Extent Of Bending Research Articles

A study of band-bending and barrier height variation in thin film n-CdSe 0.5Te 0.5 photoanode/polysulphide junctions

Polycrystalline thin films of n-CdSe 0.5Te 0.5 were deposited in a vacuum of 5 × 10 −5 torr by thermal flash evaporation with a deposition rate of 20 ± 1 A ̊ s −1 on indium oxide coated glass plates [ σ = 1.25 × 10 4 (Ω cm) −1 ] held at a temperature of 473 K. The change in the pH value of the polysulphide electrolyte from 12.5 to 8.0 leads to a fall in the extent of band bending from 680 meV to 420 meV and decrease in the barrier height from 690 meV to 430 meV. The barrier heights as calculated from Mott-Schottky plots and current-voltage plots are compared. From the reverse saturation current ( I 0) variation with temperature, it is found that the barrier height decreases from 690 meV to 430 meV with decrease in pH of the electrolyte from 12.5 to 8.0. The variation of diode ideality factor n, with temperature was also studied. It was found that the diode ideality factor n, decreases with increase of temperature, viz. from 3.00 to 2.00 with rise in temperature from 300 K to 333 K. This is due to the additional injection of electrons from the bulk into the junction region because of increase in temperature.

Machining‐Induced Surface Residual Stress Behavior in Al2O3–SiC Nanocomposites

The machining and subsequent annealing behavior of an Al2O3‐SiC nanocomposite (A12O3+ 5 vol% 0.2 μm SiC particles) was compared to that of single‐phase A12O3. The machining‐induced residual line force was determined by measuring the extent of elastic bending in thin disk specimens, and the surface roughness was evaluated by profilometry. The results showed that, when the two materials were subjected to the same grinding conditions, they developed compressive residual stresses and surface roughness values of similar magnitude. The maximum thickness of the residual stress layers was estimated to be ∼ 10 μm for the A12O3 and ∼12 μm for the nanocomposite. A direct linear correlation was observed between the residual force and the surface roughness for different machining treatments. Annealing of the machined samples produced complete relaxation of residual stresses in the single‐phase Al2O3, whereas only partial stress relaxation occurred for the nanocomposite.

The effect of interfacial instabilities on the strength of the interface in two‐layer plastic structures

AbstractWe have experimentally investigated the coupling between interfacial instabilities and mechanical interlocking in polymeric films consisting of the incompatible polymer pair of polypropylene/high‐density polyethylene and the compatible polymer pair of linear low‐density polyethylene/high‐density polyethylene. Our experimental results show that mechanical interlocking between the two phases can be achieved by controlling the extent of interfacial instabilities by properly selecting the initial disturbance frequency and amplitude as well as the layer depth ratio. Additionally, it has been shown that strength enhancement of the interface due to mechanical interlocking is directly proportional to the extent of wave bending in the processing apparatus. In fact, it has been demonstrated that in our test geometry maximum strength enhancement can be achieved at dimensionless wavenumbers near unity that correspond to disturbances with the largest growth rates. Overall, it has been shown that mechanical interlocking induced by a controlled amount of interfacial instabilities (i.e., based on knowledge of the stability of the interface and growth/decay rate of interfacial waves) can significantly increase the interfacial strength of two layer polymeric structures consisting of incompatible and compatible polymer pairs. Moreover, this effect is more pronounced in incompatible polymer pairs that possess negligible interfacial strength in absence of mechanical interlocking.

Helical periodicity of GA-alternating triple-stranded DNA.

Homopurine-homopyrimidine tracts (18 or 28 bp) containing predominantly GA-alternating sequences were inserted between two bent DNA loci composed of six (dA)6.(dT)6 repeats. For each homopurine tract, the DNA length between the bent DNA loci was varied by one base pair over a full helical turn. The two series of bent DNA fragments were electrophoresed in 5% polyacrylamide gel to measure the gel mobilities, which reflected the overall extent of DNA bending of each DNA fragment. By comparing the gel mobilities between the two series of bent DNA fragments, the helical periodicity of the GA-alternating duplex was determined to be 10.4 bp/turn. The two series of bent DNA fragments were also electrophoresed upon formation of the intermolecular triplex at the homopurine.homopyrimidine tracts. Comparison of the gel mobilities between the two series of DNA fragments showed that the helical periodicity of triplexed DNA of GA-alternating sequence was 11.2 bp/turn. Triplexed DNA with homopurine and homopyrimidine oligodeoxyribonucleotides had the same helical periodicity, while hybrid triplex DNA associated with homopyrimidine oligoribonucleotide had a slightly more wound structure with 11.1 bp/turn.

