Central Bending Research Articles

Sequence-induced curvature of Tenebrio molitor satellite DNA

Single satellite DNA constitutes about 50% of the Tenebrio molitor genome. Electrophoresis of 142 base pair long satellite monomers on nondenaturating polyacrylamide gel shows retarded mobility, a characteristic of fragments with sequence-induced DNA curvature. Migrational analysis of circularly permuted satellite monomers revealed the existence of 2 bend centers in the monomer sequence. We calculated the trajectory of DNA helix axis according to the algorithm of De Santis et al [14]. This model predicts that T molitor naked satellite DNA forms a solenoid structure with left-handed superhelix. One turn of the superhelix has approximately 310 base pairs and a 33 nm pitch. Point mutations found in the satellite DNA (1.8%) influence bending characteristics, but do not distort the general geometry of satellite superhelix.

Intrinsic bends and integration host factor binding at F plasmid oriT

F plasmid oriT DNA extending from the F kilobase coordinate 66.7 (base pair [bp] 1 on the oriT sequence map) rightward to bp 527 was analyzed for intrinsic bends (by permutation assays) and for binding of integration host factor (IHF) (by gel retardation and DNase footprinting). Intrinsic bending of the 527-bp fragment (bend center approximately at bp 240) was represented as a composite of at least two components located near bp 170 and near bp 260. IHF bound primarily to a site extending from bp 165 to 195 and with lower affinity to a site extending from bp 287 to 319. The intrinsic curvature and sequences to which IHF binds (IHF is known to bend DNA) may play a structural role in oriT function.

The NF-ϰB transcription factor induces DNA bending which is modulated by its 65-kD subunit

This study describes a novel functional property of the eukaryotic transcription factor NF-kappa B in altering the DNA structure. We observed that the binding of purified NF-kappa B to DNA was facilitated by spermine and cations which are known to promote DNA bending, and by a nick in one position at the 3'-end of the binding site. Furthermore, the position of the NF-kappa B binding sequence 5'-GGGACTTTCC-3' (kappa B motif) within circularly permutated DNA fragments had a profound influence on the mobility of NF-kappa B-DNA complexes in a gel retardation assay while the mobility of unbound DNA fragments did not depend on the position of the kappa B motif. The mobility effect was slightly reduced at increased temperature. These observations suggested that binding of NF-kappa B to DNA induces bending. The estimated bending angle induced by the 50-kD DNA binding subunit of NF-kappa B (p50) was smaller than that induced by p50 which was associated with the 65-kD non-DNA binding subunit (p65). Moreover, the presence of p65 appeared to result in a shift of the bending center from the middle towards the 3'-end of the kappa B motif. This shows a role for the p65 subunit of NF-kappa B in modulating the extent and altering the position of protein-induced DNA bending.

Methylation strongly enhances DNA bending in the replication origin region of the Escherichia coli chromosome.

Two-dimensional gel electrophoresis, at high and low temperatures, and gel mobilities of circularly permuted DNA segments showed a large bending locus about 50 bp downstream from the right border of the 245 bp oriC box, a minimal essential region of autonomous replication on the Escherichia coli chromosome. Bending was strongly enhanced by Dam methylation. In DNA from a Dam- strain, the mobility anomaly arising from altered conformation was much reduced, but was raised to the original level by methylation in vivo or in vitro. Enhancement of the mobility anomaly was also observed by hybrid formation of the Dam- strand with the Dam+ strand. Near the bending center, GATC, the target of Dam methylase, occurs seven times arranged essentially on the same face of the helix with 10.5 bp per turn. We concluded that small bends at each Dam site added up to the large bending detectable by gel electrophoresis.

