| G-quadruplexes (G4s) are nucleic acid structures formed from pi-stacked planar sets of four Hoogsteen hydrogen bonded guanine bases. G4s emerged as potential therapeutic targets based on their ability to modulate gene expression and inhibit the ability of telomerase to elongate chromosomal telomeres. Raman spectroscopy, polarized Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS), and other optical spectroscopic techniques were used to characterize the G4s formed by four different DNA sequences: human telomeric (HT), thrombin-binding aptamer (TBA), nuclease hypersensitive element III1 region of the c- Myc gene promoter (Myc), and a single loop-isomer of Myc (MycL1).;Reported herein are the first polarized Raman spectra and Raman depolarization ratios for four different G4s: HT with Na+, HT with K +, TBA, and MycL1. In the interpretation of the Raman spectra, a conformational analysis of NMR models of the G4s from the PDB was integrated, revealing different amounts of localized B and Z DNA character in each G4. In addition, drop deposition Raman spectroscopy of the G4 sequences without cations confirmed that G4 formation is dependent on hydration.;The first SERS spectra of the G4s formed by HT with Na+ and K+, Myc, and MycL1 are reported, along with additional SERS spectra of the TBA G4. SERS spectra of the G4- forming sequences on silver nanoparticles with and without cations were analyzed using multivariate analysis (MVA), including principal components analysis, naive Bayes analysis, and linear discriminant analysis. The analyses revealed structural differences between the G4s and the different orientations with which the G4-forming sequences adsorbed to silver nanoparticles.;MVA was also used to characterize SERS spectra from living human fibroblast and melanoma cells incubated for different amounts of time with different sizes of gold nanoparticles. Changes in SERS spectra dependent on cell type, incubation time, and nanoparticle size were observed.;Additional work includes Raman and SERS studies of eight different G4-binding molecules in the porphyrin family, SERS detection of two different porphyrins in living human melanoma cells, single-molecule (SM) fluorescence and SM SERS of respective model compounds rhodamine 6G and 4-mercaptopyridine, and parallel factor analysis of advanced glycation end product fluorescence excitation-emission matrices. |
