Journal articles: 'Cruciform structure'

1

Ait Saada, Anissia, Alex B. Costa, Ziwei Sheng, Wenying Guo, James E. Haber, and Kirill S. Lobachev. "Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures." Nucleic Acids Research 49, no. 7 (March 27, 2021): 3932–47. http://dx.doi.org/10.1093/nar/gkab168.

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Abstract Palindromic sequences are a potent source of chromosomal instability in many organisms and are implicated in the pathogenesis of human diseases. In this study, we investigate which nucleases are responsible for cleavage of the hairpin and cruciform structures and generation of double-strand breaks at inverted repeats in Saccharomyces cerevisiae. We demonstrate that the involvement of structure-specific nucleases in palindrome fragility depends on the distance between inverted repeats and their transcriptional status. The attack by the Mre11 complex is constrained to hairpins with loops <9 nucleotides. This restriction is alleviated upon RPA depletion, indicating that RPA controls the stability and/or formation of secondary structures otherwise responsible for replication fork stalling and DSB formation. Mus81-Mms4 cleavage of cruciforms occurs at divergently but not convergently transcribed or nontranscribed repeats. Our study also reveals the third pathway for fragility at perfect and quasi-palindromes, which involves cruciform resolution during the G2 phase of the cell cycle.

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Timsit, Youri, and Dino Moras. "Cruciform structures and functions." Quarterly Reviews of Biophysics 29, no. 4 (December 1996): 279–307. http://dx.doi.org/10.1017/s0033583500005862.

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In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

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Nag, Dilip K., and Alicia Kurst. "A 140-bp-Long Palindromic Sequence Induces Double-Strand Breaks During Meiosis in the Yeast Saccharomyces cerevisiae." Genetics 146, no. 3 (July 1, 1997): 835–47. http://dx.doi.org/10.1093/genetics/146.3.835.

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Palindromic sequences have the potential to form hairpin or cruciform structures, which are putative substrates for several nucleases and mismatch repair enzymes. A genetic method was developed to detect such structures in vivo in the yeast Saccharomyces cerevisiae. Using this method we previously showed that short hairpin structures are poorly repaired by the mismatch repair system in S. cerevisiae. We show here that mismatches, when present in the stem of the hairpin structure, are not processed by the repair machinery, suggesting that they are treated differently than those in the interstrand base-paired duplex DNA. A 140-bp-long palindromic sequence, on the contrary, acts as a meiotic recombination hotspot by generating a site for a double-strand break, an initiator of meiotic recombination. We suggest that long palindromic sequences undergo cruciform extrusion more readily than short ones. This cruciform structure then acts as a substrate for structure-specific nucleases resulting in the formation of a double-strand break during meiosis in yeast. In addition, we show that residual repair of the short hairpin structure occurs in an MSH2-independent pathway.

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Nobile, C., J. Nickol, and R. G. Martin. "Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA." Molecular and Cellular Biology 6, no. 8 (August 1986): 2916–22. http://dx.doi.org/10.1128/mcb.6.8.2916.

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Nucleosomes were reconstituted in vitro from a fragment of DNA spanning the simian virus 40 minimal replication origin. The fragment contains a 27-base-pair palindrome (perfect inverted repeat). DNA molecules with stable cruciform structures were generated by heteroduplexing this DNA fragment with mutants altered within the palindromic sequence (C. Nobile and R. G. Martin, Int. Virol., in press). Analyses of the structural features of the reconstituted nucleosomes by the DNase I footprint technique revealed two alternative DNA-histone arrangements, each one accurately phased with respect to the uniquely labeled DNA ends. As linear double-stranded DNA, a unique core particle was formed in which the histones strongly protected the regions to both sides of the palindrome. The cruciform structure seemed to be unable to associate with core histones and, therefore, an alternative phasing of the histone octamer along the DNA resulted. Thus, nucleosome positioning along a specific DNA sequence appears to be influenced in vitro by the secondary structure (linear or cruciform) of the 27-base-pair palindrome. The formation of cruciform structures in vivo, if they occur, might therefore represent a molecular mechanism by which nucleosomes are phased.

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5

Nobile, C., J. Nickol, and R. G. Martin. "Nucleosome phasing on a DNA fragment from the replication origin of simian virus 40 and rephasing upon cruciform formation of the DNA." Molecular and Cellular Biology 6, no. 8 (August 1986): 2916–22. http://dx.doi.org/10.1128/mcb.6.8.2916-2922.1986.

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Nucleosomes were reconstituted in vitro from a fragment of DNA spanning the simian virus 40 minimal replication origin. The fragment contains a 27-base-pair palindrome (perfect inverted repeat). DNA molecules with stable cruciform structures were generated by heteroduplexing this DNA fragment with mutants altered within the palindromic sequence (C. Nobile and R. G. Martin, Int. Virol., in press). Analyses of the structural features of the reconstituted nucleosomes by the DNase I footprint technique revealed two alternative DNA-histone arrangements, each one accurately phased with respect to the uniquely labeled DNA ends. As linear double-stranded DNA, a unique core particle was formed in which the histones strongly protected the regions to both sides of the palindrome. The cruciform structure seemed to be unable to associate with core histones and, therefore, an alternative phasing of the histone octamer along the DNA resulted. Thus, nucleosome positioning along a specific DNA sequence appears to be influenced in vitro by the secondary structure (linear or cruciform) of the 27-base-pair palindrome. The formation of cruciform structures in vivo, if they occur, might therefore represent a molecular mechanism by which nucleosomes are phased.

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6

Leach, David R. F. "Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair." BioEssays 16, no. 12 (December 1994): 893–900. http://dx.doi.org/10.1002/bies.950161207.

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7

Polishchuk, M. A., and M. V. Polishchuk. "Unmanned cruciform winged glider dynamics and control." Journal of «Almaz – Antey» Air and Space Defence Corporation, no. 3 (September 30, 2018): 55–60. http://dx.doi.org/10.38013/2542-0542-2018-3-55-60.

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Tha paper focuses on the problems of unmanned cruciform winged glider dynamics and control in autonomous flight conditions, and studies the wing aspect ratio effect on its flight performance. The winged glider control structure in the longitudinal and lateral axes is proposed. We carried out a comparative analysis of the ballistic flight ranges of models of different configurations, as well as the flight ranges of models of different configurations in the operating conditions of the control system of the proposed structure. As a result, the structure of the unmanned winged glider targeting system is proposed. The targeting system in the longitudinal axis, unlike the samples used in currently operating models, consists of two subsystems responsible for the unmanned winged glider best range gliding at the first flight phase and the direct aimpoint guidance at the second, i.e. final, flight stage

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Fridlyander, I. N., E. A. Tkachenko, A. Galliot, J. Koshorst, V. Y. Valkov, and V. V. Budanov. "Structure and Properties of 1933 Cruciform Large Fitting Blanks." Materials Science Forum 331-337 (May 2000): 1365–68. http://dx.doi.org/10.4028/www.scientific.net/msf.331-337.1365.

