Extracellular matrix (ECM) is a dynamic scaffold that provides both structural support and functional integrity to various tissues and organs. By serving as a natural reservoir to a variety of resident cells, ECM actively interacts with these residing cells and regulates their behaviors ranging from differentiation and proliferation to migration and regeneration. Due to its dynamic nature, ECM constantly undergoes remodeling as the local tissues experience either physiological or pathological changes, such as aging and fibrosis. Therefore, understanding the changes occur in ECM may help the development of clinically translated stem cell applications for conditions like aging and fibrosis. In this thesis, we examine the changes that ECM undergoes with aging and pathogenesis by using two different organ systems, skeletal muscles and skin. Specifically, in the first study, we determine the biochemical changes of ECM in muscles of both wild type and dystrophic mice at various ages. We also demonstrate the structural changes of ECM associated with aging and muscle pathology. In the second study, we establish a decellularized skin model to study the effect of extracellular matrix on fibroblast behavior in an effort to understand the role of ECM on fibrosis progression. Our results show that aging and disease have a tremendous effect on biochemical composition of ECM in skeletal muscles. Also, we demonstrate that the decellularized skin model has the potential of studying the role of ECM properties on skin fibrosis, and decellularized tissue has an effect on activation of fibroblasts

A family of quinazoline-based fluorescent nucleoside analogues is synthesized for photophysical studies and applications in probing nucleic acid structure, dynamics, and recognition. These size-expanded U analogues exhibit fluorescent emission wavelengths that span 155 nm, from 335 to 490 nm. Each nucleoside has unique characteristic response to changes in its microenvironment. These distinct features lead to a variety of applications in biological assays, many of which have been explored. The fluorescent nucleoside analogues are useful in Förster Resonance Energy Transfer (FRET) experiments. The 5- methoxyquinazoline-2,4(1H,3H)-dione based nucleoside acts as the donor fluorophore to commercially available 7- diethylaminecoumarin. The FRET pair is used in a robust analysis and discovery platform for antibiotics targeting the bacterial ribosomal RNA A-site. The emissive U surrogate is incorporated into a model RNA construct of the A-site and the aminoglycosides are labeled with the 7- diethylaminecoumarin fluorescence acceptor. Titrating the coumarin labeled aminoglycosides into the emissive A-site construct shows a decrease in donor emission and concurrent increase of the acceptor emission. Titration curves faithfully generate EC50 values. Titration of unlabeled ligands into the pre-formed FRET complex yields valuable data regarding competitive displacement of aminoglycosides. Furthermore, an orthogonal FRET assembly reports antibiotic affinities to two different RNA targets. A binder was labeled with a fluorophore that acts both as an acceptor for the emissive nucleoside on the bacterial A-site and a donor fluorophore for the terminally-labeled human A-site. Unlabeled drugs were used to dissociate the labeled antibiotic. The nucleoside based on 5-aminoquinazoline-2,4(1H,3H)-dione makes a good FRET acceptor to tryptophan, one of the most infrequently occurring amino acids in proteins. The FRET pair facilitates the study of RNA-protein interactions, which is demonstrated in studying the binding of the Rev peptide to the RRE. Additionally, upon incorporation into a RNA oligonucleotide, 5-aminoquinazoline-2,4(1H,3H)-dione detects the presence of a RNA bulge by fluorescence enhancement and hypsochromic wavelength shift. In another single fluorophore experiment, the fluorescent U-analogue 7-aminoquinazoline-2,4(1H,3H)-dione detects mismatch G upon incorporation into a DNA oligonucleotide by displaying G-specific fluorescence enhancement