Статті в журналах: "Cruciform structures"

1

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.

2

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.

3

Mandal, Shankar, Sangeetha Selvam, Yunxi Cui, Mohammed Enamul Hoque, and Hanbin Mao. "Mechanical Cooperativity in DNA Cruciform Structures." ChemPhysChem 19, no. 20 (August 1, 2018): 2627–34. http://dx.doi.org/10.1002/cphc.201800480.

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4

Frappier, L., G. B. Price, R. G. Martin, and M. Zannis-Hadjopoulos. "Monoclonal antibodies to cruciform DNA structures." Journal of Molecular Biology 193, no. 4 (February 1987): 751–58. http://dx.doi.org/10.1016/0022-2836(87)90356-1.

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5

Zannis-Hadjopoulos, M., O. Novac, D. Alvarez, and G. B. Price. "14-3-3s are DNA-replication proteins." Biochemical Society Transactions 30, no. 4 (August 1, 2002): 397–401. http://dx.doi.org/10.1042/bst0300397.

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14-3-3 proteins are conserved multifunctional molecules, involved in many biological processes. Several 14-3-3 isoforms were recently shown to be cruciform DNA-binding proteins, which is a new activity ascribed to the 14-3-3 family. As cruciform-binding proteins, 14-3-3 proteins are putatively involved in the regulation of DNA replication. Inverted repeat sequences that are able to extrude into cruciform structures are a common feature of replication origins in both prokaryotes and eukaryotes. The involvement of cruciform structures in the initiation of DNA replication has been demonstrated. A leading model of 14-3-3 function proposes that they facilitate critical protein-protein interactions, thus serving as a central component of a wide variety of cellular processes.

6

Battistoni, Andrea, Luisa Leoni, Beatrice Sampaolese, and Maria Savino. "Kinetic persistence of cruciform structures in reconstituted minichromosomes." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 950, no. 2 (July 1988): 161–71. http://dx.doi.org/10.1016/0167-4781(88)90008-5.

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7

Yu, Ying Xia, Bo Lin He, and Xiao Dong Zhang. "Calculation about the Effect of Stress Concentration Coefficient on the Fatigue Properties for Welded Cruciform Joints of 16MnR Steel." Applied Mechanics and Materials 189 (July 2012): 350–54. http://dx.doi.org/10.4028/www.scientific.net/amm.189.350.

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Stress concentration coefficient of welded joints has a crucial influence on mechanical properties of welded structures. Geometrical parameters of welded joints seriously affect the stress concentration coefficient. In order to increase the mechanical properties and safety of welded structures, it has great significance for reducing stress concentration coefficient and improving the mechanical properties of welded structures by researching and improving the geometry of welded joints. In this paper, the effect of stress concentration coefficient on the fatigue properties for welded cruciform joints of 16MnR steel was analyzed by using ABAQUS finite element and MSC.Fatigue programe, and the change rule of stress concentration coefficient with the variation of the parameter was studied and the fatigue life changed with the stress concentration coefficient 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, and the fatigue life of welded cruciform joints can be improved succesfully. In order to obtain the safety welded structures, the true weld tangent line angle θ should be controlled in the angle smaller than 20o.

8

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.

9

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.

10

Farajpourbonab, Ebrahim, Hossein Showkati, and Sunil Kute. "Castellated cruciform steel columns." World Journal of Engineering 15, no. 4 (August 6, 2018): 440–49. http://dx.doi.org/10.1108/wje-04-2017-0088.