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9

Lader, Pål, Birger Enerhaug, Arne Fredheim, Pascal Klebert, and Bjørnar Pettersen. "Forces on a cruciform/sphere structure in uniform current." Ocean Engineering 82 (May 2014): 180–90. http://dx.doi.org/10.1016/j.oceaneng.2014.03.007.

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10

Gao, Xinglong, Qingbin Zhang, Qin Chen, and Wenkai Wang. "Fluid-structure Interactions on Steerable Cruciform Parachute Inflation Dynamics." IOP Conference Series: Materials Science and Engineering 751 (February 7, 2020): 012010. http://dx.doi.org/10.1088/1757-899x/751/1/012010.

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11

Wels, Michiel, Roger S. Bongers, Jos Boekhorst, Douwe Molenaar, Mark Sturme, Willem M. de Vos, Roland J. Siezen, and Michiel Kleerebezem. "Large Intergenic Cruciform-Like Supermotifs in the Lactobacillus plantarum Genome." Journal of Bacteriology 191, no. 10 (March 13, 2009): 3420–23. http://dx.doi.org/10.1128/jb.01672-08.

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ABSTRACT Twenty-four Lactobacillus plantarum supermotifs (LPSMs) with lengths from ∼800 to 1,000 nucleotides were identified in the L. plantarum genome. LPSMs were conserved in other L. plantarum strains but not in other species. Secondary structure analysis predicted that LPSMs may fold into cruciform-like structures. Preliminary experiments indicate that the LPSMs are transcribed.

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12

Sinden, R. R., G. X. Zheng, R. G. Brankamp, and K. N. Allen. "On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo." Genetics 129, no. 4 (December 1, 1991): 991–1005. http://dx.doi.org/10.1093/genetics/129.4.991.

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Abstract We have studied the deletion of inverted repeats cloned into the EcoRI site within the CAT gene of plasmid pBR325. A cloned inverted repeat constitutes a palindrome that includes both EcoRI sites flanking the insert. In addition, the two EcoRI sites represent direct repeats flanking a region of palindromic symmetry. A current model for deletion between direct repeats involves the formation of DNA secondary structure which may stabilize the misalignment between the direct repeats during DNA replication. Our results are consistent with this model. We have analyzed deletion frequencies for several series of inverted repeats, ranging from 42 to 106 bp, that were designed to form cruciforms at low temperatures and at low superhelical densities. We demonstrate that length, thermal stability of base pairing in the hairpin stem, and ease of cruciform formation affect the frequency of deletion. In general, longer palindromes are less stable than shorter ones. The deletion frequency may be dependent on the thermal stability of base pairing involving approximately 16-20 bp from the base of the hairpin stem. The formation of cruciforms in vivo leads to a significant increase in the deletion frequency. A kinetic model is presented to describe the relationship between the physical-chemical properties of DNA structure and the deletion of inverted repeats in living cells.

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13

He, Bo Lin, Ying Xia Yu, Xiao Dong Zhang, and Song Song Xia. "Calculation about Stress Concentration Coefficient of Welded Cruciform Joints of Magnesium Alloy Based on FEM." Advanced Materials Research 989-994 (July 2014): 931–34. http://dx.doi.org/10.4028/www.scientific.net/amr.989-994.931.

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Geometrical parameters of welded joint affect the stress concentration coefficient seriously. In order to increase the fatigue property of welded structure, it has great significance to reduce stress concentration coefficient of welded structures by researching and improving the geometry of welded joints. In this paper, the effects of weld tangent line angle θ on the stress concentration coefficient of welded cruciform joints of magnesium alloy were analyzed by using ABAQUS finite element program, and the change rule of stress concentration coefficient with the variation of the parameter was also researched. The calculation results indicate that reducing the weld tangent line angle θ can effectively decrease the stress concentration coefficient of welded cruciform joints, so as to improve the fatigue property of welded structures. In order to have high reliability and safety of welded structures of magnesium alloy, the true weld tangent line angle θ should be controlled less than 25°.

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14

Zhou, Caihua, Chaoxiang Xia, Shizhao Ming, Xiangjun Bi, and Tong Li. "Low-Velocity Impact Response of Discontinuous Kirigami Cruciform Sandwich Panel." International Journal of Applied Mechanics 11, no. 05 (June 2019): 1950046. http://dx.doi.org/10.1142/s1758825119500467.

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Cruciform structures have desirable energy absorption capacity. However, the engineering application is limited by the difficulties in the manufacturing process. In this paper, a kirigami approach is introduced to simplify the manufacturing process. Based on the kirigami strategy, a structure referred to as a discontinuous kirigami cruciform sandwich panel (DKC), is investigated to validate the mechanical performance in energy absorption. Experiments and numerical simulations were carried out to investigate the impact resistance of DKC under four levels of impact energy and the energy–absorption performance is evaluated by comparing to a typical energy–absorption device, pyramidal truss sandwich panel (PT). In order to reduce the initial impact force and the displacement of the bottom surface on the protected objective, the DKC is further optimized by introducing an additional cutout at the opposite end in each component plate. With the new design, the displacement of the bottom surface on the sandwich structure is reduced by 13.9%, together with a decrease of impact peak force and an increase of energy absorption.

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15

Bzymek, Malgorzata, and Susan T. Lovett. "Evidence for Two Mechanisms of Palindrome-Stimulated Deletion in Escherichia coli: Single-Strand Annealing and Replication Slipped Mispairing." Genetics 158, no. 2 (June 1, 2001): 527–40. http://dx.doi.org/10.1093/genetics/158.2.527.

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Abstract Spontaneous deletion mutations often occur at short direct repeats that flank inverted repeat sequences. Inverted repeats may initiate genetic rearrangements by formation of hairpin secondary structures that block DNA polymerases or are processed by structure-specific endonucleases. We have investigated the ability of inverted repeat sequences to stimulate deletion of flanking direct repeats in Escherichia coli. Propensity for cruciform extrusion in duplex DNA correlated with stimulation of flanking deletion, which was partially sbcD dependent. We propose two mechanisms for palindrome-stimulated deletion, SbcCD dependent and SbcCD independent. The SbcCD-dependent mechanism is initiated by SbcCD cleavage of cruciforms in duplex DNA followed by RecA-independent single-strand annealing at the flanking direct repeats, generating a deletion. Analysis of deletion endpoints is consistent with this model. We propose that the SbcCD-independent pathway involves replication slipped mispairing, evoked from stalling at hairpin structures formed on the single-stranded lagging-strand template. The skew of SbcCD-independent deletion endpoints with respect to the direction of replication supports this hypothesis. Surprisingly, even in the absence of palindromes, SbcD affected the location of deletion endpoints, suggesting that SbcCD-mediated strand processing may also accompany deletion unassociated with secondary structures.

