In sperm chromatin, DNA exists in a highly condensed state reaching a final volume roughly twenty times that of a somatic nucleus. For the vast majority (>90%) of sperm DNA in mammals, somatic-like histones are first replaced by transition proteins which in turn are replaced by arginine-rich protamines. This near crystalline organization of the DNA in mature sperm is thought crucial for both the transport and protection of genetic information since all DNA repair mechanisms are shut down. Recent studies show that increased DNA damage is linked to dysfunctions in replacing histones with protamines resulting in mispackaged DNA. This increased DNA damage correlates not only to infertility but also impacts normal embryonic development. This damage is currently poorly characterized, but is known to involve oxidative base damage by reactive oxygen species (ROS). Using a variety of biophysical methods, the effect of DNA condensation by polycations on the on free radical access and DNA damage in the packaged state was investigated. In Chapter 2, gel electrophoresis was used to quantify the ability of free radicals to damage both unpackaged and packaged DNA. DNA condensed by polycations shows significantly reduced levels of indirect damage from exposure to free radicals. Combining previous work on packaging density, it is also shown that differences in the packaged state, even by a few Angstroms, can result in significantly different degrees of damage to the DNA. In Chapter 3, we investigate the effects of protamine concentration on the ability to condense and protect DNA. Insufficient protamination is known to be a potential source of protamine dysfunction in mammalian sperm chromatin. Using gel retardation assays and UV-Vis studies, we examined the ability for DNA to condense with protamine at varying nitrogen to phosphate (N:P) charge ratios. Initial results on damage as a function of N:P are also discussed. Future work will more quantitatively determine the interrelationship between DNA packaging densities and the resulting accessibility of DNA to reactive oxygen species (ROS).

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Electro-optic (EO) polymers are an attractive alternative to inorganic nonlinear materials. EO polymers with a Pockel's coefficient, r33, greater than 320 pm/V have been recently demonstrated. In addition to their high EO activity, EO polymers have the additional benefit that their dielectric constants at optical and millimeter wave frequencies are closely matched which allow for bandwidths which are limited only by the resistive losses of traveling wave electrodes. The amorphous nature of the host polymer makes heterogeneous integration of the materials on any substrate possible. The devices which will have the most immediate impact based on these recent materials developments are EO waveguide modulators. Performance benchmarks of less than 6 dB insertion loss, sub-volt Vpi and greater than 100 GHz bandwidth have been achieved separately however, the challenge of achieving all of these benchmarks in a single device has not yet been met.The aim of this dissertation is to optimize passive materials to achieve efficient in device poling of EO polymers, optimize the chromophore loading of the active polymers and to optimize waveguide modulators for device performance within a particular system, analog RF photonic links. These optimizations were done by defining figures of merit for the materials and modulators. This research strategy has led to significant improvements in poling efficiency as well as modulators with record low insertion losses which maintain a low half-wave voltage; on the order of 1 - 2 Volts. Using this optimization strategy and state of the art EO polymers, devices which meet or surpass the benchmark performance values in all categories are expected in the near future.

This research focuses on the development of a biomimetic photosynthetic energy transduction system which can convert the light energy into a transmembrane potential gradient. This potential gradient provides energy for transmembrane proton pumping, which can be detected potentiometrically and/or spectroscopically through the changes in the optical and electrochemical properties of conductive polymers that supports a lipid bilayer. To achieve this goal, there were two major objectives: 1) Development of a pH sensitive, conducting polymer-based thin film platform as a suitable interface to couple a planar lipid membrane to an ITO electrode and as a pH transducer to detect transmembrane proton motive force (pmf). 2) Construction of an ionophore-aided, transmembrane proton transport model system in a planar supported lipid membrane.Toward the first objective, two different approaches have been used: a) to create a conducting polymer thin film, composed of alternating layers of poly(aniline) PANI and poly(acrylic acid) PAA on an ITO-coated, planar glass substrate. The electroactivity in a neutral environment and the pH dependence of the self-assembled (SA) PANI/PAA multilayer thin films were demonstrated both electrochemically and spectroscopically. Additionally, (PANI/PAA)2 films were shown to be compatible with PSLB. The polymer cushion supported lipid bilayer was found to be highly impermeable to protons, as demonstrated by the blockage of the pH response of the PANI film underneath the lipid membrane. b) to create a PANI nanowire/sol-gel hybrid thin film on an ITO-coated, planar glass substrate. Electrochemical growth of PANI nanowires through a porous sol-gel matrix was demonstrated. The PANI nanowire/sol-gel hybrid thin film with a sol-gel capping layer was found to respond to pH both potentiometrically and spectroscopically and a uniform lipid membrane was formed on the capping layer.To achieve the second objective, a ΔpH-driven transmembrane proton transport model system supported by a PANI nanowire doped sol-gel/ITO substrate with a sol-gel capping layer was developed. Ionophore valinomycin and CCCP were incorporated into the planar supported lipid bilayer (PSLB). Driven by a transmembrane pH gradient, an enhanced rate of proton transport with a proton permeability ca. 3 orders of magnitude higher than that of the lipid membrane without ionophores was demonstrated.

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A new hydrophobic hybrid silica film was synthesized by introducing one silicon precursor (as modifiers) into another precursor (network former). Hybrid films have improved properties. Hydrolysis and condensation of dimethyldiethoxysilane (DMDES) (solvent (EtOH) to DMDES molar ratio R = 4, water to DMDES molar ratio r = 4, 0.01 N HCl catalyst) was analyzed using high-resolution liquid 29Si NMR. It was found that after several hours, DMDES hydrolyzed and condensed into linear and cyclic species. Films from triethoxyfluorosilane (TEFS) have been shown to be promising interlayer dielectric materials for future integrated circuit applications due to their low dielectric constant and high mechanical properties (i.e., Young's modulus (E) and hardness (H)). Co-condensing with TEFS, linear structures from DMDES hydrolysis and condensation reactions rendered hybrid films hydrophobic, and cyclic structures induced the formation of pores. Hydrophobicity characterized by contact angle, thermal stability by thermogravimetric analysis (TGA), Fourier transform Infrared spectroscopy (FTIR), contact angle, and dynamic secondary ion mass spectroscopy (DSIMS), dielectric constant determined by impedance measurement, and mechanical properties (E and H) determined by nanoindentation of TEFS and TEFS + DMDES films were compared to study the effect of DMDES on the TEFS structure. Hybrid films were more hydrophobic and thermally stable. DMDES incorporation affected the dielectric constant, but showed little enhancement of mechanical properties.