Hydroxyl radical footprints and half-site arrangements of binding sites for the CysB transcriptional activator of Salmonella typhimurium

CysB is a transcriptional activator for the cysteine regulon and negatively autoregulates its own gene, cysB. Transcription activation also requires an inducer, N-acetyl-L-serine. CysB is known to bind to activation sites just upstream of the -35 regions of the positively regulated cysJIH, cysK, and cysP promoters and to a repressor site centered at about +1 in the cysB promoter. Additional accessory sites have been found in positively regulated promoters. The hydroxyl radical footprinting experiments reported here indicate that the activation sites CBS-J1, CBS-K1, and CBS-P1 in the cysJIH, cysK, and cysP promoters are composed of two convergently oriented 19-bp half-sites separated by 1 or 2 bp. N-Acetyl-L-serine stimulates binding to these sites as well as to the accessory sites CBS-J2 and CBS-P2, both of which share a similar topology with activation sites. A second topology is found in the accessory site CBS-K2 and the repressor site CBS-B, which contain divergently oriented 19-bp half-sites separated by one or two helical turns. N-Acetyl-L-serine inhibits binding to these two sites. A third topology is present in the cysK and cysP promoters, where an additional half-site is oriented toward the activation site and separated from it by one helical turn. Here, CysB binds to all three half-sites, bending the DNA, and N-acetyl-L-serine decreases the extent of bending. The marked dissimilarities of these half-site arrangements and of their responses to N-acetyl-L-serine suggest that CysB, a homotetramer, binds to them with different combinations of subunits.

Stress protection afforded by a cast on plate fixation of the distal forelimb in the horse in vitro.

Six forelimb specimens from three adult horses had the fetlock joint fused by application of a dorsal plate and by a screw placed in lag fashion through the metacarpus to each proximal sesamoid bone. Five specimens were instrumented on the central dorsal surface of the plate with a single rosette strain gage, and the plate of the sixth specimen was instrumented with four longitudinally oriented single-axis strain gages. The specimens were loaded axially in compression to 4,000 N in a cast (test 1), in a cast with a heel block (test 2), and uncast (test 3). The principal angle of strain in all specimens, in all tests, closely approximated the vertical axis at loads < 1,000 N. The principal angle in uncast specimens was significantly different at loads > 1,000 N than the cast specimens (P < .05). At loads > 3,000 N, the principal angle in test 3 closely approximated the horizontal axis, indicating a change from tension to compression on the dorsal surface of the plate, whereas the principal angle of the cast specimens was unchanged. Specimens in a cast (tests 1 and 2) suffered less surface deformation than did uncast specimens (test 3). Therefore, the cast changed the direction and extent of bending at the point of fixation, and thereby decreased the deformation of the plate. This effect would lead to greater fatigue life of the implant in the cast specimens compared with the uncast specimens.

Protonation of fused aromatic systems: Ab initio study of some model Wheland intermediates

AbstractStructure and properties of Wheland's intermediates are studied in some model systems. The effect of the annelated small ring is simulated by bending two vicinal CH bonds in benzene toward each other. The extent of bending describes the ring‐size effect of a small fused fragment molecule. The electrophilic substituent is represented by a proton. Calculations at the HF/6‐31G* and MP2/HF/6–31G* levels of sophistication confirm the Mills–Nixon (MN) hypothesis. It is conclusively shown that ß‐complexes are more stable than are α‐protonated species. The results are interpreted in terms of the ground‐state density distribution dictated by rehybridization and of the transition structure π‐electron redistribution triggered by protonation. Their effects are additive to a large extent as far as CC bond distances are concerned. Energetic properties are determined by the interplay of two characteristic π‐electron localization patterns, one caused by the initial angular strain and the accompanying rehybridization related to the ground state and the other one occurring during formation of the proton σ‐complex. This interplay destabilizes α‐intermediates relative to ß‐intermediates. © 1994 John Wiley &amp; Sons, Inc.

DNA bending by retinoid X receptor-containing retinoid and thyroid hormone receptor complexes.

