Nonlinear optics and wavelength translation via cavity-optomechanics

The field of cavity-optomechanics explores the interaction of light with sound in an ever increasing array of devices. This interaction allows the mechanical system to be both sensed and controlled by the optical system, opening up a wide variety of experiments including the cooling of the mechanical resonator to its quantum mechanical ground state and the squeezing of the optical field upon interaction with the mechanical resonator, to name two.

In this work we explore two very different systems with different types of optomechanical coupling. The first system consists of two microdisk optical resonators stacked on top of each other and separated by a very small slot. The interaction of the disks causes their optical resonance frequencies to be extremely sensitive to the gap between the disks. By careful control of the gap between the disks, the optomechanical coupling can be made to be quadratic to first order which is uncommon in optomechanical systems. With this quadratic coupling the light field is now sensitive to the energy of the mechanical resonator and can directly control the potential energy trapping the mechanical motion. This ability to directly control the spring constant without modifying the energy of the mechanical system, unlike in linear optomechanical coupling, is explored.

Next, the bulk of this thesis deals with a high mechanical frequency optomechanical crystal which is used to coherently convert photons between different frequencies. This is accomplished via the engineered linear optomechanical coupling in these devices. Both classical and quantum systems utilize the interaction of light and matter across a wide range of energies. These systems are often not naturally compatible with one another and require a means of converting photons of dissimilar wavelengths to combine and exploit their different strengths. Here we theoretically propose and experimentally demonstrate coherent wavelength conversion of optical photons using photon-phonon translation in a cavity-optomechanical system. For an engineered silicon optomechanical crystal nanocavity supporting a 4 GHz localized phonon mode, optical signals in a 1.5 MHz bandwidth are coherently converted over a 11.2 THz frequency span between one cavity mode at wavelength 1460 nm and a second cavity mode at 1545 nm with a 93% internal (2% external) peak efficiency. The thermal and quantum limiting noise involved in the conversion process is also analyzed and, in terms of an equivalent photon number signal level, are found to correspond to an internal noise level of only 6 and 4 times 10x^-3 quanta, respectively.

We begin by developing the requisite theoretical background to describe the system. A significant amount of time is then spent describing the fabrication of these silicon nanobeams, with an emphasis on understanding the specifics and motivation. The experimental demonstration of wavelength conversion is then described and analyzed. It is determined that the method of getting photons into the cavity and collected from the cavity is a fundamental limiting factor in the overall efficiency. Finally, a new coupling scheme is designed, fabricated, and tested that provides a means of coupling greater than 90% of photons into and out of the cavity, addressing one of the largest obstacles with the initial wavelength conversion experiment.

Nuclear weak interaction rates during stellar evolution and collapse

Nuclear weak interaction rates, including electron and positron emission rates, and continuum electron and positron capture rates , as well as the associated v and –/v energy loss rates are calculated on a detailed grid of temperature and density for the free nucleons and 226 nuclei with masses between A = 21 and 60. Gamow-Teller and Fermi discrete-state transition matrix element systematics and the Gamow-Teller T^< →/← T^> resonance transitions are discussed in depth and are implemented in the stellar rate calculations. Results of the calculations are presented on an abbreviated grid of temperature and density and comparison is made to terrestrial weak transition rates where possible. Neutron shell blocking of allowed electron capture on heavy nuclei during stellar core collapse is discussed along with several unblocking mechanisms operative at high temperature and density. The results of one-zone collapse calculations are presented which suggest that the effect of neutron shell blocking is to produce a larger core lepton fraction at neutrino trapping which leads to a larger inner-core mass and hence a stronger post-bounce shock.

