Conformational flexibility of DNA: polymorphism and handedness

It is shown that left-handed duplexes are possible for A, B, and D forms of DNA. These duplexes are stereochemically satisfactory and are consistent with the observed x-ray intensity data. On scrutiny the refined right-handed models of B and D DNA by Arnott and coworkers are found to be stereochemically unacceptable. It was possible to formulate a stereochemical guideline for molecular model building based on theory and analysis of single-crystal structure data of dinucleoside monophosphate and higher oligomers. This led to both right- and left-handed DNA duplexes. The right-handed B and D DNA duplexes so obtained are stereochemically superior to earlier models and agree well with the observed x-ray intensity data. The observation that DNA can exist in either handedness for all the polymorphous forms of DNA at once explained A in equilibrium B and B in equilibrium D transitions. Hence it is confirmed that polymorphism of DNA is a reflection on the conformational flexibility inherent in DNA, the same cause that ultimately allows DNA in either handedness. The possibility of various types of right- and left-handed duplexes generated by using dinucleoside monophosphate and trinucleoside diphosphate as repeating units resulted in a variety of models, called RL models. All these models have alternating right and left helical segments and inverted stacking at the bend region as suggested by us earlier. It turns out that the B-Z DNA model of Wang et al. is only an example of RL models.

Crystalline A-DNA: The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)

An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its 5-bromouracil-containing analogue, 2. The structure of the isomorphous crystals (space group P61) was solved by a search technique based on packing criteria and R-factor calculations, with use of only low order data. At the present stage of refinement the R factors are 31 % for 1 and 28 % for 2 at a resolution of 2.25 A (0.225 nm). The molecules interact through their minor grooves by hydrogen bonding and base to sugar van der Waals contacts. The stable A conformation observed in the crystal may have some structural relevance to promoter regions where the T-A-T-A sequence is frequently found.

Heat-Transfer During Polymer Combustion

The nature of surface and subsurface reactions in polymer combustion is poorly underst0od.l During the burning of thermoplastic polymers a melt layer is observed on the surface, and below the melt layer there is thermal wave penetration. But the exact thickness of the melt layer and the thickness of the thermal wave penetration have not been precisely measured, although a qualitative idea has been given.

Use of S1 nuclease and formamide in combination for the reassociation studies on GC-rich DNA

The optimal parameters in the use of nuclease S1 in DNA reassociation kinetics in the presence of formamide have been determined. The conditions are especially suitable for the study of DNA rich in mole percent GC. A 10-fold dilution of the reassociation samples leading to a decrease in both NaCl and formamide concentrations, consequently resulting in a lowering of Tm by only 1.5°C, and the S1 digestion at temperatures identical to the reassociation assay in order to retain the stability of the duplex, are two important aspects of this system. Under these conditions, the kinetics of reassociation followed the theoretically predicted pattern, while the earlier reported methods have shown lower values.

Fibre diffraction of lithium DNA shows structural variability and deviation from a regular helical structure for the B-form

Recently, reports have appeared which show structural variations in B-DNA and indicate deviations from a uniform helical structure. We report for the first time that these indications are also present in the B-form fibre diffraction patterns for the lithium salt of natural DNA. We have used an improved method of controlling the salt concentration in the fibres. Our results are based on the appearance and disappearance of meridional reflections on different layer lines depending upon the salt.

Base specific binding of deoxyguanylate and deoxycytidylate antibodies to double stranded DNA

Antibodies raised in rabbits against daoxyguanylate and daoxycytidylate bind to 3H-(lambda) double stranded DNA and the binding is base specific. The concentrations of antibody populations that bind to double stranded DNA are much less than those binding to denatured DNA. Due to their low concentrations, these antibodies ware not detected in earlier studies. These antibodies are expected to be useful to probe the conformational flexibilities of double stranded DNAs.

Use of narrow-pore filters in He II transfer devices - new results

With the aim of finding simple methods for the fabrication of He II refilling devices, He II flow has been studied through filters made from various fine powders (oxides and metals, grain sizes in the range 0.05–2 μm) by compacting them under pressure. The results obtained for the different states of He II flow, especially in the “breakthrough” and “easy flow” range, are explained by the fountain effect, He II hydrodynamics and the choking effect. According to the results, pressedpowder filters can be classified into three groups with different flow characteristics, of which the “good transfer filters” with a behaviour neatly described by simple theory are suitable for use in He II refilling devices.