Retinoid X receptors (RXR) have been identified as common subunits in the regulation of multiple hormonal signaling pathways. Using circular permutation and phasing analysis of specific response elements, we present evidence that RXR-retinoic acid receptor and RXR-thyroid hormone receptor heterodimer or RXR-RXR homodimer complexes induce directed DNA bends when bound to their cognate response elements. The extent of DNA bending induced by the RXR alpha-containing complexes varied and depended on the structure of the DNA-binding sites and the RXR partners. The overall bending orientation for RXR-containing complexes is directed toward the major groove of the DNA helix at the center of hormone response elements. Our observation implicates DNA bending as a possible mechanism underlying transcriptional regulation of distinct retinoid and thyroid hormone responsive genes.

DNA bending by retinoid X receptor-containing retinoid and thyroid hormone receptor complexes.

Retinoid X receptors (RXR) have been identified as common subunits in the regulation of multiple hormonal signaling pathways. Using circular permutation and phasing analysis of specific response elements, we present evidence that RXR-retinoic acid receptor and RXR-thyroid hormone receptor heterodimer or RXR-RXR homodimer complexes induce directed DNA bends when bound to their cognate response elements. The extent of DNA bending induced by the RXR alpha-containing complexes varied and depended on the structure of the DNA-binding sites and the RXR partners. The overall bending orientation for RXR-containing complexes is directed toward the major groove of the DNA helix at the center of hormone response elements. Our observation implicates DNA bending as a possible mechanism underlying transcriptional regulation of distinct retinoid and thyroid hormone responsive genes.

Cyclopentadienylideneketene: Theoretical confirmation of a key infrared band

Optimized structures and harmonic vibrational frequencies have been obtained at the MP2/6-31G* level for cyclopentadienylideneketene ( 1), propadienone ( 2) and difluoropropadienone ( 3). It is found that 1 is a strongly bent molecule, the extent of bending being similar to that in 2. Theoretical predictions for 1, in conjunction with theoretical and experimental vibrational frequency data for 2 and 3, provide strong support for the assignment of a 2085 cm −1 absorption band, often seen in the infrared spectrum of benzyne, to the ketenic stretching frequency of 1.

Bending-incompetent variants of Flp recombinase mediate strand transfer in half-site recombinations: role of DNA bending in recombination

One key feature of the interaction of Flp recombinase with its target site ( FRT) is the large bend introduced in the substrate as a result of protein binding. The extent of bending was found to depend on the phasing and spacing of the Flp monomers occupying the two Flp-binding elements ( FBE) bordering the strand-exchange region (spacer) of the substrate. The relative mobilities of the Flp complexes formed by the two permuted substrate fragments, containing the FRT site near the end or in the middle, corresponded to a DNA bend of approx. 140° when each of the two FBEs flanking the spacer was occupied by a protein monomer. The estimated bend angle was the same when the reference DNA fragment with the FRT site at the end was substituted by one with the site in the middle, but containing a 4-bp insertion within the spacer. We used a combination of wild-type Flp and Flp variants that were competent or incompetent in DNA bending, together with full, or half FRT sites, to ask whether bending is a conformational requirement for catalysis, namely cleavage and exchange of strands. We obtained the following results: in full-site ( FRT) vs. full-site recombinations or in full-site vs. half-site (half FRT) recombinations, there was a large difference in the reactivity between Flp and a bending-incompetent Flp variant. This difference virtually disappeared when reactions were done with half- FRT sites. We conclude that bending is not a prerequisite for catalysis, but represents the manner in which the substrate accommodates the Flp protomer-protomer interactions that are pertinent to catalysis.

Solution studies on the structure of bent DNA in the cAMP receptor protein-lac DNA complex.

Cyclic AMP receptor protein is involved in the regulation of more than 20 genes. A step in the mechanism of activation of transcription is to induce a significant bending of the DNA upon complex formation between specific DNA and the protein. The induced DNA bending and a structure of the protein-DNA complex were studied by fluorescence energy transfer in 50 mM Tris, 1 mM EDTA, and 50 mM KCl at pH 7.8 and 20 degrees C. The symmetry of the DNA bend was estimated by measuring the efficiency of transfer between the protein and a label on either the upstream or the downstream end of a lac DNA fragment. The results show that the bend, despite the asymmetry in the DNA sequence, is symmetrical, for the fragments which length ranges from 26 to 40 bp. Using fluorescence energy transfer, the extent of DNA bending was estimated by measuring the end-to-end distance of the DNA fragment which was labeled with a donor-acceptor pair on two opposite ends. Both steady-state and time-resolved measurements showed that in a 26 bp lac DNA fragment complexed with cyclic AMP receptor protein, the end-to-end distance is about 77 A which corresponds to a bending angle of 80 degrees or 100 degrees, depending on the actual contour length between the fluorophores in the free DNA fragment. The results using longer DNA fragments show no measurable amount of energy transfer; thus, it is very unlikely that the DNA completely wraps around the CRP molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