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Giguère, Jean-Benoît, Joël Boismenu-Lavoie, and Jean-François Morin. "Cruciform Alkynylated Anthanthrene Derivatives: A Structure–Properties Relationship Case Study." Journal of Organic Chemistry 79, no. 6 (March 10, 2014): 2404–18. http://dx.doi.org/10.1021/jo402674m.

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17

Leonard, M. W., and R. K. Patient. "Evidence for torsional stress in transcriptionally activated chromatin." Molecular and Cellular Biology 11, no. 12 (December 1991): 6128–38. http://dx.doi.org/10.1128/mcb.11.12.6128.

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The existence of torsional stress in eukaryotic chromatin has been controversial. To determine whether it could be detected, we probed the structure of an alternating AT tract. These sequences adopt cruciform geometry when the DNA helix is torsionally strained by negative supercoiling. The single-strand-specific nuclease P1 was used to determine the structure of an alternating AT sequence upstream of the Xenopus beta-globin gene when assembled into chromatin in microinjected Xenopus oocytes. The pattern of cleavage by P1 nuclease strongly suggests that the DNA in this chromatin template is under torsional stress. The cruciform was detected specifically in the most fully reconstituted templates at later stages of chromatin assembly, suggesting that negative supercoiling is associated with chromatin maturation. Furthermore, the number of torsionally strained templates increased dramatically at the time when transcription of assembled chromatin templates began. Transcription itself has been shown to induce supercoiling, but the requisite negative supercoiling for cruciform extrusion by (AT)n in oocytes was not generated in this way since the characteristic P1 cutting pattern was retained even when RNA polymerase elongation was blocked with alpha-amanitin. Thus, torsional stress is associated with transcriptional activation of chromatin templates in the absence of ongoing transcription.

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Leonard, M. W., and R. K. Patient. "Evidence for torsional stress in transcriptionally activated chromatin." Molecular and Cellular Biology 11, no. 12 (December 1991): 6128–38. http://dx.doi.org/10.1128/mcb.11.12.6128-6138.1991.

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The existence of torsional stress in eukaryotic chromatin has been controversial. To determine whether it could be detected, we probed the structure of an alternating AT tract. These sequences adopt cruciform geometry when the DNA helix is torsionally strained by negative supercoiling. The single-strand-specific nuclease P1 was used to determine the structure of an alternating AT sequence upstream of the Xenopus beta-globin gene when assembled into chromatin in microinjected Xenopus oocytes. The pattern of cleavage by P1 nuclease strongly suggests that the DNA in this chromatin template is under torsional stress. The cruciform was detected specifically in the most fully reconstituted templates at later stages of chromatin assembly, suggesting that negative supercoiling is associated with chromatin maturation. Furthermore, the number of torsionally strained templates increased dramatically at the time when transcription of assembled chromatin templates began. Transcription itself has been shown to induce supercoiling, but the requisite negative supercoiling for cruciform extrusion by (AT)n in oocytes was not generated in this way since the characteristic P1 cutting pattern was retained even when RNA polymerase elongation was blocked with alpha-amanitin. Thus, torsional stress is associated with transcriptional activation of chromatin templates in the absence of ongoing transcription.

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19

Cheung, Andrew K. "Palindrome Regeneration by Template Strand-Switching Mechanism at the Origin of DNA Replication of Porcine Circovirus via the Rolling-Circle Melting-Pot Replication Model." Journal of Virology 78, no. 17 (September 1, 2004): 9016–29. http://dx.doi.org/10.1128/jvi.78.17.9016-9029.2004.

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ABSTRACT Palindromic sequences (inverted repeats) flanking the origin of DNA replication with the potential of forming single-stranded stem-loop cruciform structures have been reported to be essential for replication of the circular genomes of many prokaryotic and eukaryotic systems. In this study, mutant genomes of porcine circovirus with deletions in the origin-flanking palindrome and incapable of forming any cruciform structures invariably yielded progeny viruses containing longer and more stable palindromes. These results suggest that origin-flanking palindromes are essential for termination but not for initiation of DNA replication. Detection of template strand switching in the middle of an inverted repeat strand among the progeny viruses demonstrated that both the minus genome and a corresponding palindromic strand served as templates simultaneously during DNA biosynthesis and supports the recently proposed rolling-circle “melting-pot” replication model. The genome configuration presented by this model, a four-stranded tertiary structure, provides insights into the mechanisms of DNA replication, inverted repeat correction (or conversion), and illegitimate recombination of any circular DNA molecule with an origin-flanking palindrome.

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20

Hsu, Ming-Ta. "Electron microscopic evidence for the cruciform structure in intracellular SV40 DNA." Virology 143, no. 2 (June 1985): 617–21. http://dx.doi.org/10.1016/0042-6822(85)90400-3.

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21

Brázda, Václav, Jan Coufal, Jack C. C. Liao, and Cheryl H. Arrowsmith. "Preferential binding of IFI16 protein to cruciform structure and superhelical DNA." Biochemical and Biophysical Research Communications 422, no. 4 (June 2012): 716–20. http://dx.doi.org/10.1016/j.bbrc.2012.05.065.

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Zhao, Dan, Cun Xin, Tao Jin, Xiaopeng Yan, Shenggguo Ma, and Zhihua Wang. "Evolution of face-centered-cubic polycrystalline plastic anisotropy under biaxial loading by crystal plasticity finite element method." Engineering Computations 37, no. 3 (September 23, 2019): 895–908. http://dx.doi.org/10.1108/ec-12-2018-0573.

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Purpose The purpose of this study to analyze the plastic anisotropy of 6061 aluminum alloy with finite deformation using crystal plasticity finite element method. Design/methodology/approach A representative volume element (RVE) model was constructed by Voronoi tessellation. In this model, grain shapes, grain orientations and distribution of grains were involved. The mechanical response of the component under composite loading was tested using specify cruciform specimen. Moreover, different stress and strain states in the specific central region were analyzed to reveal the effects of complex loading. Findings We calculated the influence of misorientation of adjacent grains as well as the evolution of the micro structure’s plastic deformation on the macroscopic deformation of the structure. Geometry design for the cruciform specimen helps obtain a homogenous distribution of the stress and strain at the specimen center. In this process, the initial grain orientation is also an important factor, and the larger misorientations between special grains may cause greater stress concentration. Originality/value The influence of micro-scale factors on macro-scale plastic anisotropy of AA6061 is analyzed using RVE model and cruciform specimen, and they offer a reference for related research.

