SecA ATPase is a critical member of the Sec system, which is important in the translocation of membrane and secreted polypeptides/proteins in bacteria. Small molecule inhibitors can be very useful research tools as well as leads for future antimicrobial agent development. Based on previous virtual screening work, we optimized the structures of two hit compounds and obtained SecA ATPase inhibitors with IC50 in the single digit micromolar range. These represent the first low micromolar inhibitors of bacterial SecA and will be very useful for mechanistic studies. Post synthetic modification is an important and efficient way of DNA functionalization especially in DNA aptamer selection. In this research, the feasibility of norbornene (Neo) modified thymidine triphosphate incorporation was described. Besides, substituted tetrazines have been found to undergo facile inversed electron demand Diels-Alder reactions with "tunable" reaction rates. This finding paves the way to utilize tetrazine conjugation reactions for not only DNA but also other labeling work.

Near-infrared (NIR) fluorescence imaging has emerged as an attractive non-invasive approach for direct visualization of diseases which depends on the development of stable, highly specific and sensitive optical probes. The NIR region of the electronic spectrum offers a reduction in the background autofluorescence and an increase in the tissue penetration depth. Cyanine dyes have often been considered promising contrast optic agents owing to their photophysical properties. Herein the synthesis of various penta- and heptamethine benzothiazole cyanine dyes has been described and their in vivo imaging efficacy was determined. Varying functionalities on the benzothiazole aromatic ring and changing substituents on the benzothiazolium nitrogen atom reflected subsequent changes in the imaging pattern and have resulted in the development of promising brain targeting agents.

The development of small-molecules which target nucleic acids, more specifically the minor groove of DNA, in a sequence specific manner and control gene expression are currently being investigated as potential therapeutic compounds for the treatment of various diseases, including cancer, as well as viral and bacterial infections. The naturally occurring compounds netropsin and distamycin have been shown to demonstrate antitumor and antibacterial properties. Currently, there are synthetic efforts to create pyrrole and imidazole-containing polyamide derivatives of netropsin and distamycin that show potential as medicinal agents. Synthetic pyrrole and imidazole-containing polyamides are potentially useful for targeting and modulating the expression of genes, including those associated with cancer cell growth. The key challenges that must be overcome to realize this goal of using synthetic polyamides in the treatment of disease are the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. As part of a systematic study within the authors’ laboratory, our goal is to develop polyamides which can be synthesized readily yet possess excellent sequence specificity, stronger binding affinity, high solubility in biological media and enhanced cell penetration and nuclear localization properties. There is a need to develop a library of modified polyamides which target DNA and exhibit improved biological properties. The present study is a systematic examination of the binding properties of various modified synthetic polyamide compounds. The synthetic polyamide derivatives presented have more potential as therapeutic candidates over other synthetic polyamides because of their increased water solubility, smaller molecular weights, and molecular design, thus, allowing them to penetrate into cells and localize in the nucleus.

Bacterial quorum sensing is regarded as a novel target for the design of antimicrobials. Based on lead structures identified from HTS, 39 analogues have been synthesized and evaluated in Vibrio haveyi. Potent inhibitors with IC50 values at single-digit micromolar concentrations for AI-2 mediated quorum sensing have been identified. On the second project, post-synthesis modifications of DNA provide easy functionalizations for expanded applications such as aptamer selection. A CBT-modified thymidine analogue (CBT-TTP) has been synthesized and used for enzymatic incorporation into DNA. Post-synthesis modifications through condensation with 1,2-aminothiol for installation of a boronic acid moiety or a fluorophore have been achieved. On the third project, H2S has been recognized as an important gasotransmitter and its concentration is relevant to a variety of diseases. A novel fluorescent probe (DNS-Az) has been developed for quantitation of H2S in aqueous solutions. This probe has been used to measure H2S concentrations in the blood.

Since single nanopores were firstly proposed as a potential rapid and low-cost tool for DNA sequencing in 1990s (PNAS, 1996, 93, 13770), extensive studies on both biological and synthetic nanopores and nanochannels have been reported. Nanochannel based stochastic sensing at single molecular level has been widely reported through the detection of transient ionic current changes induced by geometry blockage due to analytes translocation. Novel properties, including ion current rectification (ICR), memristive and memcapacitive behaviors were reported. These fundamental properties of nanochannels arise from the nanoscale dimensions and enables applications not only in single molecule sensing, but also in drug delivery, electrochemical energy conversion, concentration enrichment and separation, nanoprecipitation, nanoelectronics etc. Electrostatic interactions at nanometer-scale between the fixed surface charges and mobile charges in solution play major roles in those applications due to high surface to volume ratio. However, the knowledge of surface charge density (SCD) at nanometer scale is inaccessible within nanoconfinement and often extrapolated from bulk planar values. The determination of SCD at nanometer scale is urgently needed for the interpretation of aforementioned phenomena. This dissertation mainly focuses on the determination of SCD confined at a nanoscale device with known geometry via combined electroanalytical measurements and theoretical simulation. The measured currents through charged nanodevices are different for potentials with the same amplitude but opposite polarities, which deviates away from linear Ohm's behavior, known as ICR. Through theoretical simulation of experiments by solving Poisson and Nernst-Planck equations, the SCD within nanoconfinement is directly quantified for the first time. An exponential gradient SCD is introduced on the interior surface of a conical nanopre based on the gradient distribution of applied electric field. The physical origin is proposed based on the facilitated deprotonation of surface functional groups by the applied electric field. The two parameters that describe the non-uniform SCD distribution: maximum SCD and distribution length are determined by fitting high- and low-conductivity current respectively. The model is validated and applied successfully for quantification and prediction of mass transport behavior in different electrolyte solutions. Furthermore, because the surface charge distribution, the transport behaviors are intrinsicaly heterogeneous at nanometer scale, the concept is extended to noninvasively determine the surface modification efficacy of individual nanopore devices. Preliminary results of single molecule sensing based on streptavidin-iminobiotin are included. The pH dependent binding affinity of streptavidin-iminobiotin binding is confirmed by different current change signals ("steps" and "spikes") observed at different pHs. Qualitative concentration and potential dependence have been established. The chemically modified nanopores are demonstrated to be reusable through regenerating binding surface.