Characterization of the neural mechanisms supporting the implementation of cognitive control in human decision making

Humans are particularly adept at modifying their behavior in accordance with changing environmental demands. Through various mechanisms of cognitive control, individuals are able to tailor actions to fit complex short- and long-term goals. The research described in this thesis uses functional magnetic resonance imaging to characterize the neural correlates of cognitive control at two levels of complexity: response inhibition and self-control in intertemporal choice. First, we examined changes in neural response associated with increased experience and skill in response inhibition; successful response inhibition was associated with decreased neural response over time in the right ventrolateral prefrontal cortex, a region widely implicated in cognitive control, providing evidence for increased neural efficiency with learned automaticity. We also examined a more abstract form of cognitive control using intertemporal choice. In two experiments, we identified putative neural substrates for individual differences in temporal discounting, or the tendency to prefer immediate to delayed rewards. Using dynamic causal models, we characterized the neural circuit between ventromedial prefrontal cortex, an area involved in valuation, and dorsolateral prefrontal cortex, a region implicated in self-control in intertemporal and dietary choice, and found that connectivity from dorsolateral prefrontal cortex to ventromedial prefrontal cortex increases at the time of choice, particularly when delayed rewards are chosen. Moreover, estimates of the strength of connectivity predicted out-of-sample individual rates of temporal discounting, suggesting a neurocomputational mechanism for variation in the ability to delay gratification. Next, we interrogated the hypothesis that individual differences in temporal discounting are in part explained by the ability to imagine future reward outcomes. Using a novel paradigm, we imaged neural response during the imagining of primary rewards, and identified negative correlations between activity in regions associated the processing of both real and imagined rewards (lateral orbitofrontal cortex and ventromedial prefrontal cortex, respectively) and the individual temporal discounting parameters estimated in the previous experiment. These data suggest that individuals who are better able to represent reward outcomes neurally are less susceptible to temporal discounting. Together, these findings provide further insight into role of the prefrontal cortex in implementing cognitive control, and propose neurobiological substrates for individual variation.

Neuronal mechanism of state control in Drosophila melanogaster

The changes in internal states, such as fear, hunger and sleep affect behavioral responses in animals. In most of the cases, these state-dependent influences are “pleiotropic”: one state affects multiple sensory modalities and behaviors; “scalable”: the strengths and choices of such modulations differ depending on the imminence of demands; and “persistent”: once the state is switched on the effects last even after the internal demands are off. These prominent features of state-control enable animals to adjust their behavioral responses depending on their internal demands. Here, we studied the neuronal mechanisms of state-controls by investigating energy-deprived state (hunger state) and social-deprived state of fruit flies, Drosophila melanogaster, as prototypic models. To approach these questions, we developed two novel methods: a genetically based method to map sites of neuromodulation in the brain and optogenetic tools in Drosophila.

These methods, and genetic perturbations, reveal that the effect of hunger to alter behavioral sensitivity to gustatory cues is mediate by two distinct neuromodulatory pathways. The neuropeptide F (NPF) – dopamine (DA) pathway increases sugar sensitivity under mild starvation, while the adipokinetic hormone (AKH)- short neuropeptide F (sNPF) pathway decreases bitter sensitivity under severe starvation. These two pathways are recruited under different levels of energy demands without any cross interaction. Effects of both of the pathways are mediated by modulation of the gustatory sensory neurons, which reinforce the concept that sensory neurons constitute an important locus for state-dependent control of behaviors. Our data suggests that multiple independent neuromodulatory pathways are underlying pleiotropic and scalable effects of the hunger state.

In addition, using optogenetic tool, we show that the neural control of male courtship song can be separated into probabilistic/biasing, and deterministic/command-like components. The former, but not the latter, neurons are subject to functional modulation by social experience, supporting the idea that they constitute a locus of state-dependent influence. Interestingly, moreover, brief activation of the former, but not the latter, neurons trigger persistent behavioral response for more than 10 min. Altogether, these findings and new tools described in this dissertation offer new entry points for future researchers to understand the neuronal mechanism of state control.

Active interaction control for civil structures

This thesis presents a civil engineering approach to active control for civil structures. The proposed control technique, termed Active Interaction Control (AIC), utilizes dynamic interactions between different structures, or components of the same structure, to reduce the resonance response of the controlled or primary structure under earthquake excitations. The primary control objective of AIC is to minimize the maximum story drift of the primary structure. This is accomplished by timing the controlled interactions so as to withdraw the maximum possible vibrational energy from the primary structure to an auxiliary structure, where the energy is stored and eventually dissipated as the external excitation decreases. One of the important advantages of AIC over most conventional active control approaches is the very low external power required.

