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.

Polypurine-polypyrimidine sequences adopt unwound structure in pBR322 form V DNA as probed by single-hit analysis of HpaII sites.

Structure at the polypurine-polypyrimidine sequences flanking the HpaII sites (CCGG) in pBR322 form V DNA was probed employing single-hit analysis using HpaII restriction endonuclease. Reduced cleavage efficiency of HpaII sites flanked by polypurine-polypyrimidine sequences suggested that under high torsional stress these sequences adopt unwound structures rendering these sites insensitive to restriction enzyme cleavage. In addition to polypurine-polypyrimidine sequences. HpaII sites flanked by alternating purine-pyrimidine sequence, a potential motif of left handed Z-DNA, were also found to be resistant to HpaII cleavage. Results obtained from various studies implicating structure sensitivity of restriction endonucleases and methylases were compiled and a direct correlation was observed between the occurrence of altered sites in a domain and its G/C content in pBR322 form V DNA.

Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Synthesis of Layered Perovskite Oxides, ACa2-xLaxNb3-xTix010 (A = K, Rb, Cs), and Characterization of New Solid Acids, HCa2-xLaxNb3-xTixOlo (0 < x d 2), Exhibiting Variable Bronsted Acidity?

Layered perovskite oxides of the formula ACa~,La,Nb3-,Ti,010 (A = K, Rb, Cs and 0 < x d 2) have been prepared. The members adopt the structures of the parent ACazNb3010. Interlayer alkali cations in the niobium-titanium oxide series can be ion-exchanged with Li+, Na+, NH4+, or H+ to give new derivatives. Intercalation of the protonated derivatives with organic bases reveals that the Bronsted acidity of the solid solution series, HC~ ~ , L ~ ,N~ ~ , T ~ ,dOep~eOnd, s on the titanium content. While the x = 1 member (HCaLaNbzTiOlo) is nearly as acidic as the parent HCazNb3010, the x = 2 member (HLazNbTizOlo) is a weak acid hardly intercalating organic bases with pKa - 11.3. The variation of acidity is probably due to an ordering of Nb/Ti atoms in the triple octahedral perovskite slabs, [Ca~,La,Nb~,Ti,0~0], such that protons are attached to NbO6 octahedra in the x = 1 member and to Ti06 octahedra in the x = 2 member.

Hybrid Polypeptides: Gabapentin as a Stereochemically Constrained gamma-Amino Acid Residue

The design of folded structures in peptides containing the higher homologues of alpha-amino acid residues requires the restriction of the range of local conformational choices In alpha-amino acids stereochemically constrained residues like alpha,alpha-dialkylated residue, aminoisobutyric acid (Aib), and D-Proline ((D)Pro) have proved extremely useful in the design of helices and hairpins in short peptides Extending this approach, backbone substitution and cyclization are anticipated to bc useful in generating conformationally constrained beta- and gamma-residues This brief review provides a survey of work on hybrid peptide sequences concerning the conformationally constrained gamma-amino acid residue 1-aminomethyl cyclohexane acetic acid, gabapentin (Gpn) This achiral, beta,beta-disubstituted, gamma-residue strongly favors gauche-gauche conformations about the C-alpha-C-beta (0(2)) and C-alpha-C-gamma (0(1)) bonds, facilitating local folding The Gpn residue can adopt both C-7 (NH1 -> CO1) and C-9 (CO1 (I)<- NH1+I) hydrogen bonds which are analogous to the C-5 and C7 (gamma-turn) conformations at alpha-residues In conjunction with adjacent residues, Gpn may be used in ay and gamma alpha segments to generate C-12 hydrogen bonded conformations which may be considered as expanded analogs of conventional beta-turns The structural characterization of C-12 helices, C-12/C-10 helices with mixed hydrogen bond directionalities and beta-hairpins incorporating Gpn residues at the turn segment is illustrated (C) 2010 Wiley Periodicals, Inc Biopolymers (Pept Sci) 94 733-741 2010

Memory Bandwidth and Power Reduction Using Lossy Reference Frame Compression in Video Encoding

Large external memory bandwidth requirement leads to increased system power dissipation and cost in video coding application. Majority of the external memory traffic in video encoder is due to reference data accesses. We describe a lossy reference frame compression technique that can be used in video coding with minimal impact on quality while significantly reducing power and bandwidth requirement. The low cost transformless compression technique uses lossy reference for motion estimation to reduce memory traffic, and lossless reference for motion compensation (MC) to avoid drift. Thus, it is compatible with all existing video standards. We calculate the quantization error bound and show that by storing quantization error separately, bandwidth overhead due to MC can be reduced significantly. The technique meets key requirements specific to the video encode application. 24-39% reduction in peak bandwidth and 23-31% reduction in total average power consumption are observed for IBBP sequences.

CAITG 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.