Bending fluctuations of an elastic line on a curved surface

In an ongoing effort to model the mechanical behavior of the nucleosome core particle in terms of elasticity theory, we study the bending fluctuations of an elastic line (nucleosomal DNA) confined to a curved surface (outside surface of the histone octamer). We define what is meant by a bending fluctuation by generalizing from the plane, where a relaxed elastic line is a segment of a straight line, a fluctuation carries the straight segment to an arc of a circle, and the measure of the extent of bending is the total curvature of the arc. It is then natural to measure the extent of a bending fluctuation on a general surface by the total geodesic curvature of the arc into which the elastic line is carried by the fluctuation. The path of the bent elastic line must satisfy a differential equation on the surface, which is derived by variational methods. The bending energy per unit length scales with the square of the extent of bending (Hooke’s law) if the surface is a plane or a sphere, but not generally. For application to the nucleosome core particle, bending fluctuations on a cylinder are analyzed. A relaxed elastic line on a cylinder can follow a circumferential trajectory only if its length l does not exceed a critical value lcrit. For subcritical lengths, a fluctuational bend away from the circumferential path requires an amount of energy that does not conform to Hooke’s law. The energy vanishes at the critical length (to lowest order in the square of the bending angle) and the mean-square thermal bending amplitude diverges, an event that could be related to conformational changes of the nucleosome core particle. A formal analogy between bending of an elastic line on a cylinder and the Landau theory of second-order phase transitions is explored in detail.

Thyroid hormone responsiveness in human growth hormone-related genes. Possible correlation with receptor-induced DNA conformational changes.

Triiodothyronine (T3) induces the transcription of the human chorionic somatomammotropin (hCS) promoter transfected into rat pituitary (GC) cells, but does not stimulate the homologous human growth hormone (hGH) promoter. As demonstrated by forward and reverse mutagenesis, this differential T3 responsiveness is due to subtle structural differences in a T3 response element located between nucleotides -64 and -44 of the 5'-flanking DNA of the hGH and hCS promoters. Synthetic hCS(-70/-40) DNA binds thyroid hormone receptors with a 4-fold higher affinity than the corresponding hGH T3 response element, indicating that small differences in receptor binding properties are reflected by major differences in T3 responsiveness. Analysis of circular permutation fragments containing the native hGH and hCS or mutated hCS(-70/-40) sequences demonstrates that the thyroid hormone receptor induces DNA bending. The extent of bending shows a possible correlation with the function of these sequences, suggesting that the receptor-induced changes in DNA conformation may be required for thyroid hormone receptor action.

Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity

We report measurements of the relative binding affinity of CAP for DNA sequences which have been systematically mutated in the region flanking the consensus binding site. Our experiments focus on the locus one helical turn from the dyad axis where DNA bending toward the minor groove is induced upon C-AP binding. The binding free energy and extent of bending are moderately well correlated for the set of 56 sequences. Changes in binding affinity spanning a factor of about 50 could be accounted for by additive contributions of dinucleotides; with a few exceptions, the relative ranking of dinucleotide contributions to binding and bending are similar. We conclude that dinucleotides are the smallest independent unit required for quantitative interpretation of CAP-induced DNA bending and binding in the distal domains of the CAP consensus binding site. The imperfect correlation between binding strength and extent of bending implies that sequence changes affect protein binding strength not only by altering the DNA deformation energy required to form the complex, but also by affecting directly the free energy of interaction between protein and DNA.

Dynamical fine structure of proteins and nucleic acids via molecular simulation

We have recently been investigating the dynamical fine structure of DNA oligonucleotides and protein structures based on molecular dynamics simulation. Recent results via d(CGCGAATTCGCG) and HIV-1 protease will be presented with an emphasis on new methods for tire analysis of aspects of structure which originate uniquely in dynamical motions. The results are compared with corresponding crystal structures and NMR data. A dynamical definition of persistence length is proposed for the analysis of oligonucleotide structures, and used to analyze the extent of axis bending in simulations as compared with crystal structures. In the protease, molecular dynamics results provide evidence for domain-domain interactions that are possibly significant in the functional energetics. Analysis of domain correlations via dynamical cross correlation maps will be discussed.

Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins

The extent of DNA bending induced by 434 repressor, its amino terminal DNA binding domain (R1-69), and 434 Cro was studied by gel shift assay. The results show that 434 repressor and R1-69 bend DNA to the same extent. 434 Cro-induced DNA bends are similar to those seen with the 434 repressor proteins. On approximately 265 base pair fragments, the cyclic AMP receptor protein of Escherichia coli (CRP) produces larger mobility shifts than does 434 repressor. This indicates that the 434 proteins bend DNA to a much smaller extent than does CRP. The effects of central operator sequence on intrinsic and 434 protein-induced DNA bending was also examined by gel shift assay. Two 434 operators having different central sequences and affinities for 434 proteins display no static bending. The amount of gel shift induced by 434 repressor on these operators is identical, showing that the 434 repressor bends operators with different central sequences to the same extent. Hence, mutations in the central region of the operator do not influence the bent structure of the unbound or bound operator.

Determination of the extent of DNA bending by an adenine-thymine tract

We determined the magnitude of the bend induced in DNA by an adenine-thymine tract by measuring the rate of cyclization of DNA oligonucleotides containing phased A tracts. A series of linear multimers with 2-bp single-stranded ends, in which the (A.T)6 tracts are separated by CG2-3C sequences and are positioned 10 and 11 bp apart alternately, were prepared from 21 bp long synthetic duplexed deoxyoligonucleotides. The cyclization rates of the multimers (105-210 bp) and the bimolecular association rate of the 84 bp long multimer were measured in the presence of DNA ligase. From the rate constants of the cyclization and bimolecular association reactions, ring closure probabilities were obtained for the multimers. The systematically bent molecules were simulated by Monte Carlo methods, and the ring closure probabilities were calculated for a given set of junction bend angles. By comparing the calculated values of ring closure probabilities to experimental values and adjusting the junction bend angles to fit experimental values, the extent of bending at the junctions (or the extent of bending for an adenine tract) was determined. We conclude that an A6 tract bends the DNA helix by 17-21 degrees.

Bending studies of DNA site-specifically modified by cisplatin, trans-diamminedichloroplatinum(II) and cis-[Pt(NH 3) 2 ( N3-cytosine) Cl] +

Duplex oligonucleotides containing a single intrastrand {Pt(NH 3) 2} 2+ cross-link or monofunctional adduct and either 15 or 22 bp in length were synthesized and chemically characterized. The platinum-modified and unmodified control DNAs were polymerized in the presence of DNA ligase and the products studied on 8% native polyacrylamide gels. The extent of DNA bending caused by the various platinum-DNA adducts was revealed by their gel mobility shifts relative to unplatinated controls. The bifunctional adducts cis-[Pt (NH 3) 2{d(GpG)}] +, cis-[Pt(NH 3) 2{d(ApG)}] +, and cis-[Pt(NH 3) 2{d(G*pTpG*)}], where the asterisks denote the sites of platinum binding, all bend the double helix, whereas the adduct trans-[Pt(NH 3) 2{d(G*pTpG*) }] imparts a degree of flexibility to the duplex. When modified by the monofunctional adduct cis-[Pt(NH 3) 2( N3-cytosine) (dG)]Cl the helix remains rod-like. These results reveal important structural differences in DNAs modified by the antitumor drug cisplatin and its analogs that could be important in the biological processing of the various adducts in vivo.

Asymmetric DNA Bending Induced by the Yeast Multifunctional Factor TUF

TUF is a yeast regulatory factor that binds to conserved DNA sequence elements involved in gene activation or silencing as well as in telomere function. Using gel electrophoresis analyses, we show here that TUF induces DNA bending at a site located upstream of the recognition sequence (rpg box). Several point mutations in the rpg box reduced TUF binding strength without affecting the extent of bending. Selective proteolysis of TUF.DNA complexes further suggested the existence of two separate protein domains involved in DNA bending and specific DNA recognition. DNA bending may be an important feature of multifunctional factors that could help them to recruit other proteins for the formation of multiprotein complexes.