Sequence-related structural DNA anomalies affect restriction enzyme activity and DNA polymerase I binding

DNA serves as a target molecule for several types of enzymes and may assume a wide variety of structural motifs depending upon the local sequence. The BssHII restriction site (GC)3 resides in a 9bp region of alternating pyrimidine and purine residues within the &phis;X174 genome. Such sequences are known to demonstrate non-canonical helical behavior under the appropriate conditions. The kinetics of BssHII cleavage was investigated in supercoiled and linear plasmid DNA, and in a 323bp DNA fragment obtained via amplification of &phis;X174. The rate of enzyme cleavage was enhanced in the supercoiled form and in the presence of 50μM cobalt hexamine. Similarly, cobalt hexamine was also found to enhance TaqI activity directly adjacent to the (GC)3 region. ^ Initial DNA polymerase I binding studies (including a gel mobility shift assay and a protection assay) indicated a notable interaction between DNA polymerase I and the BssHII site. An in-depth study revealed that equilibrium binding of DNA polymerase I to the T7 RNA polymerase promoter was comparable to that of the (GC)3 site, however the strongest interaction was observed with a cruciform containing region. Increasing the ionic strength of the solution environment, including the addition of DNA polymerase I reaction buffer significantly decreased the equilibrium dissociation constant values. ^ It is suggested that the region within or around the BssHII site experiences a conformational change generating a novel structure under the influence of supercoiled tension or 50μM cobalt hexamine. It is proposed that this transition may enhance enzyme activity and binding by providing an initial enzyme-docking site—the rate-limiting step in restriction enzyme kinetics. The high binding potential of DNA polymerase I for each of the motifs described, is hypothesized to be due to recognition of the structural DNA anomalies by the 3′–5′ exonuclease domain. ^

The correlation of structure and electronic properties near the surface of transition metal oxides

The strong couplings between different degrees of freedom are believed to be responsible for novel and complex phenomena discovered in transition metal oxides (TMOs). The physical complexity is directly responsible for their tunability. Creating surfaces/interfaces add an additional ' man-made' twist, approaching the quantum phenomena of correlated materials. ^ The dissertation focused on the structural and electronic properties in proximity of surface of three prototype TMO compounds by using three complementary techniques: scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and low energy electron diffraction, particularly emphasized the effects of broken symmetry and imperfections like defects on the coupling between charge and lattice degrees of freedom. ^ Ca1.5Sr0.5RuO4 is a layered ruthenate with square lattice and at the boundary of magnetic/orbital instability in Ca2-xSrxRuO4. That the substitution of Sr 2+ with Ca2+ causing RuO6 rotation narrows the dxy band width and changes the Fermi surface topology. Particularly, the γ(dxy) Fermi surface sheet exhibited hole-like in Ca1.5Sr0.5RuO4 in contrast to electron-like in Sr2RuO4, showing a strong charge-lattice coupling. ^ Na0.75CoO2 is a layered cobaltite with triangular lattice exhibiting extraordinary thermoelectric properties. The well-ordered CoO2-terminated surface with random Na distribution was observed. However, lattice constants of the surface are smaller than that in bulk. The surface density of states (DOS) showed strong temperature dependence. Especially, an unusual shift of the minimum DOS occurs below 230 K, clearly indicating a local charging effect on the surface. ^ Cd2Re2O7 is the first known pyrochlore oxide superconductor (Tc ∼ 1K). It exhibited an unusual second-order phase transition occurring at TS1 = 200 K and a controversial first-order transition at TS2 = 120 K. While bulk properties display large anomalies at TS1 but rather subtle and sample-dependent changes at TS2, the surface DOS near the EF show no change at T s1 but a substantial increase below TS2---a complete reversal as the signature for the transitions. We argued that crystal imperfections, mainly defects, which were considerably enhanced at the surface, resulted in the transition at TS2. ^

Structural Characterization of Metal Hydrides for Energy Applications

Hydrogen can be an unlimited source of clean energy for future because of its very high energy density compared to the conventional fuels like gasoline. An efficient and safer way of storing hydrogen is in metals and alloys as hydrides. Light metal hydrides, alanates and borohydrides have very good hydrogen storage capacity, but high operation temperatures hinder their application. Improvement of thermodynamic properties of these hydrides is important for their commercial use as a source of energy. Application of pressure on materials can have influence on their properties favoring hydrogen storage. Hydrogen desorption in many complex hydrides occurs above the transition temperature. Therefore, it is important to study the physical properties of the hydride compounds at ambient and high pressure and/or high temperature conditions, which can assist in the design of suitable storage materials with desired thermodynamic properties. ^ The high pressure-temperature phase diagram, thermal expansion and compressibility have only been evaluated for a limited number of hydrides so far. This situation serves as a main motivation for studying such properties of a number of technologically important hydrides. Focus of this dissertation was on X-ray diffraction and Raman spectroscopy studies of Mg2FeH6, Ca(BH4) 2, Mg(BH4)2, NaBH4, NaAlH4, LiAlH4, LiNH2BH3 and mixture of MgH 2 with AlH3 or Si, at different conditions of pressure and temperature, to obtain their bulk modulus and thermal expansion coefficient. These data are potential source of information regarding inter-atomic forces and also serve as a basis for developing theoretical models. Some high pressure phases were identified for the complex hydrides in this study which may have better hydrogen storage properties than the ambient phase. The results showed that the highly compressible B-H or Al-H bonds and the associated bond disordering under pressure is responsible for phase transitions observed in brorohydrides or alanates. Complex hydrides exhibited very high compressibility suggesting possibility to destabilize them with pressure. With high capacity and favorable thermodynamics, complex hydrides are suitable for reversible storage. Further studies are required to overcome the kinetic barriers in complex hydrides by catalytic addition. A comparative study of the hydride properties with that of the constituting metal, and their inter relationships were carried out with many interesting features.^

Critical Analysis on the Structural and Magnetic Properties of Bulk and Nanocrystalline Cu-Fe-O

Nanocrystalline and bulk samples of “Fe”-doped CuO were prepared by coprecipitation and ceramic methods. Structural and compositional analyses were performed using X-ray diffraction, SEM, and EDAX. Traces of secondary phases such as CuFe2O4, Fe3O4, and α-Fe2O3 having peaks very close to that of the host CuO were identified from the Rietveld profile analysis and the SAED pattern of bulk and nanocrystalline Cu0.98Fe0.02O samples. Vibrating Sample Magnetometer (VSM) measurements show hysteresis at 300 K for all the samples. The ferrimagnetic Neel transition temperature () was found to be around 465°C irrespective of the content of “Fe”, which is close to the value of cubic CuFe2O4. High-pressure X-Ray diffraction studies were performed on 2% “Fe”-doped bulk CuO using synchrotron radiation. From the absence of any strong new peaks at high pressure, it is evident that the secondary phases if present could be less than the level of detection. Cu2O, which is diamagnetic by nature, was also doped with 1% of “Fe” and was found to show paramagnetic behavior in contrast to the “Fe” doped CuO. Hence the possibility of intrinsic magnetization of “Fe”-doped CuO apart from the secondary phases is discussed based on the magnetization and charge state of “Fe” and the host into which it is substituted.