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23

Davison, A., and D. R. Leach. "The effects of nucleotide sequence changes on DNA secondary structure formation in Escherichia coli are consistent with cruciform extrusion in vivo." Genetics 137, no. 2 (June 1, 1994): 361–68. http://dx.doi.org/10.1093/genetics/137.2.361.

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Abstract The construction in bacteriophage lambda of a set of long DNA palindromes with paired changes in the central sequence is described. Identical palindrome centers were previously used by others to test the S-type model for cruciform extrusion in vitro. Long DNA palindromes prevent the propagation of carrier phage lambda on a wild-type host, and the sbcC mutation is sufficient to almost fully alleviate this inviability. The plaque areas produced by the palindrome containing phages were compared on an Escherichia coli sbcC lawn. Central sequence changes had a greater effect upon the plaque area than peripheral changes, implying that the residual palindrome-mediated inviability in E. coli sbcC is center-dependent and could be due to the formation of a cruciform structure. The results argue strongly that intrastrand pairing within palindromes is critical in determining their effects in vivo. In addition, the same data suggests that DNA loops in vivo may sometimes contain two bases only.

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24

Panayotatos, N., and A. Fontaine. "A native cruciform DNA structure probed in bacteria by recombinant T7 endonuclease." Journal of Biological Chemistry 262, no. 23 (August 1987): 11364–68. http://dx.doi.org/10.1016/s0021-9258(18)60968-8.

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25

Kurahashi, Hiroki, Hidehito Inagaki, Kouji Yamada, Tamae Ohye, Mariko Taniguchi, Beverly S. Emanuel, and Tatsushi Toda. "Cruciform DNA Structure Underlies the Etiology for Palindrome-mediated Human Chromosomal Translocations." Journal of Biological Chemistry 279, no. 34 (June 20, 2004): 35377–83. http://dx.doi.org/10.1074/jbc.m400354200.

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Goldstein, Joshua N., and Sandra K. Weller. "In Vitro Processing of Herpes Simplex Virus Type 1 DNA Replication Intermediates by the Viral Alkaline Nuclease, UL12." Journal of Virology 72, no. 11 (November 1, 1998): 8772–81. http://dx.doi.org/10.1128/jvi.72.11.8772-8781.1998.

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ABSTRACT Herpes simplex virus type 1 (HSV-1) DNA replication intermediates exist in a complex nonlinear structure that does not migrate into a pulsed-field gel. Genetic evidence suggests that the product of the UL12 gene, termed alkaline nuclease, plays a role in processing replication intermediates (R. Martinez, R. T. Sarisky, P. C. Weber, and S. K. Weller, J. Virol. 70:2075–2085, 1996). In this study we have tested the hypothesis that alkaline nuclease acts as a structure-specific resolvase. Cruciform structures generated with oligonucleotides were treated with purified alkaline nuclease; however, instead of being resolved into linear duplexes as would be expected of a resolvase activity, the artificial cruciforms were degraded. DNA replication intermediates were isolated from the well of a pulsed-field gel (“well DNA”) and treated with purified HSV-1 alkaline nuclease. Although alkaline nuclease can degrade virion DNA to completion, digestion of well DNA results in a smaller-than-unit-length product that migrates as a heterogeneous smear; this product is resistant to further digestion by alkaline nuclease. The smaller-than-unit-length products are representative of the entire HSV genome, indicating that alkaline nuclease is not inhibited at specific sequences. To further probe the structure of replicating DNA, well DNA was treated with various known nucleases; our results indicate that replicating DNA apparently contains no accessible double-stranded ends but does contain nicks and gaps. Our data suggest that UL12 functions at nicks and gaps in replicating DNA to correctly repair or process the replicating genome into a form suitable for encapsidation.

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HOSAKA, Fuji, Atsushi NAKAHARA, Tsutomu TAKAHASHI, László BARANYI, and Masataka SHIRAKASHI. "Structure of longitudinal vortices shedding periodically from two cylinders in a cruciform arrangement." Journal of the Visualization Society of Japan 16, Supplement2 (1996): 159–62. http://dx.doi.org/10.3154/jvs.16.supplement2_159.

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Nehls, Benjamin S., Frank Galbrecht, Askin Bilge, Ullrich Scherf, and Tony Farrell. "Synthesis and Properties of Oligo-/Polymers Based on a “Flexible” Swivel-Cruciform Structure." Macromolecular Symposia 239, no. 1 (June 2006): 21–29. http://dx.doi.org/10.1002/masy.200690099.

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Bass, B. R., W. J. McAfee, J. W. Bryson, and W. E. Pennell. "An Investigation of Cladding Effects on Shallow-Flaw Fracture Toughness of Reactor Pressure Vessel Steel Under Prototypic Biaxial Loading." Journal of Pressure Vessel Technology 121, no. 3 (August 1, 1999): 257–68. http://dx.doi.org/10.1115/1.2883701.

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Potential structural-integrity benefits or liabilities of the stainless steel cladding on the inner surface of a reactor pressure vessel (RPV) are important considerations in the effort to refine or improve safety assessment procedures applied to RPVs. Clad-beam tests were carried out to investigate and quantify effects of the clad structure on fracture initiation toughness of through-clad shallow surface flaws in RPV material. A cruciform beam specimen was developed at ORNL to introduce a prototypic, far-field, out-of-plane biaxial stress component that provides a linear approximation of the nonlinear stress distribution generated by thermo-mechanical loading transients in an RPV. The cruciform specimens (102-mm-thick test section) were fabricated from RPV shell segments available from a canceled pressurized-water reactor plant. The specimens were tested under biaxial load ratios ranging from 0.0 (uniaxial) to 1.0 (full biaxial), the ratio being defined as the total load applied to the transverse beam arms divided by that applied to the longitudinal arms. The test results imply that biaxial loading is effective in reducing the shallow-flaw fracture toughness of the clad/heat-affected zone/structural-weld region of the RPV shell below that determined from uniaxial loading conditions. The lowest toughness value from the clad cruciform specimens tested under biaxial loading is only slightly above the ASME Section XI KIc curve. For all biaxiality ratios, the test results imply that shallow-flaw fracture toughness data from the RPV structural weld material are significantly lower than that obtained from a high-yield strength plate material.

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Cao, Dongliang, Peng Zhang, Pei Liu, Shaonan Cui, and Na Sun. "New conjugated cruciform chromophores with D-π-A structure: Synthesis, characterization and theoretical calculation." Journal of Molecular Structure 1076 (November 2014): 396–402. http://dx.doi.org/10.1016/j.molstruc.2014.07.066.

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Li, Dong Xia, Bao Chun Jia, and Yan Zhi Zhu. "Enhancement of the Fatigue Property of the Crack of Cruciform Welded Joints by TIG-Dressing." Advanced Materials Research 146-147 (October 2010): 1419–22. http://dx.doi.org/10.4028/www.scientific.net/amr.146-147.1419.