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Purpose The main function of the castellation process is making I-sections stiffer by increasing the height of web and supplying a higher moment capacity of primary axis than plain-webbed members of the same weight. In addition, it optimizes the use of heavy, costly constructional steel material and provides good services accessibility. The purpose of this study was to investigate the strength and buckling behavior of axially loaded castellated cruciform steel columns using finite element analysis. Although a significant body of research exists on the failure of different columns, there is no proper criterion introduced to determine the point of buckling in the equilibrium path of an imperfect column. Design/methodology/approach This paper considers a wide range of practical geometric dimensions and various end conditions using ANSYS software. Findings are reported for about 224 samples of castellated cruciform I-shaped sections, and a simplified approach to evaluate buckling capacity of castellated columns, using the slenderness-load curve, is developed. In addition, the axial compressive capacities of those steel sections are investigated numerically in the current study. Findings The results of nonlinear analyses of these columns revealed that the load-carrying capacity of castellated cruciform steel columns far outweighs and is more appropriate than that of the traditional cruciform steel columns. In the present paper, new geometric criteria have been introduced having the ability to cover different types of columns. It shows the critical load of columns in the range of elastic and inelastic behavior. Practical implications This study can provide a background for practical engineering applications and design specifications for steel structures with castellated sections. In the present paper, new geometric criteria have been introduced having the ability to cover different types of columns. It shows the critical load of columns showing both elastic and inelastic behavior. Because this method showed reliable performance, it can be used during experimental tests for detecting buckling point. Originality/value This study can provide background for practical engineering applications and design specifications for steel structures with castellated sections; also, a physical criterion has been defined for calculating the buckling load of real columns.

11

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.

12

Gong, Genfei, Ning Zhao, Debin Ni, Jianyou Chen, Yan Shen, Mingkui Wang, and Guoli Tu. "Dopant-free 3,3′-bithiophene derivatives as hole transport materials for perovskite solar cells." Journal of Materials Chemistry A 4, no. 10 (2016): 3661–66. http://dx.doi.org/10.1039/c6ta00032k.

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13

Zhao, Weidong, Guoqing Feng, Wenchao Liu, and Huilong Ren. "Research on Fatigue Properties of Typical Welded Joints of DH36 Steel at −60 °C." Applied Sciences 10, no. 11 (May 28, 2020): 3742. http://dx.doi.org/10.3390/app10113742.

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As the development of the polar region continues to increase, the fatigue properties of structures at low temperature are increasingly receiving researcher attention. This study aimed to investigate the fatigue properties of T-welded and cruciform welded joints at −60 °C. Logarithmic S–N curves based on the hot-spot stress of the T-welded and cruciform welded joints at 50% and 95% confidence levels were obtained at −60 °C. The test results showed that the fatigue properties of T-welded joints were almost 2–7% better than those of the cruciform welded joints at −60 °C. Factors that affected the fatigue properties of welded joints, such as the stress concentration factor, microstructure, Vickers hardness profiles, and fractography, were also studied and the test results showed that the fatigue properties of cruciform welded joints at −60 °C were 57.215% better than at room temperature.

14

Grunder, Sergio, Roman Huber, Viviana Horhoiu, Maria Teresa González, Christian Schönenberger, Michel Calame, and Marcel Mayor. "New Cruciform Structures: Toward Coordination Induced Single Molecule Switches." Journal of Organic Chemistry 72, no. 22 (October 2007): 8337–44. http://dx.doi.org/10.1021/jo7013998.

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15

LILLEY, D., G. GOUGH, L. HALLAM, and K. SULLIVAN. "The physical chemistry of cruciform structures in supercoiled DNA molecules." Biochimie 67, no. 7-8 (July 1985): 697–706. http://dx.doi.org/10.1016/s0300-9084(85)80157-7.

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16

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°.

17

Nag, D. K., and T. D. Petes. "Physical detection of heteroduplexes during meiotic recombination in the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 4 (April 1993): 2324–31. http://dx.doi.org/10.1128/mcb.13.4.2324.

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We describe a general physical method for detecting the heteroduplex DNA that is formed as an intermediate in meiotic recombination in the yeast Saccharomyces cerevisiae. We use this method to study the kinetic relationship between the formation of heteroduplex DNA and other meiotic events. We show that strains with the rad50, but not the rad52, mutation are defective in heteroduplex formation. We also demonstrate that, although cruciform structures can be formed in vivo as a consequence of heteroduplex formation between DNA strands that contain different palindromic insertions, small palindromic sequences in homoduplex DNA are rarely extruded into the cruciform conformation.

