The binding of antibiotics to DNA

Issued as Report of research, Project no. G-41-63

Methods to improve the remediation of polycyclic aromatic hydrocarbons (pahs) in aerobic and anaerobic environments

Oil spills occur regularly in terrestrial environments and crude oil can contain many compounds that are highly resistant to degradation. Among these compounds are high levels of polycyclic aromatic hydrocarbons (PAHs) which are not only toxic but can also be carcinogenic and/or mutagenic. The first chapter of this dissertation includes an extensive review chapter on the variables affecting the anaerobic degradation of hydrocarbons, with a particular focus on PAHs. Electron acceptors, electron donors, temperature, salinity, pH all play key roles in determining the possibility effective of effective degradation occurring. Thus, by addressing solutions, such as biostimulation, improving environmental variables for optimal growth and enzymatic rates, and increasing the supply of the electron acceptors needed for anaerobic respiration help to remove obstacles to biodegradation. Additionally, the use of co-substrates or techniques such as bioaugmentation can further enhance this endeavor. Aerobic hydrocarbon degradation also has its challenges, especially for complex aromatic compounds such as PAH.s Electrokinetics (EK) is a remediation technology can be used to make species more accessible such as contaminants, nutrients, electrons acceptors, and electron donors. EK technology can be used to migrate certain contaminants but can also greatly enhance the aerobic degradation of PAHs primarily by increasing bioavailability and nutrient delivery. Studies were conducted to examine differences in electromigration rates for sand and clay. Two dyes, a red dye with anionic properties (FD&C 40) and a green dye with both anionic and cationic properties, composed of turmeric and Spirulina Blue were analyzed separately. The component of the green dye found to readily migrate is Spirulina Blue, consisting primarily of the protein pigment C-phycocyanin. The red dye in both sand and clay moves towards the anode, as predicted, and the rate between the two media was found to be approximately ten-fold. The green dye, having amphoteric qualities, can accept or donate protons, and can thus become strongly positively or negatively charged depending upon the pH of the system. It was found that due to a shifting pH gradient over time (in sand), this dye was initially anionic and thus migrated towards the anode but ceased migration after 48-72 hours due to a shift to a positive charge. Additional studies were conducted to observe how pH gradients in both sand and soil change over time. It is discovered that the rate at which the pH changes is dependent upon system variables including the current applied, which appears to absent from the literature, and that the initial semi-linear trend does not match the final gradient typically reported. The final study investigates the potential of EK technology to enhance biodegradation. In order to do so, a sandy soil, spiked with three compounds (fluorene, phenanthrene, fluoranthene) is placed within self-designed electrokinetic setups and an initial experiment shows a high possibility of PAH degradation but is unconfirmable. A second experiment attempts to verify the general findings of the first experiment and employs the use of a surfactant (Brij-35), which is thought to increase microbial movement throughout the contaminated soil and possibly reduce the sorption of PAHs to soil particles, both thereby increasing bioavailability and degradation rates. While biological activity is very apparent in this experiment, no degradation is observed and this may be due to a presence of carbonaceous materials (i.e. organic matter) within the soil. This yields an additional variable that must be taken into consideration in future in-situ studies or remediation projects. Overall it is found that many factors need to be taken into consideration for both aerobic and anaerobic biodegradation of PAHs. Increasing favorable growth conditions and increasing bioavailability can greatly help with this endeavor. Electrokinetics is an efficient means of ensuring this takes place but very specific designs or methods may be needed and pH gradients and extremes are found to provide significant obstacles to certain implementation but the results found in these experiments may be helpful to shed light on means of maintaining biological or chemical degradation experiments in an in-situ environment

DNA conformation and protein DNA interaction

Issued as Preliminary report, Project no. G-41-B05 (continues G-41-B04; continued by G-41-B06

Transmission of conformational stability through adjacent regions of DNA

Issued as Final report, Project no. G-41-64

Interaction of RNA polymerase with DNA

Issued as Summary progress report, Project no. G-41-B02 (continuation of G-41-B01; continued by G-41-B03

Phase Transition of DNA-Linked Gold Nanoparticle

Melting and hybridization of DNA-capped gold nanoparticle networks are investigated with optical absorption spectroscopy. Single-stranded, 12-base DNA-capped gold nanoparticles are linked with complementary, single-stranded, 24-base linker DNA to form particle networks. Compared to free DNA, a sharp melting transition is seen in these networked DNA-nanoparticle systems. The sharpness is explained by percolation transition phenomena.Comment: 9 pages, 4 figures, submitte

Influence of ribose 2′-O-methylation on GpC conformation by classical potential energy calculations

Potential energy calculations were employed to examine the effect of ribose 2′-O-methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker-C(3′)-endo, ω′ and ω,g−g−, bases-anti) is the global minimum, and a helix-reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g− g− helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′-O-methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates

Small instrumentation grant

Issued as Final progress report, Project G-32-62

Statistical Theory of Force Induced Unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the stiffness of single strand of DNA and the potential depth $D$. We used constant extension ensemble to calculate the average force needed to stretch a base pair $y$ distance apart. A very large peak around $y = 1 {\rm \AA}$ is found. The value of $F(y)$ needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance. The effect of mismatching in the base pairs on the peak height and position is investigated. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of "an eye" when a base pair far from ends is stretched are investigated.Comment: Minor changes in figures, published versio