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The effect of TIG-dressing on fatigue strength in support of the fillet weld of offshore platform was investigated experimentally in the paper. According to the causes in which most cracks are produced in actual structure, the model tests have been performed based upon cruciform weld bead characteristic. The TIG-dressing technique parameters were established by the actual structure and the fatigue specimen tests were done also. The life estimation equation after TIG-dressing is presented by least square method. The fatigue life used by TIG-dressing has increased over 100%. Therefore the TIG-technique gives a big potential for engineering application.

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Gao, Song, Li Xu, Da Zheng Wang, and Fei Ma. "Research of Stress Assessment Based on Singularity Strength." Applied Mechanics and Materials 496-500 (January 2014): 1147–51. http://dx.doi.org/10.4028/www.scientific.net/amm.496-500.1147.

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Hull structure has sharp corners with singularity which tends to produce fatigue cracks and cause structural damages. Its not straightforward to assess FE analysis results of stiffened plating structures because of the stress singularities that are inherent in the overall geometry. This paper concentrates on the analysis of a simple planar right angled cruciform corner and a 135-degree sheet corner through a series of FE analyses using ANSYS. The aim is to try and provide an understanding of the nature of the singularities. Through the understanding a simple method is proposed to estimate the singular stress at the corners using as named as singularity strength which is based on notch-stress intensity factor theory. Finally the estimation methods of as are given for the 2D corners.

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Farah, Joseph A., Edgar Hartsuiker, Ken-ichi Mizuno, Kunihiro Ohta, and Gerald R. Smith. "A 160-bp Palindrome Is a Rad50·Rad32-Dependent Mitotic Recombination Hotspot inSchizosaccharomyces pombe." Genetics 161, no. 1 (May 1, 2002): 461–68. http://dx.doi.org/10.1093/genetics/161.1.461.

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AbstractPalindromic sequences can form hairpin and cruciform structures that pose a threat to genome integrity. We found that a 160-bp palindrome (an inverted repeat of 80 bp) conferred a mitotic recombination hotspot relative to a control nonpalindromic sequence when inserted into the ade6 gene of Schizosaccharomyces pombe. The hotspot activity of the palindrome, but not the basal level of recombination, was abolished by a rad50 deletion, by a rad50S “separation of function” mutation, or by a rad32-D25A mutation in the nuclease domain of the Rad32 protein, an Mre11 homolog. We propose that upon extrusion of the palindrome the Rad50·Rad32 nuclease complex recognizes and cleaves the secondary structure thus formed and generates a recombinogenic break in the DNA.

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Koide, Mizuyasu, Tsutomu Takahashi, Masataka Shirakashi, and Sheikh Ahmad Zaki Bin Shaikh Salim. "Three-dimensional structure of longitudinal vortices shedding from cruciform two-cylinder systems with different geometries." Journal of Visualization 20, no. 4 (February 16, 2017): 753–63. http://dx.doi.org/10.1007/s12650-017-0419-5.

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Du, Guangyin, Han Xia, Jun Cai, Huangsong Pan, and Changshen Sun. "Liquefiable Ground Treatment Using Cruciform Section Probe Resonant Compaction Method: A Case Study in the Xitong Expressway, Eastern China." Advances in Civil Engineering 2020 (January 30, 2020): 1–11. http://dx.doi.org/10.1155/2020/6564193.

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The foundation treatment of liquefiable soil has always been an important part of construction. Sand liquefaction decreases the foundation capacity and can cause severe building, highway, or bridge engineering accidents. This study used self-developed cruciform section probe resonant compaction equipment (CSPRCE) to evaluate the applicability and reinforcement effect of the Xitong Expressway foundation. The cone penetration test (CPT) results showed that this soil was liquefiable ground requiring treatment before construction. Laboratory tests illustrated that the clay particle content was nearly 10% in the surface layer, indicating that the traditional resonant compaction probe (RCP) would not provide effective reinforcement; therefore, we adopted the new resonant compaction method (RCM) for the reinforcement process. The CPT and standard penetration test (SPT) results after foundation reinforcement indicated that the cruciform section probe resonant compaction method (CSPRCM) is suitable for treating the Xitong Expressway liquefiable foundation. Before reinforcement, 7-8 liquefiable soil layers were observed, whereas after reinforcement, no foundation testing points were liquefiable. Cone resistance and unit sleeve friction resistance were both improved by a factor of nearly 3 after the CSPRCM reinforcement. The CSPRCM has wider applicability than traditional vibrating compaction methods, especially for sites with a high content of silt and clay particles. The strengthening mechanism of the CSPRCM is a vibration hammer that generates vibrational energy to obliterate the original soil structure and render the sand completely liquefied; the soil particles then rearrange to form a new structure.

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Zhang, Tong, Chunyu Zhang, Xiaoting Li, Meng Liang, Weixiao Bian, Yan Zhang, Kunpeng Wang, and Pengchong Xue. "Fluorescence response of cruciform D–π–A–π–D phenothiazine derivatives to mechanical force." CrystEngComm 21, no. 28 (2019): 4192–99. http://dx.doi.org/10.1039/c9ce00568d.

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Sharma, Sudha. "Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases." Journal of Nucleic Acids 2011 (2011): 1–15. http://dx.doi.org/10.4061/2011/724215.

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In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

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Limansky, A. P. "Study of cruciform structure in supercoiled pUC8 plasmid DNA by atomic force microscopy and computer modelling." Biopolymers and Cell 18, no. 5 (September 20, 2002): 401–5. http://dx.doi.org/10.7124/bc.00061d.

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Losch, Florian O., Anne Bredenbeck, Verena M. Hollstein, Peter Walden, and Paul Wrede. "Evidence for a large double-cruciform DNA structure on the X chromosome of human and chimpanzee." Human Genetics 122, no. 3-4 (July 19, 2007): 337–43. http://dx.doi.org/10.1007/s00439-007-0405-4.

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Jagelská, Eva B., Václav Brázda, Petr Pečinka, Emil Paleček, and Miroslav Fojta. "DNA topology influences p53 sequence-specific DNA binding through structural transitions within the target sites." Biochemical Journal 412, no. 1 (April 25, 2008): 57–63. http://dx.doi.org/10.1042/bj20071648.

