<p>Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(<em>R</em>-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.</p>

No / Biarylpyrimidines are characterized as selective ligands for higher-order nucleic acid structures. A concise and efficient synthesis has been devised incorporating Suzuki biaryl cross-coupling of dihalopyrimidines. Two ligand series are described based on the parent thioether 4,6-bis[4-[[2-(dimethylamino)ethyl]mercapto]-phenyl]pyrimidine (la) and amide 4,6-bis(4[(2-(dimethylamino)ethyl)carboxamido]phenyl)pyrimidine (2a) compounds. In UV thermal denaturation studies with the poly(dA)·[poly(dT)]2 triplex structure, thioethers showed stabilization of the triplex form (¿Tm ¿ 20 °C). In contrast, amides showed duplex stabilization (¿Tm ¿ 15 °C) and either negligible stabilization or specific destabilization (¿Tm = -5 °C) of the triplex structure. Full spectra of nucleic acid binding preferences were determined by competition dialysis. The strongest interacting thioether bound preferentially to the poly(dA)·[poly(dT)]2 triplex, Kapp = 1.6 x 105 M-1 (40 x Kapp for CT DNA duplex). In contrast, the strongest binding amide selected the (T2G20T2)4 quadruplex structure, Kapp = 0.31 x 105 M-1 (6.5 x Kapp for CT DNA duplex).

The thesis begins with a brief introduction and relevant literature references. The novelty of synthesis, methodology and results of the work reported in the thesis and highlighted subsequently. The thesis consist of three parts, Part A of the thesis consist of five chapters describing new methods of synthesis of orthovanadates, mainly dealing with the structure and photocatalytic properties of synthesized materials. Part B of the thesis consist of two chapters dealing with an unique crystallization methodology for subliming and low melting organic compounds and the crystal structure determination via single crystal X-ray diffraction. Part C consists of one chapter presenting the ab-initio approach of structure determination via powder X-ray diffraction methods. Chapter 1 of the thesis presents the synthesis of three zircon type lanthanide orthovanadates, LnVO4 (Ln = Ce, Pr and Nd) via a new solution based approach at room temperature and photodegradation of a variety of water pollutants have been investigated. Chapter 2 describes the importance of microwave synthesis to produce nano particles of the zircon type lanthanide orthovanadates LnVO4. The importance of the surface area in photocatalysis is evaluated. Chapter 3 consist of the synthesis of a series of new compounds, Ln0.95φ0.05Mo0.15V0.85O4 (Ln = Ce, Pr and Nd) via solid state method. The photocatalytic activities of these compounds are investigated both under UV exposure and sunlight. Chapter 4 presents the synthesis of MxCe1-xVO4+ (M = Li, Ca and Fe) with x = 0.1, 0.25 and 0.05 respectively. Different kinds of dyes and organics are degraded under UV radiation and the specificity towards the same are evaluated. Chapter 5 describes a comparative photocatalytic conversion of cyclohexane and benzene to cyclohexanol, cyclohexanone and phenol respectively by LnVO4, LnMo0.15V0.85O4 and MxCe1-xVO4+ (Ln = Ce, Pr and Nd, M= Li, Ca and Fe with x = 0.1, 0.25 and 0.05 respectively). Kinetics of above photoconversions are established by proposing a mechanism and determining the rate constants. Chapter 6 describes the development of a novel apparatus for the crystallization of anhydrous adenine, whose structure has not been solved over the last few decades. The crystal structure is solved via single crystal X-ray diffraction. Chapter 7 presents a modified design for crystallization of low melting organic compounds and co-crystals. A new polymorph of anhydrous thymine has been grown with this apparatus and its structure has been analyzed and compared with the known form of thymine. Chapter 8 presents the ab-initio approach of structure determination via powder X-ray diffraction methods. The methodology of using the direct space approach for the determination of the crystal structure of N-(2-fluorophenyl) benzamide (a drug intermediate), which could not yield good quality single crystals, is outlined.

First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.