18

Nag, D. K., and T. D. Petes. "Physical detection of heteroduplexes during meiotic recombination in the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 4 (April 1993): 2324–31. http://dx.doi.org/10.1128/mcb.13.4.2324-2331.1993.

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We describe a general physical method for detecting the heteroduplex DNA that is formed as an intermediate in meiotic recombination in the yeast Saccharomyces cerevisiae. We use this method to study the kinetic relationship between the formation of heteroduplex DNA and other meiotic events. We show that strains with the rad50, but not the rad52, mutation are defective in heteroduplex formation. We also demonstrate that, although cruciform structures can be formed in vivo as a consequence of heteroduplex formation between DNA strands that contain different palindromic insertions, small palindromic sequences in homoduplex DNA are rarely extruded into the cruciform conformation.

19

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.

20

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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21

Mandal, Shankar, Sangeetha Selvam, Yunxi Cui, Mohammed Enamul Hoque, and Hanbin Mao. "Cover Feature: Mechanical Cooperativity in DNA Cruciform Structures (ChemPhysChem 20/2018)." ChemPhysChem 19, no. 20 (October 19, 2018): 2600. http://dx.doi.org/10.1002/cphc.201800843.

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22

West, S. C., and A. Korner. "Cleavage of cruciform DNA structures by an activity from Saccharomyces cerevisiae." Proceedings of the National Academy of Sciences 82, no. 19 (October 1, 1985): 6445–49. http://dx.doi.org/10.1073/pnas.82.19.6445.

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23

Chen, Shou Hui, and Zheng Guo. "On the Tensile Experiments of the Woven Membrane Materials under Bi-Axial Loads." Advanced Materials Research 146-147 (October 2010): 14–17. http://dx.doi.org/10.4028/www.scientific.net/amr.146-147.14.

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As a kind of flexible fabric reinforced composites, the woven membrane materials suffer from the bi-axial tensile loads in the application of the lightweight structures. Therefore, the experiments under bi-axial tensile loads are essential for the acquaintance of the mechanical characters of the membrane materials. This paper has summarized thoroughly the details of the bi-axial tensile tests, especially the in-plane cruciform tests. The aspects include the shape and configuration of the cruciform sample, the practice of the applied stresses and the testing of the strains in the two axial directions. It could be expected to be the reference for the establishment of the testing standard of the bi-axial tensile experiment for the membrane materials.

24

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.

25

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.

26

Grunder, Sergio, Roman Huber, Songmei Wu, Christian Schönenberger, Michel Calame, and Marcel Mayor. "Novel Cruciform Structures as Model Compounds for Coordination Induced Single Molecule Switches." CHIMIA International Journal for Chemistry 64, no. 3 (March 31, 2010): 140–44. http://dx.doi.org/10.2533/chimia.2010.140.

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27

Elborough, Kieran M., and Stephen C. West. "Specific binding of cruciform DNA structures by a protein from human extracts." Nucleic Acids Research 16, no. 9 (1988): 3603–16. http://dx.doi.org/10.1093/nar/16.9.3603.

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28

Grunder, Sergio, Roman Huber, Songmei Wu, Christian Schönenberger, Michel Calame, and Marcel Mayor. "Oligoaryl Cruciform Structures as Model Compounds for Coordination-Induced Single-Molecule Switches." European Journal of Organic Chemistry 2010, no. 5 (February 2010): 833–45. http://dx.doi.org/10.1002/ejoc.200901150.

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29

Brázda, Václav, Rob C. Laister, Eva B. Jagelská, and Cheryl Arrowsmith. "Cruciform structures are a common DNA feature important for regulating biological processes." BMC Molecular Biology 12, no. 1 (2011): 33. http://dx.doi.org/10.1186/1471-2199-12-33.