Compressible second-order boundary layers for three-dimensional stagnation point flows with mass transfer

All the second-order boundary-layer effects have been studied for the steady laminar compressible 3-dimensional stagnation-point flows with variable properties and mass transfer for both saddle and nodal point regions. The governing equations have been solved numerically using an implicit finite-difference scheme. Results for the heat transfer and skin friction have been obtained for several values of the mass-transfer rate, wall temperature, and also for several values of parameters characterizing the nature of stagnation point and variable gas properties. The second-order effects on the heat transfer and skin friction at the wall are found to be significant and at large injection rates, they dominate over the results of the first-order boundary layer, but the effect of large suction is just the opposite. In general, the second-order effects are more pronounced in the saddle-point region than in the nodal-point region. The overall heat-transfer rate for the 3-dimensional flows is found to be more than that of the 2-dimensional flows.

Left-handed helices for DNA: studies on poly[d(I-C)]

Earlier, we showed that, for the D form (n = 8 and h = 3.03 A, where n is number of nucleotide units per turn and h is height per nucleotide unit) of poly[d(A-T)], both right- and left-handed double helical models are stereochemically satisfactory and give good agreement with the observed fiber diffraction data. It was also noted that the conformations of the right- and left-handed D-DNA models are very similar to those of the right- and left-handed B-DNA models. This observation was consistent with the D leads to B transition in the solid phase. As a continuation of our earlier studies, we have carried out similar experiments with poly[d(I-C)]. We could obtain a crystalline D-form pattern (n = 8, h = 3.13 A) of the fiber at 75% relative humidity (r.h.); the hydrated (r.h. approximately equal to 95%) form of the same fiber gave the classical B-form pattern (n = 10, h = 3.40 A). In the present report, we show that both right- and left-handed double-helical models are consistent with the fiber diffraction data of poly[d(I-C)] in the D-form. Theoretical energy calculations also suggest that the right- and left-handed B- and D-DNA models are almost equally stable. Hence, we conclude that the right- and left-handed double-helical models of poly[d(I-C)] in a given form (B or D) are equally likely and that the fiber diffraction data do not permit discrimination.

Heat transfer in a MHD flow between eccentric disks rotating at different speeds

Heat transfer in a MHD flow between two infinite eccentric disks rotating with different speeds is considered when the plates are maintained at different temperatures. The results for the corresponding nonmagnetic case presented wrongly by Banerjee and Borkakati [7] are corrected. It is observed that the eccentric rotation reduces the heat transfer on the disks.

sopB of Salmonella enterica serovar Typhimurium is a potential DNA vaccine candidate in conjugation with live attenuated bacteria

The immune response against Salmonella is multi-faceted involving both the innate and the adaptive immune system. The characterization of specific Salmonella antigens inducing immune response could critically contribute to the development of epitope based vaccines for Salmonella. We have tried to identify a protective T cell epitope(s) of Salmonella, as cell mediated immunity conferred by CD8+ T cells is the most crucial subset conferring protective immunity against Salmonella. It being a proven fact that secreted proteins are better in inducing cell mediated immunity than cell surface and cytosolic antigens, we have analyzed all the genbank annotated Salmonella pathogenicity island 1 and 2 secreted proteins of Salmonella enterica serovar Typhimurium (S. typhimurium) and S. enterica serovar Typhi (S. typhi). They were subjected to BIMAS and SYFPEITHI analysis to map MHC-I and MHC-II binding epitopes. The huge profile of possible T cell epitopes obtained from the two classes of secreted proteins were tabulated and using a scoring system that considers the binding affinity and promiscuity of binding to more than one allele, SopB and SifB were chosen for experimental confirmation in murine immunization model. The entire SopB and SifB genes were cloned into DNA vaccine vectors and were administered along with live attenuated Salmonella and it was found that SopB vaccination reduced the bacterial burden of organs by about 5-fold on day 4 and day 8 after challenge with virulent Salmonella and proved to be a more efficient vaccination strategy than live attenuated bacteria alone.

Boundary-layer convective heat transfer in a convergent channel

In this paper the numerical solution of the heat transfer problem in a convergent channel with uniform and non-uniform wall temperatures under boundary-layer approximations has been presented. Also, a semi-analytical solution for uniform wall temperature has been obtained.

MHD Flow with Heat and Mass Transfer Due to a Point Sink

The magnetofluid dynamic steady incompressible laminar boundary layer flow for a point sink with an applied magnetic field and mass transfer has been studied. The two-point boundary-value problem governed by self-similar equations has been solved numerically. It is observed that the magnetic field increases the skin friction, but reduces the heat transfer and mass flux diffusion. However, the skin friction, heat transfer and mass flux diffusion increase due to suction and the effect of injection is just opposite. Prandtl and Schmidt numbers affect the temperature and concentration, respectively.