Investigation of the ceriumIV oxidation of poly(vinyl alcohol)

AbstractInitiation of ceric ion‐induced grafting from poly(vinyl alcohol) (PVOH) was studied by examining the formation and lifetime of colored complexes between ceriumIV and (1) a commercial PVOH, (2) a diol‐free PVOH, and (3) several model 1,2‐diols. UV/visible spectroscopy was employed using a wavelength of 520 nm. Results showed that the 1,2‐diols, which are an inherent defect in PVOH, are the sites most reactive toward ceric ion. The observed rate constant for the reaction was found to increase with decreasing [CeIV] until the maximum rate was reached at which time reaction took place exclusively with 1,2‐diols. The activation energy for oxidation of commercial PVOH at the maximum rate was 15.4 kcal/mol while that for diol‐free PVOH was 22.4 kcal/mol. The 1,2‐diols of PVOH displayed a high equilibrium constant for complexation with ceric ion, compared to the model 2,3‐butanediol. It was suggested that the PVOH chain segments bring about crowding of the diol group, and this leads to a higher equilibrium constant for complexation. The lowest energy conformation of a PVOH chain segment containing a 1,2‐diol linkage was calculated using the CHEMLAB‐II molecular design program, and the 1,2‐diol was predicted to be at the center of a sharp bend in the chain brought about by its presence.

Dual loci of DNA bending in the bovine papillomavirus upstream regulatory region

Recombinant clones containing all or portions of the bovine papillomavirus (BPV) upstream regulatory region (URR) were constructed. When analyzed by polyacrylamide gel electrophoresis, the cloned URR sequences exhibited electrophoretic properties characteristic of DNA containing bend sites. Two distinct bend centers were identified, mapping to approximately 7477 and 7790 respectively on the BPV genome. No other loci of static DNA bending were detected in the URR region of the BPV genome.

DNA bending is induced by a transcription factor that interacts with the human c-FOS and alpha-actin promoters.

Conserved sequence elements in the human cardiac and skeletal alpha-actin promoters that contain the CC(A + T-rich)6GG motif have been shown to regulate transcription of these genes. A similar sequence is found in the serum response element of the human c-FOS gene. In this study, we demonstrate that indistinguishable proteins bind to each of five CC(A + T-rich)6GG elements examined in the human cardiac and skeletal alpha-actin promoters and the c-FOS serum response element. Using electrophoretic techniques, we show that these factors induce a stable bend in the DNA upon binding, and the bend center is shown to coincide with the CC(A + T-rich)6GG element. In addition, the ability to bend DNA is retained by a small proteolytic fragment of the protein, suggesting that the DNA-binding domain of the protein is resistant to proteases and is sufficient to bend DNA.

Protein-induced bending of the simian virus 40 origin of replication

A 3· S protein, isolated from mammalian nuclei, specifically binds to DNA fragments containing the simian virus 40 (SV40) origin of replication. Two distinct nucleoprotein complexes are formed, a complex with high electrophoretic mobility carrying probably only one protein molecule, and a complex with reduced electrophoretic mobility carrying probably two protein molecules per DNA fragment. Band shift competition as well as methylation interference assays locate the binding site of the protein in the A + T-rich “late” region of the origin between SV40 nucleotides 13 and 35. The late origin binding (LOB) protein and T antigen bind simultaneously to adjacent sites in the origin. Using circularly permuted DNA fragments of identical lengths we show that the LOB protein induces pronounced bending of the origin fragment. The bending center maps at the 5′ end of the adenine tract with one bound protein molecule and at the 3′ end when two LOB proteins are bound to one origin fragment.

Cis-acting elements involved in the regulated expression of a human hsp70 gene

Expression of reporter genes under the control of upstream sequences of a human hsp70 gene was examined in microinjected Xenopus oocytes, transfected monkey COS and human HeLa cells. The genes were strictly heat-regulated in all three cell systems. A 69 nucleotide long segment of hsp70 5′ non-transcribed sequence that included at least one functional heat shock regulation sequence was sufficient for heat-controlled expression in Xenopus and monkey cells but not in human HeLa cells. An additional segment of about 200 nucleotides in length was required for optimal activity. This segment contains two heat shock regulation elements, each of which appears to contribute to the overall activity in heat-treated human cells. Upstream non-transcribed sequences of the human hsp70 gene are capable of conferring heat regulation on a heterologous promoter. The potential roles in transcription regulation of a bending center in the TATA box region, a CCAAT-like sequence and some of many potential Sp1 binding sites in the hsp70 5′ non-transcribed region were investigated.