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The tumour suppressor protein p53 is one of the most important factors regulating cell proliferation, differentiation and programmed cell death in response to a variety of cellular stress signals. P53 is a nuclear phosphoprotein and its biochemical function is closely associated with its ability to bind DNA in a sequence-specific manner and operate as a transcription factor. Using a competition assay, we investigated the effect of DNA topology on the DNA binding of human wild-type p53 protein. We prepared sets of topoisomers of plasmid DNA with and without p53 target sequences, differing in their internal symmetry. Binding of p53 to DNA increased with increasing negative superhelix density (−σ). At −σ≤0.03, the relative effect of DNA supercoiling on protein–DNA binding was similar for DNA containing both symmetrical and non-symmetrical target sites. On the other hand, at higher −σ, target sites with a perfect inverted repeat sequence exhibited a more significant enhancement of p53 binding as a result of increasing levels of negative DNA supercoiling. For −σ=0.07, an approx. 3-fold additional increase in binding was observed for a symmetrical target site compared with a non-symmetrical target site. The p53 target sequences possessing the inverted repeat symmetry were shown to form a cruciform structure in sufficiently negative supercoiled DNA. We show that formation of cruciforms in DNA topoisomers at −σ≥0.05 correlates with the extra enhancement of p53–DNA binding.

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Gimble, J. M., and E. E. Max. "Human immunoglobulin kappa gene enhancer: chromatin structure analysis at high resolution." Molecular and Cellular Biology 7, no. 1 (January 1987): 15–25. http://dx.doi.org/10.1128/mcb.7.1.15.

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The murine immunoglobulin kappa gene enhancer has previously been found to coincide with a region of altered chromatin structure reflected in a DNase I hypersensitivity site detectable on Southern blots of B-cell DNA. We examined the chromatin structure of the homologous region of human DNA using the high-resolution electroblotting method originally developed for genomic sequence analysis by G. Church and W. Gilbert (Proc. Natl. Acad. Sci. USA 81:1991-1995, 1984). Analysis of DNA isolated from cells treated in vivo with dimethyl sulfate revealed two B-cell-specific sites of enhanced guanine methylation. Both sites are located within perfect inverted repeats theoretically capable of forming cruciform structures; one of these repeats overlaps an enhancer core sequence. No enhancement or protection of guanine methylation was observed within sequences similar to sites of altered methylation previously described in the immunoglobulin heavy-chain enhancer. Treatment of isolated nuclei with DNase I or a variety of restriction endonucleases defined a B-cell-specific approximately 0.25-kilobase region of enhanced nuclease susceptibility similar to that observed in the murine kappa enhancer. The 130-base-pair DNA segment that shows high sequence conservation between human, mouse, and rabbit DNAs lies at the 5' end of the nuclease-susceptible region.

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Gimble, J. M., and E. E. Max. "Human immunoglobulin kappa gene enhancer: chromatin structure analysis at high resolution." Molecular and Cellular Biology 7, no. 1 (January 1987): 15–25. http://dx.doi.org/10.1128/mcb.7.1.15-25.1987.

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The murine immunoglobulin kappa gene enhancer has previously been found to coincide with a region of altered chromatin structure reflected in a DNase I hypersensitivity site detectable on Southern blots of B-cell DNA. We examined the chromatin structure of the homologous region of human DNA using the high-resolution electroblotting method originally developed for genomic sequence analysis by G. Church and W. Gilbert (Proc. Natl. Acad. Sci. USA 81:1991-1995, 1984). Analysis of DNA isolated from cells treated in vivo with dimethyl sulfate revealed two B-cell-specific sites of enhanced guanine methylation. Both sites are located within perfect inverted repeats theoretically capable of forming cruciform structures; one of these repeats overlaps an enhancer core sequence. No enhancement or protection of guanine methylation was observed within sequences similar to sites of altered methylation previously described in the immunoglobulin heavy-chain enhancer. Treatment of isolated nuclei with DNase I or a variety of restriction endonucleases defined a B-cell-specific approximately 0.25-kilobase region of enhanced nuclease susceptibility similar to that observed in the murine kappa enhancer. The 130-base-pair DNA segment that shows high sequence conservation between human, mouse, and rabbit DNAs lies at the 5' end of the nuclease-susceptible region.

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Czubinski, Jaroslaw, Jakub Barciszewski, Miroslaw Gilski, Kamil Szpotkowski, Janusz Debski, Eleonora Lampart-Szczapa, and Mariusz Jaskolski. "Structure of γ-conglutin: insight into the quaternary structure of 7S basic globulins from legumes." Acta Crystallographica Section D Biological Crystallography 71, no. 2 (January 23, 2015): 224–38. http://dx.doi.org/10.1107/s1399004714025073.

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γ-Conglutin from lupin seeds is an unusual 7S basic globulin protein. It is capable of reducing glycaemia in mammals, but the structural basis of this activity is not known. γ-Conglutin shares a high level of structural homology with glycoside hydrolase inhibitor proteins, although it lacks any kind of inhibitory activity against plant cell-wall degradation enzymes. In addition, γ-conglutin displays a less pronounced structural similarity to pepsin-like aspartic proteases, but it is proteolytically dysfunctional. Only one structural study of a legume 7S basic globulin, that isolated from soybean, has been reported to date. The quaternary assembly of soybean 7S basic globulin (Bg7S) is arranged as a cruciform-shaped tetramer comprised of two superposed dimers. Here, the crystal structure of γ-conglutin isolated fromLupinus angustifoliusseeds (LangC) is presented. The polypeptide chain of LangC is post-translationally cleaved into α and β subunits but retains its covalent integrity owing to a disulfide bridge. The protomers of LangC undergo an intricate quaternary assembly, resulting in a ring-like hexamer with noncrystallographicD3symmetry. The twofold-related dimers are similar to those in Bg7S but their assembly is different as a consequence of mutations in a β-strand that is involved in intermolecular β-sheet formation in γ-conglutin. Structural elucidation of γ-conglutin will help to explain its physiological role, especially in the evolutionary context, and will guide further research into the hypoglycaemic activity of this protein in humans, with potential consequences for novel antidiabetic therapies.

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Vežić, Pavuša. "Memorije križnoga tlocrta na tlu Istre i Dalmacije." Ars Adriatica, no. 3 (January 1, 2013): 21. http://dx.doi.org/10.15291/ars.459.

