Molecular Mechanics Studies of Homopolymeric and Mixed Sequence Py.Pu*Pu Triple Helices,

DNA triple helices containing two purine strands and one pyrimidine strand (C.G*G and T.A*A) have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that in the C.G*G case the structure with a parallel orientation of the third strand, resulting from Hoogsteen hydrogen bonds between the third strand and the Watson-Crick duplex, is energetically the most favourable while in the T.A*A case the antiparallel orientation of the third strand, resulting from reverse Hoogsteen hydrogen bonds, is energetically the most favourable. These studies when extended to the mixed sequence triplexes, in which the second strand is a mixture of G and A, correspondingly the third strand is a mixture of G and APT, show that though the parallel orientation is still energetically more favourable, the antiparallel orientation becomes energetically comparable with an increasing number of thymines in the third strand. Structurally, for the mixed triplexes containing G and T in the third strand, it is seen that the basepair non-isomorphism between the C.G*G and the T.A*T triplets can be overcome with some changes in the base pair parameters without much distortion of either the backbone or the hydrogen bonds.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

A new model for coalescence efficiency of drops in stirred dispersions

A model for coalescence efficiency of two drops embedded in an eddy has been developed. Unlike the other models which consider only head-on collisions, the model considers the droplets to approach at an arbitrary angle. The drop pair is permitted to undergo rotation while they approach each other. For coalescence to occur, the drops are assumed to approach each other under a squeezing force acting over the life time of eddy but which can vary with time depending upon the angle of approach. The model accounts for the deformation of tip regions of the approaching drops and, describes the rupture of the intervening film, based on stability considerations while film drainage is continuing under the combined influence of the hydrodynamic and van der Waals forces. The coalescence efficiency is defined as the ratio of the range of angles resulting in coalescence to the total range of all possible approach angles. The model not only reconciles the contradictory predictions made by the earlier models based on similar framework but also brings out the important role of dispersed-phase viscosity. It further predicts that the dispersions involving pure phases can be stabilized at high rps values. Apart from explaining the hitherto unexplained experimental data of Konno et al. qualitatively, the model also offers an alternate explanation for the interesting observations of Shinnar.

Coherent rainfall zones of the Indian region

We have delineated rainfall zones for the Indian region that are coherent with respect to the variations of the summer monsoon rainfall. Within each zone, the time series of the summer monsoon rainfall at every pair of stations are significantly positively correlated, and the mean interseries correlation for each zone is high. The interseries correlation data set is analysed in order to delineate the rainfall zones, using an objective method specifically developed for the purpose. Each of the zonal averages are shown to be representative of the zone as a whole. We suggest that this regionalization is appropriate for study of the variation of the summer monsoon rainfall over the Indian region on interannual and larger scales.

CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Molecular expression for dielectric friction on a rotating dipole: Reduction to the continuum theory

Recently we presented a microscopic expression for dielectric friction on a rotating dipole. This expression has a rather curious structure, involving the contributions of the transverse polarization modes of the solvent and also of the molecular length scale processes. It is shown here that under proper limiting conditions, this expression reduces exactly to the classical continuum model expression of Nee and Zwanzig [J. Chem. Phys. 52, 6353 (1970)]. The derivation requires the use of the asymptotic form of the orientation‐dependent total pair correlation function, the neglect of the contributions of translational modes of the solvent, and also the use of the limit that the size of the solvent molecules goes to zero. Thus, the derivation can be important in understanding the validity of the continuum model and can also help in explaining the results of a recent computer simulation study of dielectric relaxation in a Brownian dipolar lattice.

Molecular theory of underdamped dielectric relaxation: understanding collective effects in dipolar liquids

A molecular theory of underdamped dielectric relaxation of a dense dipolar liquid is presented. This theory properly takes into account the collective effects that are present (due to strong intermolecular correlations) in a dipolar liquid. For small rigid molecules, the theory again leads to a three-variable description which, however, is somewhat different from the traditional version. In particular, two of the three parameters are collective in nature and are determined by the orientational pair correlation function. A detailed comparison between the theory and the computer simulation results of Neria and Nitzan is performed and an excellent agreement is obtained without the use of any adjustable or free parameter - the calculation is fully microscopic. The theory can also provide a systematic description of the Poley absorption often observed in dipolar liquids in the high-frequency regime.

NDDO-based CI methods for the prediction of electronic spectra and sum-over-states molecular hyperpolarization

NDDO-based (AM1) configuration interaction (CI) calculations have been used to calculate the wavelength and oscillator strengths of electronic absorptions in organic molecules and the results used in a sum-over-states treatment to calculate second-order-hyperpolarizabilities. The results for both spectra and hyperpolarizabilities are of acceptable quality as long as a suitable CI-expansion is used. We have found that using an active space of eight electrons in eight orbitals and including all single and pair-double excitations in the CI leads to results that agree well with experiment and that do not change significantly with increasing active space for most organic molecules. Calculated second-order hyperpolarizabilities using this type of CI within a sum-over-states calculation appear to be of useful accuracy.