In this thesis, the AIC concept is introduced and a new AIC algorithm, termed Optimal Connection Strategy (OCS) algorithm, is proposed. The efficiency of the OCS algorithm is demonstrated and compared with two previously existing AIC algorithms, the Active Interface Damping (AID) and Active Variable Stiffness (AVS) algorithms, through idealized examples and numerical simulations of Single- and Multi-Degree-of Freedom systems under earthquake excitations. It is found that the OCS algorithm is capable of significantly reducing the story drift response of the primary structure. The effects of the mass, damping, and stiffness of the auxiliary structure on the system performance are investigated in parametric studies. Practical issues such as the sampling interval and time delay are also examined. A simple but effective predictive time delay compensation scheme is developed.

Interaction of aqueous inorganic orthophosphate and phosphate rock

An experimental study was made of the interaction of phosphate rock and aqueous inorganic orthophosphate, calcium, and hydroxyl ions. A model of the reaction was developed by observing electron diffraction patterns in conjunction with concentration changes of chemical components. The model was applied in explaining the performance of batch suspensions of powdered phosphate rock and packed columns of granular phosphate rock. In both cases the reaction consisted initially of a rapid nucleation phase that occurred in a time period of minutes. In the batch system the calcium phosphate nuclei then ripened into larger micro-crystals of hydroxyapatite, which eventually became indistinguishable from the original phosphate rock surface. During column operation the high supersaturation ratio that existed after the rapid nucleation phase resulted in a layer of small nuclei that covered a slowly growing hydroxyapatite crystal.

The column steady-state rate constant was found to increase with increasing temperature, pH, and fluoride concentration, and to decrease with increasing concentrations of magnesium sulfate, ammonium chloride, and bicarbonate ion.

An engineering feasibility study indicated that, based on economic considerations, nucleation of apatite on phosphate rock ore has a potential use as a wastewater phosphate removal treatment process.

Studies of the serotonin type 3A receptor and the chemical preparation of tRNA

This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT₃AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.

In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT₃A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT₃AR, which establishes a binding orientation for these drugs.

In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT₃A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.

In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.

Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, K_B, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT₃A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.

Conduction-electron localized-moment interaction in palladium-silicon base amorphous alloys containing transition metals

The electrical and magnetic properties of amorphous alloys obtained by rapid quenching from the liquid state have been studied. The composition of these alloys corresponds to the general formula M_xPd_80-xSi₂₀, in which M stands for a metal of the first transition series between chromium and nickel and x is its atomic concentration. The concentration ranges within which an amorphous structure could be obtained were: from 0 to 7 for Cr, Mn and Fe, from 0 to 11 for Co and from 0 to 15 for Ni. A well-defined minimum in the resistivity vs temperature curve was observed for all alloys except those containing nickel. The alloys for which a resistivity minimum was observed had a negative magnetoresistivity approximately proportional to the square of the magnetization and their susceptibility obeyed the Curie-Weiss law in a wide temperature range. For concentrated Fe and Co alloys the resistivity minimum was found to coexist with ferromagnetism. These observations lead to the conclusion that the present results are due to a s-d exchange interaction. The unusually high resistivity minimum temperature observed in the Cr alloys is interpreted as a result of a high Kondo temperature and a large s-d exchange integral. A low Fermi energy of the amorphous alloys (3.5 eV) is also responsible for the anomalies due to the s-d exchange interaction.

Silicide formation and the interaction of metals with polycrystalline Si

The main factors affecting solid-phase Si-metal interactions are reported in this work. The influence of the orientation of the Si substrates and the presence of impurities in metal films and at the Si-metal interface on the formation of nickel and chromium silicides have been demonstrated. We have observed that the formation and kinetic rate of growth of nickel silicides is strongly dependent on the orientation and crystallinity of the Si substrates; a fact which, up to date, has never been seriously investigated in silicide formation. Impurity contaminations in the Cr film and at the Si-Cr interface are the most dominant influencing factors in the formation and kinetic rate of growth of CrSi₂. The potentiality and use of silicides as a diffusion barrier in metallization on silicon devices were also investigated.