Effective action and adiabatic expansions for the 1-D and 2-D hubbard models at half-filling

We analyze here the occurrence of antiferromagnetic (AFM) correlations in the half-filled Hubbard model in one and two space dimensions using a natural fermionic representation of the model and a newly proposed way of implementing the half-filling constraint. We find that our way of implementing the constraint is capable of enforcing it exactly already at the lowest levels of approximation. We discuss how to develop a systematic adiabatic expansion for the model and how Berry's phase contributions arise quite naturally from the adiabatic expansion. At low temperatures and in the continuum limit the model gets mapped onto an O(3) nonlinear sigma model (NLsigma). A topological, Wess-Zumino term is present in the effective action of the ID NLsigma as expected, while no topological terms are present in 2D. Some specific difficulties that arise in connection with the implementation of an adiabatic expansion scheme within a thermodynamic context are also discussed, and we hint at possible solutions.

Generating synchronizable test sequences based on finite-statemachine with distributed ports

In the area of testing communication systems, the interfaces between systems to be tested and their testers have great impact on test generation and fault detectability. Several types of such interfaces have been standardized by the International Standardization Organization (ISO). A general distributed test architecture, containing distributed interfaces, has been presented in the literature for testing distributed systems based on the Open Distributing Processing (ODP) Basic Reference Model (BRM), which is a generalized version of ISO distributed test architecture. We study in this paper the issue of test selection with respect to such an test architecture. In particular, we consider communication systems that can be modeled by finite state machines with several distributed interfaces, called ports. A test generation method is developed for generating test sequences for such finite state machines, which is based on the idea of synchronizable test sequences. Starting from the initial effort by Sarikaya, a certain amount of work has been done for generating test sequences for finite state machines with respect to the ISO distributed test architecture, all based on the idea of modifying existing test generation methods to generate synchronizable test sequences. However, none studies the fault coverage provided by their methods. We investigate the issue of fault coverage and point out a fact that the methods given in the literature for the distributed test architecture cannot ensure the same fault coverage as the corresponding original testing methods. We also study the limitation of fault detectability in the distributed test architecture.

Modified Crack Closure Integral (MCCI) For 3-D Problems Using 20-Noded Brick Elements

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

Hydrogen-bond-directed self-assembly of D-(+)-dibenzoyltartaric acid and 4-aminopyridine: optical nonlinearities and stoichiometry-dependent novel structural features

Attempts to prepare hydrogen-bond-directed nonlinear optical materials from a 1:1 molar mixture Of D-(+)-dibenzoyltartaric acid (DBT, I) and 4-aminopyridine (4-AP, II) resulted in two salts of different stoichiometry. One of them crystallizes in an unusual 1.5:1 (acid:base) monohydrate salt form III while the other one crystallizes as 1:1 (acid:base) salt IV. Crystal structures of both of the salts were determined from single-crystal X-ray diffraction data. The salt III crystallizes in a monoclinic space group C2 with a = 30.339(l), b = 7.881(2), c = 14.355(1) angstrom, beta = 97.48(1)degrees, V = 3403.1(9) angstrom3, Z = 4, R(w) = 0.058, R(w)= 0.058. The salt IV also crystallizes in a monoclinic space group P2(1) with a = 7.500(1), b = 14.968(2), c = 10.370(1) angstrom, beta = 102.67(1)degrees, V = 1135.9(2) angstrom3, Z = 2, R = 0.043, R(w) = 0.043. Interestingly, two DBT molecules with distinctly different conformation are present in the same crystal lattice of salt III. Extensive hydrogen-bonding interactions are found in both of the salts, and both of them show SHG intensity 1.4-1.6 times that of urea.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Modified crack closure integral (MCCI) for 3-d problems using 20 noded brick elememnts

The Modified Crack Closure Integral (MCCI) technique based on Irwin's crack closure integral concept is very effective for estimation of strain energy release rates G in individual as well as mixed-mode configurations in linear elastic fracture mechanics problems. In a finite element approach, MCCI can be evaluated in the post-processing stage in terms of nodal forces and displacements near the crack tip. The MCCI expressions are however, element dependent and require a systematic derivation using stress and displacement distributions in the crack tip elements. Earlier a general procedure was proposed by the present authors for the derivation of MCCI expressions for 3-dimensional (3-d) crack problems modelled with 8-noded brick elements. A concept of sub-area integration was proposed to estimate strain energy release rates at a large number of points along the crack front. In the present paper a similar procedure is adopted for the derivation of MCCI expressions for 3-d cracks modelled with 20-noded brick elements. Numerical results are presented for centre crack tension and edge crack shear specimens in thick slabs, showing a comparison between present results and those available in the literature.

3-D Warping in Four-Bar Laminated Linkages

This paper deals with the evaluation of the component-laminate load-carrying capacity, i.e., to calculate the loads that cause the failure of the individual layers and the component-laminate as a whole in four-bar mechanism. The component-laminate load-carrying capacity is evaluated using the Tsai-Wu-Hahn failure criterion for various layups. The reserve factor of each ply in the component-laminate is calculated by using the maximum resultant force and the maximum resultant moment occurring at different time steps at the joints of the mechanism. Here, all component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically nonlinear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and nonlinear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional nonlinearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the nonlinear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the nonlinear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict more quickly and accurately than would otherwise be possible. Local 3-D stress, strain and displacement fields for representative sections in the component-bars are recovered, based on the stress resultants from the 1-D global beam analysis. A numerical example is presented which illustrates the failure of each component-laminate and the mechanism as a whole.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.