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30

Yamamoto, Yu, Osamu Miura, and Takashi Ohyama. "Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell Integrity." International Journal of Molecular Sciences 22, no. 7 (March 26, 2021): 3399. http://dx.doi.org/10.3390/ijms22073399.

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DNA can adopt various structures besides the B-form. Among them, cruciform structures are formed on inverted repeat (IR) sequences. While cruciform formable IRs (CFIRs) are sometimes found in regulatory regions of transcription, their function in transcription remains elusive, especially in eukaryotes. We found a cluster of CFIRs within the mouse Pou5f1 enhancer. Here, we demonstrate that this cluster or some member(s) plays an active role in the transcriptional regulation of not only Pou5f1, but also Sox2, Nanog, Klf4 and Esrrb. To clarify in vivo function of the cluster, we performed genome editing using mouse ES cells, in which each of the CFIRs was altered to the corresponding mirror repeat sequence. The alterations reduced the level of the Pou5f1 transcript in the genome-edited cell lines, and elevated those of Sox2, Nanog, Klf4 and Esrrb. Furthermore, transcription of non-coding RNAs (ncRNAs) within the enhancer was also upregulated in the genome-edited cell lines, in a similar manner to Sox2, Nanog, Klf4 and Esrrb. These ncRNAs are hypothesized to control the expression of these four pluripotency genes. The CFIRs present in the Pou5f1 enhancer seem to be important to maintain the integrity of ES cells.

31

Tuling, S., L. Dala, and C. Toomer. "Lee-Side Flow Structures of Very Low Aspect Ratio Cruciform Wing–Body Configurations." Journal of Spacecraft and Rockets 50, no. 6 (November 2013): 1134–49. http://dx.doi.org/10.2514/1.a32522.

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32

Lilley, David M. J. "Structural isomerization in DNA: the formation of cruciform structures in supercoiled DNA molecules." Chemical Society Reviews 18 (1989): 53. http://dx.doi.org/10.1039/cs9891800053.

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33

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.

34

MAIER, GIULIO, VLADIMIR BULJAK, TOMASZ GARBOWSKI, GIUSEPPE COCCHETTI, and GIORGIO NOVATI. "MECHANICAL CHARACTERIZATION OF MATERIALS AND DIAGNOSIS OF STRUCTURES BY INVERSE ANALYSES: SOME INNOVATIVE PROCEDURES AND APPLICATIONS." International Journal of Computational Methods 11, no. 03 (June 2014): 1343002. http://dx.doi.org/10.1142/s0219876213430020.

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A survey is presented herein of some recent research contributions to the methodology of inverse structural analysis based on statical tests for diagnosis of possibly damaged structures and for mechanical characterization of materials in diverse industrial environments. The following issues are briefly considered: identifications of parameters in material models and of residual stresses on the basis of indentation experiments; mechanical characterization of free-foils and laminates by cruciform and compression tests and digital image correlation measurements; diagnosis, both superficially and in depth, of concrete dams, possibly affected by alkali-silica-reaction or otherwise damaged.

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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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Chasovskikh, Sergey, Alexandre Dimtchev, Mark Smulson, and Anatoly Dritschilo. "DNA transitions induced by binding of PARP-1 to cruciform structures in supercoiled plasmids." Cytometry Part A 68A, no. 1 (2005): 21–27. http://dx.doi.org/10.1002/cyto.a.20187.

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Coté, Atina G., and Susanna M. Lewis. "Mus81-Dependent Double-Strand DNA Breaks at In Vivo-Generated Cruciform Structures in S. cerevisiae." Molecular Cell 31, no. 6 (September 2008): 800–812. http://dx.doi.org/10.1016/j.molcel.2008.08.025.

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Li, Dawei, Bei Lv, Hao Zhang, Jasmine Yiqin Lee, and Tianhu Li. "Disintegration of cruciform and G-quadruplex structures during the course of helicase-dependent amplification (HDA)." Bioorganic & Medicinal Chemistry Letters 25, no. 8 (April 2015): 1709–14. http://dx.doi.org/10.1016/j.bmcl.2015.02.070.