Two phases, Ni₂Si and NiSi, form simultaneously in two distinct sublayers in the reaction of Ni with amorphous Si, while only the former phase was observed on other substrates. On (111) oriented Si substrates the growth rate is about 2 to 3 times less than that on <100> or polycrystalline Si. Transmission electron micrographs establish-·that silicide layers grown on different substrates have different microcrystalline structures. The concept of grain-boundary diffusion is speculated to be an important factor in silicide formation.

The composition and kinetic rate of CrSi₂ formation are not influenced by the underlying Si substrate. While the orientation of the Si substrate does not affect the formation of CrSi₂ , the purity of the Cr film and the state of Si-Cr interface become the predominant factors in the reaction process. With an interposed layer of Pd₂Si between the Cr film and the Si substrate, CrSi₂ starts to form at a much lower temperature (400°C) relative to the Si-Cr system. However, the growth rate of CrSi₂ is observed to be independent of the thickness of the Pd2Si layer. For both Si-Cr and Si-Pd₂Si-Cr samples, the growth rate is linear with time with an activation energy of 1.7 ± 0.1 ev.

A tracer technique using radioactive ³¹Si (T_1/2 = 2.26 h) was used to study the formation of CrSi₂ on Pd₂Si. It is established from this experiment that the growth of CrSi₂ takes place partly by transport of Si directly from the Si substrate and partly by breaking Pd₂Si bonds, making free Si atoms available for the growth process.

The role of CrSi₂ in Pd-Al metallization on Si was studied. It is established that a thin CrSi₂ layer can be used as a diffusion barrier to prevent Al from interacting with Pd₂Si in the Pd-Al metallization on Si.

As a generalization of what has been observed for polycrystalline-Si-Al interaction, the reactions between polycrystalline Si (poly Si) and other metals were studied. The metals investigated include Ni, Cr, Pd, Ag and Au. For Ni, Cr and Pd, annealing results in silicide formation, at temperatures similar to those observed on single crystal Si substrates. For Al, Ag and Au, which form simple eutectics with Si annealing results in erosion of the poly Si layer and growth of Si crystallites in the metal films.

Backscattering spectrometry with 2.0 and 2.3 MeV ⁴He ions was the main analytical tool used in all our investigations. Other experimental techniques include the Read camera glancing angle x-ray diffraction, scanning electron, optical and transmission electron microscopy. Details of these analytical techniques are given in Chapter II.

Chemical studies of viral entry mechanisms: I. Hydrophobic protein-lipid interactions during sendai virus membrane fusion. II. Kinetics of bacteriophage λ DNA injection.

Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage λ DNA injection.

Sendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125 )I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.

Examination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.

The kinetics of DNA injection by bacteriophage λ. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.

It is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.

Investigating the Role of the GET3-GET4/GET5 Interaction During Tail-Anchor Protein Targeting

The proper targeting of membrane proteins is essential to the viability of all cells. Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C-terminus, are post-translationally targeted to the endoplasmic reticulum (ER) membrane by the GET pathway (Guided Entry of TA proteins). In the yeast pathway, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 (Get4/5) complex, which tethers the co-chaperone Sgt2 to the central targeting factor, the Get3 ATPase. Although binding of Get4/5 to Get3 is critical for efficient TA targeting, the mechanisms by which Get4 regulates Get3 are unknown. To understand the molecular basis of Get4 function, we used a combination of structural biology, biochemistry, and cell biology. Get4/5 binds across the Get3 dimer interface, in an orientation only compatible with a closed Get3, providing insight into the role of nucleotide in complex formation. Additionally, this structure reveals two functionally distinct binding interfaces for anchoring and ATPase regulation, and loss of the regulatory interface leads to strong defects in vitro and in vivo. Additional crystal structures of the Get3-Get4/5 complex give rise to an alternate conformation, which represents an initial binding interaction mediated by electrostatics that facilitates the rate of subsequent inhibited complex formation. This interface is supported by an in-depth kinetic analysis of the Get3-Get4/5 interaction confirming the two-step complex formation. These results allow us to generate a refined model for Get4/5 function in TA targeting.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

On the interaction of actinomycin and DNA

Experiments have been accomplished that (a) further define the nature of the strong, G-containing DNA binding sites for actinomycin D (AMD), and (b) quantitate the in vitro inhibition of E. coli RNA polymerase activity by T7 DNA-bound AMD.