Three regions in the DNA of plasmid pLS1 show sequence-directed static bending.

Three regions showing abnormal electrophoretic mobility, which is an indication of the existence of bends in DNA, have been observed in the DNA of plasmid pLS1. These loci have been characterized by assays designed to detect sequence-directed bending in DNA (temperature-dependence migration and two dimensional electrophoresis). The first region (locus B-1) was located within a fragment that contains a proposed inhibitor countertranscribed RNA (RNAII). The second locus (B-2) contains the plasmid plus origin of replication and the third region (locus B-3) was located in the vicinity of a putative antisense RNA (RNAI) of unknown function. The centres of the first two bent DNA regions were located by circular permutation assays at nucleotides 882 (locus B-1) and 634 (locus B-2). The bend centre of locus B-1 was found to be upstream of the promoter for the putative antisense RNAII. The centre of curvature in locus B-2 was located in the vicinity of the putative promoter of the replication proteins RepA and RepB and of a sequence that has three 11-bp direct repeats. The DNA sequence at this region showed the existence of A.T tracts, with an internal repeat of 10 to 11 base pairs, for five helix turns. A complex curvature in the DNA of pLS1 at locus B-2 that may have a regulatory role in plasmid replication is postulated.

Bending of a circular cylinder containing a crack

The study of bending of cracked circular cylinders is of more significance. The bending of cylinders containing radical crack or cracks was discussed by refs. [1]–[4] and that of concentrically craked circular cylinders was studied by [5]. Continuing [6] and using complex variable methods in elasticity, this paper deals with the bending problems of a circular cylinder, containing an internal linear crack at any position under an acting force perpendicular to the crack. The general forms of displacements, stresses, and stressintensity factors, expressed in terms of series, are obtained and to this bending problems with small Ah are presented good approximate formulas for the stress-intensity factors whose variations with the center of the crack are analysed. Finally, the twist angle per unit length and the center of bending for the radically cracked circular cylinder, one of whose crack-tips is located at the origin, have been computed and the results are almost the same as that calculated in [1].

Stellar occultations by turbulent planetary atmospheres: A heuristic scattering model

A model of ray refraction by an isothermal atmosphere with a scattering screen at the center of bending is used to generate analytic results which simulate the effects of real atmospheric turbulence on occultations. Calculations are carried through for scattering which is constant with height and for exponential height dependence. The effect of the scattering is to bias the the mean intensity of the occulted source, and hence systematically to distort bending angles and height differences obtained from inversion of the intensity data. However, the effect is of order 〈 δϵ 2〉/ ϵ 2 for either model, where 〈 δϵ 2〉 is the mean square scattering angle and ϵ is the average bending angle. The effect turns out to be small for plausible turbulence, since 〈 δϵ 2〉/ gfe 2 is of approximately the same order as the relative mean square density fluctuation. Thus the random effects of turbulence are unlikely to be a source of large systematic error in occultations, provided that the data can be meaningfully averaged either temporally or over a number of occultation events.

Cathodoluminescence and electrical anisotropy from α and β dislocations in plastically deformed gallium arsenide

