Interaction of synthetic analogs of distamycin and netropsin with nucleic acids. Does curvature of ligand play a role in distamycin-DNA interactions?

Distamycin and netropsin, a class of minor groove binding nonintercalating agents, are characterized by their B-DNA and A-T basespecific interactions. To understand the CQI I ~OIT~ ~ I ~ ~aOnMd ~c hemical basis of the above specificities, the DNA-binding characteristics of a novel synthetic analogue of distamycin have been studied. The analogue, mPD derivative, has the requisite charged end groups and a number of potential hydrogen-bonding loci equal to those of distamycin. The difference in the backbone curvatures of the ligands, distamycin, the mPD derivative, and NSC 101327 (another structurally analogous compound),is a major difference between these ligands. UV and CD spectrosoopic studies reported here show the following salient features: The mPD derivative recognizes only B-DNA, to which it binds via the minor groove. On the other hand, unlike distamycin, it binds with comparable affinities to A-T and G-C base pairs in a natural DNA. These DNA-binding properties are compared with those reported earlier for distamycin and NSC 101327 [Zimmer, Ch., & Wahnert, U. (1986) Prog. Biophys. Mol. Biol. 47, 31-1121. The backbone structures of these three ligands were compared to show the progressive decrease in curvatures in the order distamycin, mPD derivative, and NSC 101327. The plausible significance of the backbone curvature vis-&vis the characteristic B-DNA and AT-specific binding of distamycin is discussed. To our knowledge, this is the first attempt (with a model synthetic analogue) to probe the possible influence of backbone curvature upon the specificity of interactions of the distamycin class of groove-binding ligands with DNA.

A matrix identity and perturbation expressions

An identity expressing formally the diagonal and off-diagonal elements of an inverse of a matrix is deduced employing operator techniques. Several well-known perturbation expressions for the self-energy are deduced as special cases. A new approximation and other applications following from the above formalism are briefly indicated through illustrations from a perturbed harmonic oscillator, chemisorption approximations and Kelly's result in the problem of electron correlation.

On computing an equivalent symmetric matrix for a nonsymmetric matrix

A real or a complex symmetric matrix is defined here as an equivalent symmetric matrix for a real nonsymmetric matrix if both have the same eigenvalues. An equivalent symmetric matrix is useful in computing the eigenvalues of a real nonsymmetric matrix. A procedure to compute equivalent symmetric matrices and its mathematical foundation are presented.

Strong metal-support interaction in nickel/niobium pentoxide and nickel/titania catalysts

EXAFS studies of Ni/Nb20, and Ni/Ti02 catalysts reduced at 773 K show evidence for the presence of a short Ni-Nb (Ti) and a long Ni-Nb (Ti) bond. The results provide evidence for considerable structural reorganization of the support in the vicinity of the Ni particles.

Interaction of water molecules in non-identical protein structures

The interaction of the protein atoms with the surrounding water oxygen atoms has been computed for 392 protein chains from 369 protein structures belonging to 90% non-homologous high resolution (<= 1.5 angstrom) protein Structures with a crystallographic R-factor <= 20%. The percentage composition of the polar atoms is found to be 36.3%. An average of 82.55% of water oxygen atoms are found to be in the primary hydration shell and 15.12% in the secondary hydration shell. The average Percentage of interactions of water oxygen atoms with the polar atoms of the main chain and side chain are 54% and 46%. respectively. The interaction of the acidic residues, aspartate and glutamate, with the water oxygen atoms is more when compared to that of the other residues.

An integer arithmetic method to compute generalized matrix inverse and solve linear equations exactly

An algorithm that uses integer arithmetic is suggested. It transforms anm ×n matrix to a diagonal form (of the structure of Smith Normal Form). Then it computes a reflexive generalized inverse of the matrix exactly and hence solves a system of linear equations error-free.

Theoretical Treatment of Interaction Parameters in Multicomponent Metallic Solutions

A new theoretical equation for interaction parameter in multicomponent metallic solutions is developed using the pseudopotential formalism coupled with the free energy of the hard sphere system. The approximate expression for the pseudopotential term is given in terms of the heat of solution at infinite dilution, to allow easy evaluation of the interaction parameter in various multicomponent systems. This theory has been applied to 23 non-ferrous alloys based on Pb, Sn, Bi and indium. Comparison with the results of previous theoretical calculations using only the hard sphere model suggests that the inclusion of the pseudopotential term yields a quantitatively more correct prediction of interaction parameters in multicomponent metallic solutions. Numerical calculations were also made for 320 Fe-base solutions relevant to steelmaking and the agreement between calculation and experimental data appears reasonable, with 90% reliability in predicting the correct sign.

