of the solutes. We attributed the observed enhancement of the amide dipoles to the reaction fields in the solvated cavities.

Our bioinspired approach and usage of amide dipoles as a principal field source allowed us to develop molecular electrets based on oligo-anthranilamides. Electrets, and specifically, dipole-polarization electrets, are the electrostatic analogues of magnets, i.e., they are systems with codirectionally ordered permanent electric dipoles. The de novo designed anthranilamides are bioinspired in the sense that, similar to protein helices, they possess permanent intrinsic dipoles resultant from the ordered orientation of amide and hydrogen bonds. Unlike the helices, however, these bioinspired oligomers have the redox properties necessary to mediating long-range charge transfer along their backbones.

Overall, the most significant contributions from my doctoral research are: (1) the optimization of polyethylene glycol surface coatings for suppressing non-specific interfacial interactions; (2) the development of an electromagnetic puller setup with a wide dynamic force range capable of simultaneously probing thousands of single-molecule protein interactions; (3) the characterization of the effects of solvent polarity on the dipole moments of amides; and (4) the demonstration of the ability of organic materials with dipole moments to rectify photoinduced charge transfer.