Thesis advisor: Larry W. McLaughlin / Nucleic acids are fundamental biomolecules responsible for all activities of a living cell. DNA serves as an instruction manual to the cell, containing blueprints and directions for all cellular processes, while RNA serves to carry out the messages held within DNA. Research into the structure, stability, and function of nucleic acids has revealed much about the origin and evolution of life. The ultimate goal of this work is to understand how molecules bind and associate within the minor groove of double stranded, helical DNA. A series of 2'-deoxyadenosine analogues are modified at the three position by replacing the N3-nitrogen with carbon. Substitution at this position is designed to emulate the effects of removing hydrogen bond acceptors, introducing steric bulk, and tethering functional groups of interest into the minor groove. These functional groups mimic small molecules that have been shown to bind within the minor groove of A-T rich sequences as well as serve as a platform for further substitution by fluorescent tags. The synthetic effort needed to obtain purine nucleosides containing each of these modifications was non-trivial. New methodologies unveiled directing and protecting strategies towards the desired isomer of these modified nucleosides in higher yields than those previously deemed acceptable. Application of these modified nucleosides into duplex DNA reveals thermodynamic parameters for how small molecules bind to the minor groove and the effects of introducing biomarkers into an unprecedented region of DNA. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

From 1997-2002, a loose collective of hip hop and R&B musicians known as The Soulquarians collaborated to produce numerous award-winning and critically-acclaimed albums. Drawn together by the heady atmosphere of collaboration with creative, like-minded peers, they were driven by a goal to create alternative sounds and representations in black music. This project has two primary goals: to historicize the collaboration of the Soulquarians and to identify and analyze aspects of their music that situated it in opposition to commercially dominant hip hop of its day. To do so, I perform close listening and analysis of recordings, interviews, liner notes, album and concert reviews, and articles on the Soulquarians and their work from contemporary print media, and draw from biographies and autobiographies of Soulquarians artists. This project contributes to music scholarship in three primary ways. First, I utilize an innovative technique to visually analyze microtiming in the groundbreaking grooves of J Dilla and D'Angelo. Using this technique, I precisely identify distinguishing timing features in drums and bass, and make them visible to the reader. By contextualizing these findings within previous scholarship on rhythm in African American music performance, I fill a gap in scholarship on groove, which has not yet described the variety of these influential rhythms. Second, I compile information from a variety of sources (web, print, liner notes, interviews) on the Soulquarians into one location. This produces a fuller picture of the collaboration than has previously been available, and facilitates access to a breadth of information on individual Soulquarians artists, and the collective. Third, I identify several musical traits that resulted from the collaborative nature of the Soulquarians’ work habits, including specific commonalities between the grooves of J Dilla and D'Angelo, and the use in Badu’s music of imitative strategies pioneered by The Roots. This presents a richer picture of artists’ working practices than is typically advanced by journalism and scholarship on hip hop. Because cooperative aspects of the Soulquarians’ working methods also characterize music communities more broadly, this description of their collaboration may serve as a corrective to popular but misguided notions of sole authorship in popular music.

Diamidines are small molecules that generally possess antiparasitic properties and bind preferentially to the minor groove of AT rich DNA. With the goal of getting a better understanding of the thermodynamic driving forces and binding affinities, a series of pentamidine analogs were investigated with various AT rich DNA by ITC, UV-Vis and fluorescence spectroscopic methods. Findings suggest that the substitution of the linker oxygen of pentamidine to a nitrogen slightly improves the binding affinity. All of the investigated compounds are entropically driven at 25 oC with non-alternating AT DNA. Additionally, the increased fluorescence of the nitrogen and sulfur linked analogs will enable future work to be done with fluorescence microscopy to help determine if and where these compounds accumulate in the target organism.