Infrared cathodoluminescence (IR-CL) micrographs were taken of surfaces perpendicular (II2) and parallel (021) to the bend axis [II2] of n-type GaAs single crystals bend at 700°C in four-point bending to introduce α (Ga) and β (As) dislocations. At the bend center, light and dark checkered patterns associated with dislocations could be observed only in the IR-CL micrographs but not by optical, standard infrared, or secondary electron emission microscopy. No significant changes related to the type of dislocation (α or β) or dislocation density were observed either in the IR-CL peak half-width or peak position at E=1.411 eV. However, decreases of 40−70% in the relative IR-CL intensity were observed in the bend samples containing predominantly α or β dislocations. To study electrical anisotropy in the deformed samples, Hall measurements as a function of temperature were made of sections cut parallel and perpendicular to the [II2] bend axis to eliminate effects due to point defects and impurities. The results indicate that relative to the unbent control sample, the conductivity and mobility of sampples with dislocations oriented parallel to the current direction were slightly enhanced, while decreases of 50−60% were noted when the dislocations were aligned perpendicular to the current direction. When oriented in the parallel mode, an increase in conductivity and mobility was noted from both types of dislocations, with the samples containing β dislocations showing a larger increase than those with α dislocations. In contrast, when the dislocations were oriented in the mobility than thoise with β dislocations. The observed electrical anisotropy is discussed in the light of current models describing specular (or difuse) electron scattering dislocations.

Economical Refuse Truck Size Determination

A method for choosing trash collection truck size to minimize cost has been developed and applied to refuse collection in South Bend, Ind., and vicinity. Time and motion data were collected on three types of collection systems presently operating in the area. These data were used for comparisons among private, municipal, and contract systems and as base data for the truck size determination in different collection districts. The most economical truck size was calculated for each collection district and for several disposal sites. For each disposal site, the total trucks of each size and the total cost are summed and presented as a function of the distance of the disposal site from the center of South Bend. Also, the most economical truck size for a given collection district is plotted as a function of the distance of the district to the disposal site and the service density in the district.

Cathodoluminescence study of plastically deformed GaAs

Infrared cathodoluminescence (IR–CL) micrographs were taken of surfaces perpendicular (11¯2) and parallel (021) to the bend axis [11¯2] of GaAs single crystals bent at 700 °C in four-point bending to introduce α-Ga and β-As dislocations. At the bend center, light and dark checkered patterns associated with dislocations could be observed only in the IR–CL micrographs but not by optical, infrared, or secondary electron emission microscopy. Dislocation densities to ρ ≈ 5 × 106 cm−2 could be determined nondestructively to within 20% of the theoretical values. No significant changes related to the type of dislocation or dislocation density were observed either in the peak half-width or peak position at E = 1.411 eV. However, decreases of 40–70% in the relative IR–CL intensity were observed in the bent samples with predominantly α or β dislocations.

Oblique bending of a bimetallic bar with a cross section bounded by circular arcs

The p re sen t paper concerns the bending of a twol ayer p r i s m a t i c ba r whose c ross sect ion is bounded by c i r c u l a r a r c s . The solution to the problem is cons t ruc ted with the aid of funct ions s i m i l a r to the bending s t r e s s function proposed by Timoshenko [1] with r e f e r ence to the bending of homogeneous rods . w Let us cons ider the e las t i c bending of the twol aye r p r i s m a t i c bar whose c ross sect ion is shown in the f igure . The side sur faces 71 and 7z as well as the boundary 3 0 between the two layers are all cy l ind r i ca l su r faces , The or igin of the r ec t angu la r coordinate sy s t em is placed in the fixed end of the ba r in such a way that the y axis coincides with the axis of symmet ry , while the x axis coincides with the c r o s s s e c t i o n chord. The force is applied to the f ree end of the bar and passes through the bend center , so that there is no to r s ion . Let the l aye r s be isot ropie , the e las t ic moduIi E~ and E 2 of the m a t e r i a l s dis t inct , and the Po isson coeff ic ients #j and P2 equal . Then, as in the bending of homogeneous rods, only three components of the s t r e s s ) t e n s o r a r e d i f ferent f rom zero, namely 0"~1), T(zlx ) , T~ly ) for layer I and the analogous components for l ayer II. Henceforth the analogous exp r e s s ions for both reg ions will contain the index i which has the value i =1 in region I and i = 2 in region II. The indices of p wil l be omit ted . The n o r m a l s t r e s s atzL)" is given by the fo rmula