The severe resistance of bacteria and fungi towards common antibiotic drugs has led to the increasing prevalence of infections due to multi-drug resistant microbes, which is one of the most serious issue faced by the healthcare system worldwide. These drug-resistant bacteria have led to significant health problems and fatalities whereas drug-resistance fungi possess significant threat to humans, livestock, and crops globally. Furthermore, this drug resistance leads to the formation of biofilms, which are thick layers of microbes embedded in extracellular polymeric matrix. They adhere to both living and nonliving surfaces, making it harder to contain or eradicate these pathogens. The conventional strategy for combating these pathogenic bacteria and fungi has its limitations and new antimicrobials are constantly required to fight the growing resistant mechanisms. Hence, there is an immediate need for an alternative strategy to combat these drug-resistant isolates. Herein, this dissertation reports the development of novel potent antimicrobial agent based on tow-dimensional layered nanomaterials dispersed in biocompatible oligonucleotide, biomolecules, polymers, and surfactant. These synthesized novel nanomaterials successfully eliminated multidrug-resistant microbes with synergistic efforts of physical interaction, membrane disintegration, depolarization and intrinsic antimicrobial properties leading to cell death. These systems were highly effective against a broad spectrum of microbes including drug-resistant gram-positive, gram-negative bacteria and fungal isolates. Furthermore, they were successful in eradication of mature biofilm as well as inhibition of biofilms on several medically relevant surfaces. Overall, these novel systems have exceptional potential as a promising alternative solution in solving current problems faced by the healthcare system sue to these pathogenic microbes. For the next direction, a different avenue was explored where a novel system based on two-dimensional layered material with antibacterial properties was analyzed for enzyme-like activity. These nanomaterials with intrinsic enzyme-like properties are commonly known as nanozymes have many advantages over natural enzymes such as low cost, scalability and high stability. A class of ultra-high temperature ceramics known as metal diborides were synthesized in biocompatible surfactant followed by analysis of their enzymatic activity and antibacterial activity. Results demonstrate this novel system possesses a unique combination of exceptionally high affinity towards hydrogen peroxide and high activity per cost. Furthermore, it is extremely potent against pathogenic bacteria and has a high degree of biocompatibility. Hence, this new system opens the door for future possible applications in biomedicine with further research.

Layered chalcogenides are a diverse class of crystalline materials that consist of covalently bound building blocks held together by van der Waals forces, including the transition metal dichalcogenides (TMDCs) and the pnictogen chalcogenides (PCs) among all. These materials, in particular, MoS2 which is the most widely studied TMDC material, have attracted significant attention in recent years due to their unique physical, electronic, optical, and chemical properties that depend on the number of layers. Due to their high aspect ratios and extreme thinness, 2D materials are sensitive to modifications via chemistry on their surfaces. For instance, covalent functionalization can be used to robustly modify the electronic properties of 2D materials, and can also be used to attach other materials or structures. Metal adsorption on the surfaces of 2D materials can also tune their electronic structures, and can be used as a strategy for removing metal contaminants from water. Thus, there are many opportunities for studying the fundamental surface interactions of 2D materials and in particular the TMDCs and PCs.

The work reported in this dissertation represents detailed fundamental studies of the covalent functionalization and metal adsorption behavior of layered chalcogenides, which are two significant aspects of the surface interactions of 2D materials. First, we demonstrate that both the Freundlich and Temkin isotherm models, and the pseudo-second-order reaction kinetics model are good descriptors of the reaction due to the energetically inhomogeneous surface MoS2 and the indirect adsorbate-adsorbate interactions from previously attached nitrophenyl (NP) groups. Second, the covalent functionalization using aryl diazonium salts is extended to nanosheets of other representative TMDC materials MoSe2, WS2, and WSe2, and of the representative PC materials Bi2S3 and Sb2S3, demonstrated using atomic force microscopy (AFM) imaging and Fourier transform infrared spectroscopy (FTIR). Finally, using AFM and X-ray photoelectron spectroscopy (XPS), it is shown that Pb, Cd Zn and Co form nanoclusters on the MoS2 surface without affecting the structure of the MoS2 itself. The metals can also be thermally desorbed from MoS2, thus suggesting a potential application as a reusable water purification technology.

DNA and RNA are generally regarded as one of the central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology witnessed the success of usage of DNA/RNA as programmable molecules to construct nano-objects with predefined shapes and dynamic molecular machines for various functions. From the perspective of structural design with nucleic acid, there are basically two types of assembly method, DNA tile based assembly and DNA origami based assembly, used to construct infinite-sized crystal structures and finite-sized molecular structures. The assembled structure can be used for arrangement of other molecules or nanoparticles with the resolution of nanometers to create new type of materials. The dynamic nucleic acid machine is based on the DNA strand displacement, which allows two nucleic acid strands to hybridize with each other to displace one or more prehybridized strands in the process. Strand displacement reaction has been implemented to construct a variety of dynamic molecular systems, such as molecular computer, oscillators, in vivo devices for gene expression control.

This thesis will focus on the computational design of structural and dynamic nucleic acid systems, particularly for new type of DNA structure design and high precision control of gene expression in vivo. Firstly, a new type of fundamental DNA structural motif, the layered-crossover motif, will be introduced. The layered-crossover allow non-parallel alignment of DNA helices with precisely controlled angle. By using the layered-crossover motif, the scaffold can go through the 3D framework DNA origami structures. The properties of precise angle control of the layered-crossover tiles can also be used to assemble 2D and 3D crystals. One the dynamic control part, a de-novo-designed riboregulator is developed that can recognize single nucleotide variation. The riboregulators can also be used to develop paper-based diagnostic devices.