Normal mode sound propagation in an ocean with random narrow-band surface waves

Normal mode sound propagation in an isovelocity ocean with random narrow-band surface waves is considered, assuming the root-mean-square wave height to be small compared to the acoustic wavelength. Nonresonant interaction among the normal modes is studied straightforward perturbation technique. The more interesting case of resonant interaction is investigated using the method of multiple scales to obtain a pair of stochastic coupled amplitude equations which are solved using the Peano-Baker expansion technique. Equations for the spatial evolution of the first and second moments of the mode amplitudes are also derived and solved. It is shown that, irrespective of the initial conditions, the mean values of the mode amplitudes tend to zero asymptotically with increasing range, the mean-square amplitudes tend towards a state of equipartition of energy, and the total energy of the modes is conserved.

Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel beta-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive chi(1) value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1 degrees C in T-m. All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (Delta Delta G(0) = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2011; 79: 244-260. (C) 2010 Wiley-Liss, Inc.

Modified conformation and physical properties in conducting polymers due to varying conjugation and solvent interactions

Small angle X-ray scattering (SAXS) studies of poly2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) with varying conjugation, and polyethylene dioxythiophene complexed with polystyrene sulfonate (PEDOT-PSS) in different solvents have shown the importance of the role of pi-electron conjugation and solvent-chain interactions in controlling the chain conformation and assembly. In MEH-PPV, by increasing the extent of conjugation from 30 to 100%, the persistence length (l(p)) increases from 20 to 66 angstrom. Moreover, a pronounced second peak in the pair distribution function has been observed in the fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. In the case of PEDOT-PSS, the chains undergo solvent induced expansion and enhanced chain organization. The clusters formed by chains are better correlated in dimethyl sulfoxide (DMSO) solution than water, as observed in the scattered intensity profiles. The values of radius of gyration and the exponent (water: 2.6, DMSO: 2.31) of power-law decay, obtained from the unified scattering function (Beaucage) analysis, give evidence for chain expansion from compact (in water) to an extended coil in DMSO solutions, which is consistent with the Kratky plot analysis. The mechanism of this transition and the increase in dc conductivity of PEDOT-PSS in DMSO solution are discussed. The onset frequency for the increase in ac conduction, as well as its temperature dependence, probes the extent of the connectivity in the PEDOT-PSS system. The enhanced charge transport in PEDOT-PSS in DMSO is attributed to the extended chain conformation, as observed in the SAXS results.

Role of Surface Texture, Roughness, and Hardness on Friction During Unidirectional Sliding

In the present investigation, experiments were conducted by unidirectional sliding of pins made of FCC metals (Pb, Al, and Cu) with significantly different hardness values against the steel plates of various surface textures and roughness using an inclined pin-on-plate sliding apparatus in ambient conditions under both the dry and lubricated conditions. For a given material pair, it was observed that transfer layer formation and the coefficient of friction along with its two components, namely adhesion and plowing, are controlled by the surface texture of the harder mating surfaces and are less dependent of surface roughness (R (a)) of the harder mating surfaces. The effect of surface texture on the friction was attributed to the variation of the plowing component of friction for different surfaces. It was also observed that the variation of plowing friction as a function of hardness depends on surface textures. More specifically, the plowing friction varies with hardness of the soft materials for a given type of surface texture and it is independent of hardness of soft materials for other type of surface texture. These variations could be attributed to the extent of plane strain conditions taking place at the asperity level during sliding. It was also observed that among the surface roughness parameters, the mean slope of the profile, Delta (a), correlated best with the friction. Furthermore, dimensionless quantifiable roughness parameters were formulated to describe the degree of plowing taking place at the asperity level.

Syntheses, spectroscopy, structures, and conformations of .lambda.3-cyclotriphosphazanes: role of negative hyperconjugation

The reactions of As-chlorocyclotriphosphazane [EtNPCl], with phenols or trifluoroethanol yield the respective aryloxy- or trifluoroethoxy-containingX 3-cyclotriphosphazanes [EtNP(OR)]3 (R = C6H4Br-4 (2),C 6H5 (3C,6 H3-Mez-3,5 (4), C6H3Mez-2,6 (5), CH2CF3 (6)) as their cis-transisomericmixtures. The products have beencharacterized by IRand NMRspectroscopy. Thecrystalstructuresofboth thecis (2a) and trans(2b) isomer_softhep-bromophenoxy derivative have been determined by X-ray diffraction. Crystal data for 2a: triclinic, P1, a = 9.872(4) A, b = 13.438(6) A, c = 13.548(8) A, CY = 117.02(5)', 0 = 96.00(6)', y = 105.38(4)O, Z = 2, final R = 0.080. Crystal data for 2b: monoclinic, P21/n, a = 12.721(6) A, b = 13.468(7) A, c = 17.882(5) A, /3 = 101.62(3)O, Z = 4, final R = 0.066. The cis isomer exhibits a chair-triaxial conformation and the trans isomer a boat-triaxial conformation. Conformational preferences of X3-cyclotriphosphazanes have been probed by both MNDO and ab initio calculations on model systems [HNPXIp (X = H, F). In addition to vicinal lone pair repulsions, negative hyperconjugative interactions involving the nitrogen lone pairs and adjacent P-X Q* orbitals are found to be important (especially when X is an electronegative substituent) in determining the conformational preferences of X3-cyclotriphosphazanes. The calculations also show that the axial - equatorial conversion at phosphorus has a large activation barrier in these systems