| The development of microarrays as an innovative tool to study biochemical samples has benefited us with a deeper understanding of DNA, RNA, and protein behaviour. This thesis will discuss the optimization and use of microarrays in order to reduce the large amounts of error inherent to this technique and to measure photochemistry in different DNA sequences. To do this, we introduced the use of a fluorescently-labeled short single stranded DNA (ssDNA) immobilized to a glass slide as an internal standard. Optimization of this technique required the correction of a number of parameters such as environmental conditions (including ambient light exposure and atmospheric ozone) and target/probe concentrations. We determined 35 μM to be the optimal concentration for the fluorescently-labeled probe and 50 μM to be the optimal concentration for the target. From these corrections, we were able to reduce the obtained error by a factor of 2 or more.;Finally, the photoluminescent properties of silicon nanoparticles as potential standards for nucleic acid microarrays were examined. The silicon nanoparticles were measured under two conditions, exposed to air and sealed. Both the sealed and exposed nanoparticles emit in two spectral regions, the near IR and the UV. The average quantum yields for the sealed sample were 17% in the UV region and 1.27% in the near IR. The average quantum yields for the exposed samples were determined to be 4.18% in the UV region and 0.48% in the near IR. The stability of these nanoparticles was investigated by measuring the effects of aging on the emission spectrum. We observed only slight decreases in the quantum yields after a period of 14 days.;In addition, the detection of DNA damage induced by UVC irradiation on microarray slides is also discussed. Three different ssDNA target sequences 5'-/Am/CGT GCA AAA AAA TTA AAA AAA A-3' (ATTA), 5'-/Am/CGT GCA AAA AAG TTG AAA AAA A-3' (GTTG), and 5'-/Am/CGT GCA AAA AAA AAA AAA AAA A-3' (AAAA) were immobilized to glass slides. The irradiation of these target sequences with UVC light produced photochemical damage, which was detected with target-specific fluorescently-labeled hairpin probes. First-order exponential decay curves were fit to the obtained data and quantitative rate constants were determined for DNA photoproduct formation. The rate constants determined were 51.59113 ± 2.14881 min (R 2 = 0.95881) for ATTA, 47.78764 ± 3.5573 min (R2 = 0.83409) for AAAA, and 53.52365 ± 1.26358 min (R2 = 0.99976) for GTTG DNA sequence. The AAAA target sequence was designed as a control sequence due to its limited photochemistry. However, here we detected photodamage induced by UVC light. |