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Generally speaking, paleochristian memoriae have emerged out of the funeral traditions of the pagan world of Antiquity with its particular expression of the cult of deceased, sustained with the culture that had come out of Christian theology and aesthetics. It came together withnew architectural forms some of which were characterized with cross-like forms, not only as a general symbol of new faith, but also as the spatial projection, model after which one had to build. It is defined by two axes that cross at the right angle, the framework of the overall architecturalcomposition, factor of building’s extension in its entire length and width, as well as the height of the building that is dominated and marked by a dome. This particular structure of the building expresses its own essence, memorial use and the Christian paradigm. Through form and function, these buildings have become a distinguished phenomenon of the Christian civilization, valued in the architecture from the late antiquity to Romanesque period.Mature form of the space intended for the cult of the deceased, particularly when small cruciform churches are in question, is remarkably expressed in the preserved chapel of St. Lawrence, widely known as the mausoleum of Galla Placidia, one of two identical buildings once located at the ends of the narthex of the Ravennate church of the Holy Cross. The lower space of Theodoric’s mausoleum in Ravenna is also cruciform, however one should also remember emperor Justinian’s cruciform tombin Constantinople church of the Holy Apostles. It was demolished in the 15 century, together with the whole complex, and is known only through historical sources.Together with the Ravennate memoriae, such tombs could have – directly or indirectly – influence the formation of the cruciform memoriae in the Adriatic cultural landscape from Late Antiquity to Romanesque period.This paper elaborates the group of approximately fifteen buildings that demonstrate – through their forms and funerary functions – perseverance of particular cruciform plan of a memoriae within the Adriatic ambiance. A particularly numerous group is that of southern Istria, which consists of the Pula cathedral baptistery, two chapels by the basilica of Sta Maria Formosa and St. Mathew’s chapel in Pula, that of St. Catharine on a nearby islet and the supposed cruciform church of St. Andrew on an island in front of Rovinj. To such a concentration of the paleochristian memoriae one should link two early-mediaeval chapels, that of St. Clement in Pula and St. Thomas’ near Rovinj. The latter’s forms were already commented by Ivan Matejčić to follow and repeat paleochristian features. Among these features there are three protruding apses similar to those of St. Catharine’s. Therefore, it seems that the forms and themeasures of pre-Romanesque chapels were taken from those of the nearby Byzantine buildings, rather than from the distant Carolingian examples in Italy or France. Earlier and later southern Istrian memoriae are treated here as a typological group with emphasized regional features and continuity. Their forms differ only in some less important details, e.g. facades being either flat or articulated with lesenes. Their common features are, on the other hand, elementary architectural composition, spatial structure that consists of four branches and the dome hidden in the drum, as well as their dimensions and proportions. An element ofparticular interest is the octagonal upper part of the dome on Pula baptistery, that on St. Catharine’s on an islet in front of Pula as well as one on St. Andrew’s on an islet in front of Rovinj. These are probably reconstructions of the older solution. Within the supposedly later construction, there is a dome, a trula, as Pietro Kandler has named it, relating it with the Longboard architecture. It is carried by squinches.This solution is, actually, the Byzantine tradition in the area of Ravennate influences. A similar dome is constructed above the cruciform chapel consecrated to St. Mary Mater Domini (Theotokos), built next to the church of St. Felix and Fortunato in Vicenza, in 6 century. It seems that the same tradition was followed by very similar buildings, Paduan chapel of San Prosdocimo, and the memory erected by Santi Apostoli in Verona. On the other hand, St. Clement’s in Pula did not have a dome of such type and this church had yet another significant difference from the other Istrian chapels, the rectangular extension of areas in front of the apses. Another example that stands out from the group is the church of St. Euphemia at Saline bay in Lim channel. It is an Early Romanesque chapel with three apses at the rear. Lateral branches are reduced; they are much shorter than the front one, and give an impression of a transept rather than cruciform branches, as in other churches of the group. The upper part of the walls give no evidence of neither vaults nor a dome.Differently from the typological unity of the paleochristian and early mediaeval Istrian memoriae, those in Dalmatia show significant variability of the theme, already noticeable at the physiognomy of the earlier examples. For instance, the small baptistery in Baška on the island of Krk is an orderly cruciform building with relatively short branches and unarticulated flat walls, similar to Pula baptistery. The ground plan of St. Martin’s on the island of Cres is considerably different. It was a considerably larger building, probably in a memorial function related to a nearby villa rustica. It also has the rectangular extension in front of the apse, like St. Clement’s at Pula. Its walls show no traces of vaulted constructions. In a later phase, it was probably used as a parish church, like some examples of Dalmatian triconchal churches. A particular articulation of the walls, different from all of the Istrian and Dalmatiancruciform memoriae, was that of St. Cyprian’s chapel at Gata. Its short branches are rectangular on the outside, while on the inside they have inscribed round apses. Therefore, the outer surfaces have narrow round niches as relief of the thickened angles. Memory of the Holy Cross at Nin also has a round apse inscribed in the rectangular body of its rear branch. However, it is flanked by two smaller protruding apses, i.e. three in total. Other branches are vaulted with a half-dome on angular squinches that are also constructed below the drum with the dome inside. Ivo Petricioli has long ago suggested that its proportions indicate influences of the early mediaeval Byzantine architecture. This is further corroborated by its outer surfaces articulated with shallow niches. These features do not appear in Carolingian architecture, so it seems that the Holy Cross should be dated into the 10th or the 11th century. It also should be related tothe influences from nearby Zadar - contemporary capitol of the Byzantine Theme of Dalmatia - with the church of St. Vitus whose features, both general form and details, are of the same type of the building. Furthermore, they should be compared with the chapel of St. Donatus at Kornić on Krk Island. This small church is of apparently different groundplan, but one could still consider it a cruciform type. Its front and rear branches are rectangular, and there are indications that the rear branch had a round apse inscribed, similarly to the memory of the Holy Cross at Nin. However, its lateral branches are relatively small round apses, protruding from the sides of the chapel. Among them, there is a relativelyspacious central section with the dome constructed on the squinches. Miljenko Jurković has plausibly dated the church in 12th century, while I believe that it confirms the continuity of the paleochristian cruciform type of the Christian memory in Istria and Dalmatia from Late Antiquity to theRomanesque period. This is proven by some contemporary constructions, such as the chapel of an unknown title at Crkvina near Kašić, near Biljani Donji, that has also been dated in Romanesque period. In spite of some individual differences all of the memoriae compared in this paper, both groups are assembled by numerousness and similarities of both cruciform plans and funerary functions. Also, the influence of Adriatic Byzantine centres, particularly that of Ravenna, Pula and Zadar, is noticeable in formation of the regional characteristics of memorial architecture in the cultural ambiance of Istria and Dalmatia, within the context of long-lasting continuity of its forms and functions, from Late Antiquity to Romanesque period.

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NAKANO, Tatsuya, Ryota SAITO, and Takashi HASEGAWA. "45-DEGREE DIRECTIONAL LOADING TEST ON SEISMIC REINFORCEMENT OF THREE DIMENSIONAL CRUCIFORM STEEL STRUCTURE USING STKR COLUMN." Journal of Structural and Construction Engineering (Transactions of AIJ) 78, no. 687 (2013): 997–1006. http://dx.doi.org/10.3130/aijs.78.997.

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46

Wu Chen-Jun, Cheng Yong-Zhi, Wang Wen-Ying, He Bo, and Gong Rong-Zhou. "Design and radar cross section reduction experimental verification of phase gradient meta-surface based on cruciform structure." Acta Physica Sinica 64, no. 16 (2015): 164102. http://dx.doi.org/10.7498/aps.64.164102.