Anthraquinone (AQ) has been used in electron transfer studies in DNA. The focus of this dissertation is the synthesis of conjugates between AQ derivatives and 2’-deoxyadenosine (dA), which can be used to induce adenine oxidation in DNA. Different AQ derivatives were attached to dA via ethynyl or ethanyl linkers. If incorporated into DNA, these short linkers should enable regiocontrol for electron transfer from adenine within the DNA duplex structure. The challenge in working with anthraquinone-2’-deoxynucleosides conjugates is that they and their intermediates are insoluble in water and only sparingly soluble in most organic solvents. A strategy used to overcome this problem was the use of either tert-butyldiphenylsilyl (TBDPS) or 4’,4-dimethoxytrityl (DMTr) 5’-protected deoxynucleosides as starting materials. A water-soluble, ethynyl-linked AQ-dA conjugate with a 3’-benzyl hydrogen phosphate was synthesized using DMTr protection. The DMTr group was not stable to the hydrogenation required to make the ethanyl-linked AQ-dA conjugate with 3’-benzyl hydrogen phosphate. Hence the latter was synthesized starting with the TBDPS protecting group. Both of these syntheses were based on the Pd coupling between ethynylanthraquinone and 8-bromodeoxyadenosine derivatives. New conjugates between AQ and A, in which the AQ moieties have been modified with formyl, trifluoroacetyl and methyl ester groups as electron withdrawing substituents were also synthesized. The synthesis of these AQ-dA conjugates was based on Pd coupling between bromoanthraquinone and 8-ethynyldeoxyadenosine derivatives. This route avoided the use of ethynylanthraquinone derivatives that had extremely low solubility and photoinstability. Other anthraquinones with electron withdrawing groups (which should provide enhanced driving force to enable respective AQ derivative to oxidize adenine) were synthesized as models. Cyclic voltammetry showed that the conjugate with the two ester groups and ethynyl linker was the most easily reduced of the derivatives synthesized. Conjugates between AQ and dU were also synthesized. Those conjugates can potentially be used to oxidize guanine or adenine or they can be used as a deep trap for an electron in reduced DNA.

The synthesis of 2,4-disubstituted pyrimidine derivatives is described. The synthetic route involved the addition reaction of lithiated intermediates, mostly heterocycles, to position 4 of 2-chloropyrimidine to give a dihydropyrimidine intermediate which was oxidized back to a pyrimidine. This was followed by nucleophilic aromatic substitution with various amines of the chlorine in the position 2. A number of compounds were prepared which showed binding towards various serotonin receptors in preliminary biological evaluation.

Protein arginine methyltransferase, PRMT, is a family of epigenetic enzymes that methylate arginine residues on histone and nonhistone substrates which result in a monomethylation, symmetric dimethylation or asymmetric dimethylation via the transfer of a methyl group from S-adenosyl-L-methionine (SAM). We discovered a novel interaction between two PRMT isoforms: PRMT1 interacts and methylates PRMT6. In this study site-directed mutagenesis was performed on selected arginines identified from tandem mass spectrometric analysis to investigate major methylation sites of PRMT6 by PRMT1. In combination with radiometric methyltransferase assays, we determined two major methylation sites. Methylations at these sites have significant effects on the nascent enzymatic activity of PRMT6 in H4 methylation. PRMTs have the ability to homodimerize which have been linked to methyltransferase activity. We designed dimerization inhibitors (DMIs) to further investigate the need for dimerization for enzyme activity. Preliminary results suggest that the monomeric form of PRMT1 retains methyltransferase activity comparable to that of the uninhibited PRMT1.

Studies on a series of polymethine cyanine dyes and analogs (1-24) show that certain near-infrared cyanines are capable of damaging DNA in the absence of light and external reducing agents. Experimental results imply that in this DNA thermal cleavage, the cyanine reduces Cu(II) to Cu(I) which reacts with O2 to generate the reactive oxygen species (ROS) O2∙- and ∙OH. The formation of these ROS is also thought to be responsible for the irreversible bleaching of the dyes in aqueous solutions. A correlation between structural features and DNA thermal cleavage activity as well as dye bleaching is suggested. Long polymethine chains appear to confer instability to cyanines in aqueous solutions and further contribute to undesired thermal DNA cleavage. These drawbacks can be overcome by introducing an electron-withdrawing group to the polymethine bridge of the cyanine dye.

Small molecules interacting with DNA is an emerging theme in scientific research due to its specificity and minimal side-effect. Moreover, a large amount of research has been done on finding compounds that can stabilize G-quadruplex DNA, a non-canonical secondary DNA structure, to inhibit cancerous cell proliferation. G-quadruplex DNA is found in the guanine-rich region of the chromosome that has an important role in protecting chromosomes from unwinding, participate in gene expression, contribute in the control replication of cells and more. In this research, rationally designed, synthetic cyanine dye derivatives, which were tested under physiologically relevant conditions, were found to selectively bind to G-quadruplex over duplex DNA and are favored to one structure over another. The interactions were observed using UV-Vis thermal melting, fluorescence titration, circular dichroism titration, and surface plasmon resonance analysis. For fluorescence and selectivity properties, cyanine dyes, therefore, have the potential to become the detections and/or therapeutic drugs to target cancers and many other fatal diseases.