It has been shown that heterocyclic diamidines, a class of minor groove binders, are promising antimicrobial agents. These compounds bind none covalently to the minor groove of A/T rich regions of the kinetoplast DNA and kill the parasite. The mechanism of action of these compounds is not well understood, yet many hypotheses have been proposed. One of the methods that improve the specificity is cooperative binding. Since there are many binding sites available in k-DNA thus the cooperativity in adjacent binding sites is desirable. A library of compounds has been scanned and few of those compounds identified that are able to bind to two adjacent A/T binding sites separated by a single G. Many biophysical methods such as isothermal titration calorimetry, surface Plasmon resonance, circular dichroism and thermal melting have been used to explore the thermodynamic profiles and binding mode of these compounds. The pulsed field gradient NMR was used to investigate the structural changes to the DNA sequence upon binding of the minor groove binders and find a correlation between their biological difference and structural changes. The molecular dynamics was applied to look at the interaction of some of the heterocyclic diamidines to the DNA with more details and predict the unknown structures.

Certain natural products, Ditamycin and Netropsin are considered as models of designing new DNA binding agents. A variety of DNA binding ligands were synthesized and accordingly characterized by different bioassays. In the series of azo-polyamide, it showed slight DNA binding affinity but has the properties of DNA photo-cleavage and recognition of mixed sequence. The carbohydrate-azo-polyamide series show the properties of DNA photo-cleavage and more effective in vitro experiment. In the quinoline series proves the attenuation effect for G-quadruplex stabilization which provides a novel strategy for development of G-quadruplex binding ligands.

The interaction of small molecules with DNA has been extensively studied and has produced a large catalogue of molecules that non-covalently bind to DNA though groove binding, intercalation, electrostatics, or a combination of these binding modes. Anthracene, acridine, and carbocyanine-based chromophores have been examined for their DNA binding properties and photo-reactivities. Their planar aromatic structures make them ideal chromophores that can be used to probe DNA structural interactions and binding patterns. We have studied DNA binding and photocleavgage properties of a bisacridine chromophore joined by a 2,6-bis(aminomethyl)pyridine copper-binding linker (Chapter II), a series of 9-aminomethyl anthracene chromophores (Chapters III and IV), both under conditions of high and low ionic strength, as well as a series of pentamethine linked symmetrical carbocyanine dyes (Chapter V). In Chapter II we present data showing that high ionic strength efficiently increases copper(II)-dependent photocleavage of plasmid DNA by the bisacridine based chromophore (419 nm, pH 7.0). In Chapters III and IV, using an pyridine N-substituted 9-(aminomethyl)anthracene (Chapter III), a bis-9-(aminomethyl)anthracene, and its mono 9-(aminomethyl)anthracene analogue (Chapter IV), pUC19 plasmid DNA was photo-converted to highly diffuse DNA fragments (350 nm, pH 7.0) in the presence of 150 mM NaCl and 260 mM KCl. Spectroscopic analyses suggest that the combination of salts promotes a change in DNA helical structure that initiate a switch in anthracene binding mode from intercalation to an external or groove binding interactions. The alteration in DNA structure and binding mode leads to an increase in the anthracene-sensitized production of DNA damaging reactive oxygen species. Finally, in Chapter V, pUC19 plasmid DNA is converted to its nicked circular and linear forms following irradiation of a series of pentamethine linked symmetrical carbocyanines (red light, pH 7.0). The data suggest that the relative levels of photocleavage arise from the different substituents on the nitrogen alkyl side chain and the pentamethine linker.

A series of combilexin-like monoamidines has been synthesized by linking an intercalative unit with the DNA minor groove binder DB 818 via “Click chemistry.” DB 818 is a dicationic minor groove binder that has shown strong binding affinity to AT sequences. The aim was to synthesize novel classes of DNA minor groove binders that are combilexin-like – minor groove binder / intercalator hybrid – as potential unique DNA binding agents and therapeutics against African Sleeping Sickness. Additionally, a series of novel benzo[d]1,3,2-diazaboroles DAPI derivatives were also synthesized and investigated. These boron compounds have the potential to be strong DNA minor groove binders because of their lower pKa and act as potential chromophores for Boron Neutron Capture Therapy.