Thermodynamic consistency of the interaction parameter formalism

The apparent contradiction between the exact nature of the interaction parameter formalism as presented by Lupis and Elliott and the inconsistencies discussed recently by Pelton and Bale arise from the truncation of the Maclaurin series in the latter treatment. The truncation removes the exactness of the expression for the logarithm of the activity coefficient of a solute in a multi-component system. The integrals are therefore path dependent. Formulae for integration along paths of constant Xi,or X i/Xj are presented. The expression for In γsolvent given by Pelton and Bale is valid only in the limit that the mole fraction of solvent tends to one. The truncation also destroys the general relations between interaction parameters derived by Lupis and Elliott. For each specific choice of parameters special relationships are obtained between interaction parameters.

Controlled photoluminescence from self-assembled semiconductor-metal quantum dot hybrid array films

Thin films of hybrid arrays of cadmium selenide quantum dots and polymer grafted gold nanoparticles have been prepared using a BCP template. Controlling the dispersion and location of the respective nanoparticles allows us to tune the exciton-plasmon interaction in such hybrid arrays and hence control their optical properties. The observed photoluminescence of the hybrid array films is interpreted in terms of the dispersion and location of the gold nanoparticles and quantum dots in the block copolymer matrix.

The role of inflammation and matrix proteins in airway remodelling

Asthma is a chronic inflammatory disorder of the airways. Remodelling in asthma is defined as the structural changes seen in the airways of asthmatics in comparison to healthy controls. Progressive loss of lung function also seen in asthma might be caused by remodelling. The research aims of this thesis were to investigate inflammation and remodelling in the airways of different types of asthmatics and smokers. The association between inflammation and remodelling was also examined in a mouse model of allergic airway inflammation. Healthy smokers showed increased numbers of macrophages in the BAL with no changes in the inflammatory cells in biopsies. Macrophages seemed to be quite quiescent, since mRNA expression for a wide variety of inflammatory mediators, especially chemokines CCL3, CCL4, CCL5 and CCL20, secreted by macrophages was significantly lower than in healthy non-smokers. Attenuated macrophage activity in the airway lumen may render smokers more susceptible to airway infections and have an impact on the development of other airway pathology. Patients with diisocyanate-induced asthma (DIA) on inhaled corticosteroids (ICS) who still had non-specific bronchial hyperreactivity (NSBHR) at the end of the follow-up showed increased expression of TNF-α, IL-6 and IL-15 mRNA in BAL cells compared to those without NSBHR. In addition to being markers for poor prognosis and possible slight glucocorticoid resistance, these cytokines might aid in guiding the treatment of DIA. The increase in the thickness of tenascin-C layer in the bronchial basement membrane (BM) was much less than usually seen in other types of asthma, which might not make tenascin-C a good marker for DIA. OVA-induced tenascin-C expression in the lung was attenuated in STAT4-/- mice with impaired Th1-type immunity compared to WT mice. Interestingly, STAT6-/- mice with impaired Th2-type immunity showed tenascin-C expression levels similar to those of WT mice. The clearest difference between these two knockout strains in response to OVA was that STAT4-/- mice exhibited no upregulation of IFN-γ and TNF-α mRNA expression. Thus, tenascin-C expression was unexpectedly more related to Th1 type reactions. In vitro studies confirmed the results. Human fibroblasts stimulated by TNF-α and IFN-γ showed increased expression of tenascin-C. Patients with newly diagnosed asthma showed increased expression of laminin α2 in the bronchial BM in comparison to patients with asthma symptoms only and healthy controls. Both patients with asthma and those with only asthma symptoms showed increased expression of the laminin β2 chain in comparison to controls. Thus, laminin α2 expression differentiated patients with clinical asthma from patients with symptoms only. Furthermore, the expression of laminin α2 and β2 was associated with NSBHR, linking very specific remodelling events to clinical findings.