Twenty-five to forty percent of the G's of crab dAT are disallowed as strong AMD binding sites. The G's are measured to be randomly distributed, and, therefore, this datum cannot be explained on the basis of steric interference alone. Poly dAC:TG binds as much AMD and as strongly as any natural DNA, so the hypothesis that the unique strong AMD binding sites are G and a neighboring purine is incorrect. The datum can be explained on the basis of both steric interference and the fact that TGA is a disallowed sequence for strong AMD binding.

Using carefully defined in vitro conditions, there is one RNA synthesized per T7 DNA by E. coli RNA polymerase. The rate of the RNA polymerase-catalyzed reaction conforms to the equation 1/rate = 1/k_A(ATP) + 1/K_G(GTP) + 1/K_C(CTP) + 1/K_U(UTP) T7 DNA-bound AMD has only modest effects on initiation and termination of the polymerase-catalyzed reaction, but a large inhibitory effect on propagation. In the presence of bound AMD, k_G and k_C are decreased, whereas k_A and k_U are unaffected. These facts are interpreted to mean that on the microscopic level, on the average, the rates of incorporation of ATP and UTP are the same in the absence or presence of bound AMD, but that the rates of incorporation of GTP and CTP are decreased in the presence of AMD.

I. Electron spin relaxation studies of manganese(II) complexes in acetonitrile. II. Nuclear spin relaxation studies of bromine in tetrabromomanganese(II) in acetonitrile

Magnetic resonance techniques have given us a powerful means for investigating dynamical processes in gases, liquids and solids. Dynamical effects manifest themselves in both resonance line shifts and linewidths, and, accordingly, require detailed analyses to extract desired information. The success of a magnetic resonance experiment depends critically on relaxation mechanisms to maintain thermal equilibrium between spin states. Consequently, there must be an interaction between the excited spin states and their immediate molecular environment which promote changes in spin orientation while excess magnetic energy is coupled into other degrees of freedom by non-radiative processes. This is well known as spin-lattice relaxation. Certain dynamical processes cause fluctuations in the spin state energy levels leading to spin-spin relaxation and, here again, the environment at the molecular level plays a significant role in the magnitude of interaction. Relatively few electron spin relaxation studies of solutions have been conducted and the present work is addressed toward the extension of our knowledge in this area and the retrieval of dynamical information from line shape analyses on a time scale comparable to diffusion controlled phenomena.

Specifically, the electron spin relaxation of three Mn⁺²3d⁵ complexes, Mn(CH₃CN)₆⁺², MnCl₄^-2 in acetonitrile has been studied in considerable detail. The effective spin Hamiltonian constants were carefully evaluated under a wide range of experimental conditions. Resonance widths of these Mn⁺² complexes were studied in the presence of various excess ligand ions and as a function of concentration, viscosity, temperature and frequency (X-band, ~9.5 Ԍ Hz and K-band, ~35 Ԍ Hz).

A number of interesting conclusions were drawn from these studies. For the Et₄NCl-₄^-2 system several relaxation mechanisms leading to resonance broadening were observed. One source appears to arise through spin-orbit interactions caused by modulation of the ligand field resulting from transient distortions of the complex imparted by solvent fluctuations in the immediate surroundings of the paramagnetic ion. An additional spin relaxation was assigned to the formation of ion pairs [Et₄N⁺…MnCl₄^-2] and it was possible to estimate the dissociation constant for this specie in acetonitrile.

The Bu₄NBr-MnBr₄^-2 study was considerably more interesting. As in the former case, solvent fluctuations and ion-pairing of the paramagnetic complex [Bu₄N⁺…MnBr₄^-2] provide significant relaxation for the electronic spin system. Most interesting, without doubt, is the onset of a new relaxation mechanism leading to resonance broadening which is best interpreted as chemical exchange. Thus, assuming that resonance widths were simply governed by electron spin state lifetimes, we were able to extract dynamical information from an interaction in which the initial and final states are the same

MnBr₄^-2 + Br^- = MnBr₄^-2 + Br^-.