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Brázda, Václav, and Miroslav Fojta. "The Rich World of p53 DNA Binding Targets: The Role of DNA Structure." International Journal of Molecular Sciences 20, no. 22 (November 9, 2019): 5605. http://dx.doi.org/10.3390/ijms20225605.

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The tumor suppressor functions of p53 and its roles in regulating the cell cycle, apoptosis, senescence, and metabolism are accomplished mainly by its interactions with DNA. p53 works as a transcription factor for a significant number of genes. Most p53 target genes contain so-called p53 response elements in their promoters, consisting of 20 bp long canonical consensus sequences. Compared to other transcription factors, which usually bind to one concrete and clearly defined DNA target, the p53 consensus sequence is not strict, but contains two repeats of a 5′RRRCWWGYYY3′ sequence; therefore it varies remarkably among target genes. Moreover, p53 binds also to DNA fragments that at least partially and often completely lack this consensus sequence. p53 also binds with high affinity to a variety of non-B DNA structures including Holliday junctions, cruciform structures, quadruplex DNA, triplex DNA, DNA loops, bulged DNA, and hemicatenane DNA. In this review, we summarize information of the interactions of p53 with various DNA targets and discuss the functional consequences of the rich world of p53 DNA binding targets for its complex regulatory functions.

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Thomas, M. J., T. M. Freeland, and J. S. Strobl. "Z-DNA formation in the rat growth hormone gene promoter region." Molecular and Cellular Biology 10, no. 10 (October 1990): 5378–87. http://dx.doi.org/10.1128/mcb.10.10.5378.

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The complete DNA sequence of the 1.7 kilobase pairs (kbp) 5' of the rat growth hormone gene (rGH) has been determined and analyzed for Z-DNA-forming potential. Regions of alternating purine-pyrimidine (APP) sequences located between -1047 and -986 [(GT)31], between -445 and -433 bp, and between -426 and -403 bp relative to the rGH RNA transcription initiation site were identified and shown to form Z-DNA in negatively supercoiled plasmids by two-dimensional gel electrophoresis. Free-energy calculations indicated that Z-DNA forms most readily in the proximal Z-DNA regions. Diethyl pyrocarbonate footprinting of physiologically supercoiled plasmid DNA confirmed the presence of Z-DNA from -444 to -404 bp spanning the two most proximal APP sequences and a short non-APP sequence in between. DNA sequence analysis also predicted a region of DNA curvature near this proximal Z-DNA region. Formation of Z-DNA in the distal Z-DNA region consisting of a (GT)31 repeat was constrained at physiological plasmid superhelical densities. This may be related to the presence of DNA sequences (-1584 to -1559) 512 bp upstream of (GT)31 that undergo cruciform formation and thereby utilize the available free energy. Removal of 580 bp containing the cruciform region resulted in Z-DNA formation within (GT)31, thus demonstrating that deletion mutations can exert topological changes at a distance within the rGH 5'-flanking region. Methylation of two specific cytosines in the rGH 5'-flanking DNA that have been associated with inhibition of rGH promoter activity had no effect on Z-DNA formation. No evidence for DNA secondary structure formation within the rGH second exon-intron or 3'-flanking region was observed. We conclude that the rGH 5'-flanking region undergoes secondary-structure formation at physiological superhelical densities, thus providing a potential mechanism(s) for modulating rGH activity.

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Thomas, M. J., T. M. Freeland, and J. S. Strobl. "Z-DNA formation in the rat growth hormone gene promoter region." Molecular and Cellular Biology 10, no. 10 (October 1990): 5378–87. http://dx.doi.org/10.1128/mcb.10.10.5378-5387.1990.

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The complete DNA sequence of the 1.7 kilobase pairs (kbp) 5' of the rat growth hormone gene (rGH) has been determined and analyzed for Z-DNA-forming potential. Regions of alternating purine-pyrimidine (APP) sequences located between -1047 and -986 [(GT)31], between -445 and -433 bp, and between -426 and -403 bp relative to the rGH RNA transcription initiation site were identified and shown to form Z-DNA in negatively supercoiled plasmids by two-dimensional gel electrophoresis. Free-energy calculations indicated that Z-DNA forms most readily in the proximal Z-DNA regions. Diethyl pyrocarbonate footprinting of physiologically supercoiled plasmid DNA confirmed the presence of Z-DNA from -444 to -404 bp spanning the two most proximal APP sequences and a short non-APP sequence in between. DNA sequence analysis also predicted a region of DNA curvature near this proximal Z-DNA region. Formation of Z-DNA in the distal Z-DNA region consisting of a (GT)31 repeat was constrained at physiological plasmid superhelical densities. This may be related to the presence of DNA sequences (-1584 to -1559) 512 bp upstream of (GT)31 that undergo cruciform formation and thereby utilize the available free energy. Removal of 580 bp containing the cruciform region resulted in Z-DNA formation within (GT)31, thus demonstrating that deletion mutations can exert topological changes at a distance within the rGH 5'-flanking region. Methylation of two specific cytosines in the rGH 5'-flanking DNA that have been associated with inhibition of rGH promoter activity had no effect on Z-DNA formation. No evidence for DNA secondary structure formation within the rGH second exon-intron or 3'-flanking region was observed. We conclude that the rGH 5'-flanking region undergoes secondary-structure formation at physiological superhelical densities, thus providing a potential mechanism(s) for modulating rGH activity.

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Wei, Guoqian, Shanshan Li, Yongxing Guo, and Zhang Dang. "Fiber Bragg Gratings Based Cyclic Strain Measuring of Weld Toes of Cruciform Joints." Applied Sciences 9, no. 14 (July 23, 2019): 2939. http://dx.doi.org/10.3390/app9142939.

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The real weld toe geometry is generally not mathematically perfect, resulting in obvious stress concentration effects, both on the weld section and along the longitudinal direction of the weld toe. The true stress-strain state at the local weld toe directly affects the fatigue performance and behavior of the welded structure. Therefore, a Fiber Bragg Grating (FBG) sensor based method for testing the cyclic strain at the weld toe was proposed. Cruciform welded joints were fabricated as specimens on which FBG sensors were arranged at several characteristic points along the weld toe curve. Strains at all the characteristic points under cyclic tensile load were measured and recorded, which showed the proposed measuring method could accurately obtain the complete local strain time histories along the weld toe. The strain time histories clearly reflected the cyclic hardening phenomenon in the early stage and the plastic yielding phenomenon in the final stage. Furthermore, based on the cyclic stress-strain constitutive model of the weld material, the stress-strain response curves of all the characteristic points were drawn. Combined with the fatigue fracture morphology, the mechanism of the unsynchronized initiation of the multiple cracks in the weld toe was investigated.

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Journal articles on the topic 'Cruciform structure'

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