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Sukackaite, Rasa, Malene Ringkjøbing Jensen, Philippe J. Mas, Martin Blackledge, Sara B. Buonomo, and Darren J. Hart. "Structural and Biophysical Characterization of Murine Rif1 C Terminus Reveals High Specificity for DNA Cruciform Structures." Journal of Biological Chemistry 289, no. 20 (March 14, 2014): 13903–11. http://dx.doi.org/10.1074/jbc.m114.557843.

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Poggi, Lucie, and Guy-Franck Richard. "Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions." Microbiology and Molecular Biology Reviews 85, no. 1 (December 23, 2020): e00110-20. http://dx.doi.org/10.1128/mmbr.00110-20.

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SUMMARYDuplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro. However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.

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Liu, Zhiguo, Lin Zhao, Yuangang Zu, Shengnan Tan, Yuanlin Wang, and Yiming Zhang. "Unusual DNA Structures Formed on Bare Highly Oriented Pyrolytic Graphite Surfaces Studied by Atomic Force Microscopy." Microscopy and Microanalysis 19, no. 3 (March 27, 2013): 544–52. http://dx.doi.org/10.1017/s1431927613000275.

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AbstractIt is important to know the detailed DNA structure on carbonaceous surfaces for further application of DNA-functionalized carbonaceous materials in diverse research areas. In this study, the topographic and structural characteristics of the separated single DNA molecules and their assembly on highly oriented pyrolytic graphite (HOPG) surfaces have been investigated by atomic force microscopy (AFM). AFM results indicate that both circular and linear DNA molecules tend to form hexagonal patterns along with some unusual structures that include node, protrusion, cruciform, parallel single-stranded DNA (ssDNA), and compact zigzag. Furthermore, parallel ssDNA patterns and their crossed structures have been obtained under high-temperature conditions. Our AFM results reveal that a bare HOPG surface can induce DNA molecules to form various unusual structures. This finding is helpful for understanding the adsorption behavior of DNA on other carbonaceous surfaces such as carbon nanotubes and graphene. In addition, the hexagonal DNA patterns in this study are similar to those formed on the alkylamine-modified HOPG surface, which implies that a bare HOPG, without any chemical modification, has a strong ability to align biomolecules. This study could expand our knowledge of the diversities of DNA structures and the aligning ability of carbonaceous surfaces.

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Hatami, Mahdi Kazemi, Amir Masoud Amini, and Kamran Fallahi. "Enhancement of Welded Joints Productivity Effect of Welding Position on Fatigue Strength." Applied Mechanics and Materials 110-116 (October 2011): 202–9. http://dx.doi.org/10.4028/www.scientific.net/amm.110-116.202.

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Welded structures are frequently used in today’s metal industry. Since fatigue is still one major reason of failures, investigation in this field is of interest to engineers. In this study experimental methods are employed to perform a fatigue evaluation concerning local weld geometry. The emphasis was on quantifying the weld toe radius as a feature in quantification of weld quality. Three different welding positions which have been led to different toe radii were analyzed. Each batch contained 12 specimens manufactured in cruciform joint and has been tested in non-load carrying status. Finally, the results of tests were compiled in Wöhler (S-N) curve and compared to reference curves introduced by IIW (International Institute of Welding). Results of this study show that local weld geometry has remarkable influence on strength of welded structures. It can be concluded that specimens with larger toe radii had more fatigue strength – as it was expected from the theory.

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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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Grunder, Sergio, Roman Huber, Songmei Wu, Christian Schönenberger, Michel Calame, and Marcel Mayor. "Oligoaryl Cruciform Structures as Model Compounds for Coordination-Induced Single-Molecule Switches (Eur. J. Org. Chem. 5/2010)." European Journal of Organic Chemistry 2010, no. 5 (February 2010): 776. http://dx.doi.org/10.1002/ejoc.201090006.