The bimolecular rate constants were obtained at six different temperatures and their magnitudes suggested that the exchange is probably diffusion controlled with essentially a zero energy of activation. The most important source of spin relaxation in this system stems directly from dipolar interactions between the manganese 3d⁵ electrons. Moreover, the dipolar broadening is strongly frequency dependent indicating a deviation between the transverse and longitudinal relaxation times. We are led to the conclusion that the 3d⁵ spin states of ion-paired MnBr₄^-2 are significantly correlated so that dynamical processes are also entering the picture. It was possible to estimate the correlation time, ^Td, characterizing this dynamical process.

In Part II we study nuclear magnetic relaxation of bromine ions in the MnBr4-2-Bu4NBr-acetonitrile system. Essentially we monitor the 79Br and 81Br linewidths in response to the [MnBr4-2]/[Br-] ratio with the express purpose of supporting our contention that exchange is occurring between "free" bromine ions in the solvent and bromine in the first coordination sphere of the paramagnetic anion. The complexity of the system elicited a two-part study: (1) the linewidth behavior of Bu4NBr in anhydrous CH3CN in the absence of MnBr4-2 and (2) in the presence of MnBr4-2. It was concluded in study (1) that dynamical association, Bu4NBr k1= Bu4N+ + Br-, was modulating field-gradient interactions at frequencies high enough to provide an estimation of the unimolecular rate constant, k1. A comparison of the two isotopic bromine linewidth-mole fraction results led to the conclusion that quadrupole interactions provided the dominant relaxation mechanism. In study (2) the "residual" bromine linewidths for both 79Br and 81Br are clearly controlled by quadrupole interactions which appear to be modulated by very rapid dynamical processes other than molecular reorientation. We conclude that the "residual" linewidth has its origin in chemical exchange and that bromine nuclei exchange rapidly between a "free" solvated ion and the paramagnetic complex, MnBr4-2.

I. Nuclear spin-internal-rotation-coupling. II. Fluorine spin-rotation interaction and magnetic shielding in fluorobenzene

Part I.

The interaction of a nuclear magnetic moment situated on an internal top with the magnetic fields produced by the internal as well as overall molecular rotation has been derived following the method of Van Vleck for the spin-rotation interaction in rigid molecules. It is shown that the Hamiltonian for this problem may be written

H_SR = Ῑ · M · Ĵ + Ῑ · M” · Ĵ”

Where the first term is the ordinary spin-rotation interaction and the second term arises from the spin-internal-rotation coupling.

The F¹⁹ nuclear spin-lattice relaxation time (T₁) of benzotrifluoride and several chemically substituted benzotrifluorides, have been measured both neat and in solution, at room temperature by pulsed nuclear magnetic resonance. From these experimental results it is concluded that in benzotrifluoride the internal rotation is crucial to the spin relaxation of the fluorines and that the dominant relaxation mechanism is the fluctuating spin-internal-rotation interaction.

Part II.

The radiofrequency spectrum corresponding to the reorientation of the F¹⁹ nuclear moment in flurobenzene has been studied by the molecular beam magnetic resonance method. A molecular beam apparatus with an electron bombardment detector was used in the experiments. The F¹⁹ resonance is a composite spectrum with contributions from many rotational states and is not resolved. A detailed analysis of the resonance line shape and width by the method of moments led to the following diagonal components of the fluorine spin-rotational tensor in the principal inertial axis system of the molecule:

F/Caa = -1.0 ± 0.5 kHz

F/Cbb = -2.7 ± 0.2 kHz

F/Ccc = -1.9 ± 0.1 kHz

From these interaction constants, the paramagnetic contribution to the F¹⁹ nuclear shielding in C₆H₅F was determined to be -284 ± ppm. It was further concluded that the F¹⁹ nucleus in this molecule is more shielded when the applied magnetic field is directed along the C-F bond axis. The anisotropy of the magnetic shielding tensor, σ_” - σ_⊥, is +160 ± 30 ppm.