A series of combilexin-like monoamidines has been synthesized by linking an intercalative unit with the DNA minor groove binder DB 818 via “Click chemistry.” DB 818 is a dicationic minor groove binder that has shown strong binding affinity to AT sequences. The aim was to synthesize novel classes of DNA minor groove binders that are combilexin-like – minor groove binder / intercalator hybrid – as potential unique DNA binding agents and therapeutics against African Sleeping Sickness. Additionally, a series of novel benzo[d]1,3,2-diazaboroles DAPI derivatives were also synthesized and investigated. These boron compounds ave the potential to be strong DNA minor groove binders because of their lower pKa and act as potential chromophores for Boron Neutron Capture Therapy.

Plank (tongue and groove) wood decking is a product that is commonly used in post and beam timber construction to transfer gravity loads on roofs and floors. In 2010, The National Building Code of Canada changed the application area of the specified concentrated roof live loads from 750 mm x 750 mm to 200 mm x 200 mm. The change was made to better reflect the area which a construction worker with equipment occupies. Preliminary analysis showed that the change in the application area of concentrated loads may have a significant impact on the design of decking systems. Little research or development has been done on plank decking since the 1950’s and 1960’s. An experimental program was undertaken at the University of Ottawa’s structural laboratory to better understand the behaviour of plank decking under uniformly distributed and concentrated loads. Non-destructive and destructive tests were conducted on plank decking systems to investigate their stiffness and failure mode characteristics under uniformly distributed as well as concentrated loads. The experimental test program was complimented with a detailed finite element model in order to predict the behaviour of a plank decking system, especially the force transfer between decks through the tongue and groove joint. The study showed that the published deflection coefficients for uniformly distributed loads can accurately predict the three types of decking layup patterns specified in the Canadian Design Standard (CSA O86, 2009). For unbalanced uniformly distributed loads on two-span continuous layup, it was found that the deflection coefficient of 0.42 was non-conservative. It was also found that under concentrated loads, the stiffness of the decking system increased significantly as more boards were added. A deflection coefficient of 0.40 is appropriate to calculate the deflection for the three types of decking layup patterns specified in the Canadian Design Standard (CSA O86, 2009) under concentrated load on an area of 200 mm by 200 mm. Significant load sharing was observed for plank decking under concentrated loads. An increase in capacity of about 1.5 to 2.5 times the capacity of the loaded boards was found. Furthermore, it was found that placing sheathing on top of a decking system had a significant effect in the case of concentrated load with an increase of over 50% in stiffness and over 100% in ultimate capacity.

Since the introduction of fiber reinforced polymers (FRP) for the repair and retrofit of concrete structures in the 1980’s, considerable research has been devoted to the feasibility of their application and predictive modeling of their performance. However, the effects of flaws present in the constitutive components and the practices in substrate preparation and treatment have not yet been thoroughly studied. This research aims at investigating the effect of surface preparation and treatment for the pre-cured FRP systems and the groove size tolerance for near surface mounted (NSM) FRP systems; and to set thresholds for guaranteed system performance. The research included both analytical and experimental components. The experimental program for the pre-cured FRP systems consisted of a total of twenty-four (24) reinforced concrete (RC) T-beams with various surface preparation parameters and surface flaws, including roughness, flatness, voids and cracks (cuts). For the NSM FRP systems, a total of twelve (12) additional RC T-beams were tested with different grooves sizes for FRP bars and strips. The analytical program included developing an elaborate nonlinear finite element model using the general purpose software ANSYS. The model was subsequently used to extend the experimental range of parameters for surface flatness in pre-cured FRP systems, and for groove size study in the NSM FRP systems. Test results, confirmed by further analyses, indicated that contrary to the general belief in the industry, the impact of surface roughness on the global performance of pre-cured FRP systems was negligible. The study also verified that threshold limits set for wet lay-up FRP systems can be extended to pre-cured systems. The study showed that larger surface voids and cracks (cuts) can adversely impact both the strength and ductility of pre-cured FRP systems. On the other hand, frequency (or spacing) of surface cracks (cuts) may only affect system ductility rather than its strength. Finally, within the range studied, groove size tolerance of +1/8 in. does not appear to have an adverse effect on the performance of NSM FRP systems.