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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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Yagi, J., S. Machida, M. Matoba, Y. Tomita, and I. Soya. "Thickness Effect Criterion for Fatigue Strength Evaluation of Welded Steel Structures." Journal of Offshore Mechanics and Arctic Engineering 115, no. 1 (February 1, 1993): 58–65. http://dx.doi.org/10.1115/1.2920090.

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From a practical point of view, some measures to reduce the thickness effect backed by a reasonable criterion are required for fabricating structures with heavy section plates. In this study, the thickness effect was investigated by systematic experiments on welded steel joints with thicknesses ranging from 10 to 80 mm. Cruciform joints and T-joints with improved weld by overall profiling or toe-grinding were tested under pulsating tension and under pulsating bending, respectively. These experimental results were analyzed together with the previous results of as-welded joints. As a result, it was concluded that the thickness effect exponents for various conditions may be classified into three categories according to the combination of joint type and loading mode. As-welded joints under bending stress have the steepest thickness effect exponent of −1/3, while as-welded joints under tension with an exponent of −1/5 is milder in thickness effect than that specified in the existing codes. If the weld profile is improved by grinding, the thickness effect becomes much milder to an exponent of −1/10. The as-weld joints with constant-sized attachments also have an exponent of −1/10. Furthermore, thickness effect dependence on fatigue life and thickness effect under random stress were investigated. Based on these results, this study proposes a new evaluation criterion for design purposes.

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Darlow, J. M., and D. R. Leach. "The effects of trinucleotide repeats found in human inherited disorders on palindrome inviability in Escherichia coli suggest hairpin folding preferences in vivo." Genetics 141, no. 3 (November 1, 1995): 825–32. http://dx.doi.org/10.1093/genetics/141.3.825.

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Abstract Unusual DNA secondary structures have been implicated in the expansion of trinucleotide repeat tracts that are associated with several human inherited disorders. We present evidence consistent with the folding of these trinucleotide repeats into hairpin loops at the center of a long DNA palindrome in vivo. Our assay utilizes a palindrome in bacteriophage lambda, the center of which determines its ability to inhibit plaque formation in a manner that is consistent with folding into a hairpin or cruciform structure. We show that central inserts of even numbers of d(CAG).d(CTG) repeats inhibit plaque formation more than do odd numbers. Both d(CAG)2.d(CTG)2 and d(CGG)2.d(CCG)2 central sequences behave like DNA sequences known to form two-base loops in vitro, suggesting that they may also form compact and stable loops. By contrast, repeats of d(GAC).d(GTC) do not show any evidence consistent with unusual loop stability. These results agree with in vitro evidence that the unstable repeats can form hairpin secondary structures and suggest a favored position of folding. We discuss the potential roles of secondary structures, DNA replication and recombination in models of repeat tract expansion.

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Wang, Min, and Hong Zhen Guo. "Study on the Interface Characteristic of Superplastic Diffusion Bonding Joint of Dissimilar Steels." Materials Science Forum 551-552 (July 2007): 157–62. http://dx.doi.org/10.4028/www.scientific.net/msf.551-552.157.

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Magnesium alloys show promise in meeting the demand for materials of lighter weight and higher rigidity. Mg alloys are hard to process and normally require grain refining for improved formability and mechanical properties. To process these fine-grained Mg alloys effectively, it is important to relate their load stress and mechanical properties to changes in their microstructures. Using a biaxial tensile machine and cruciform specimens, to evaluate the mechanical properties, microstructure, and plasticity, in a high temperature biaxial stress state, used of AZ31 Mg alloy sheet. With biaxial deformation, grain boundary slide occurred more frequently than with uniaxial deformation, causing grain boundary separation and formation of micro-voids between the grains. In the vicinity of the cracks and at the locations of grain boundary separation, although deformation temperature at higher than the recrystallization temperature, fine grains (about 2 μm) showing in duplex grain structures were formed locally. The formation of duplex grain structures as a result of local formation of fine grains during the deformation process is a major issue to be solved from the viewpoint of plasticity processing.

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Noda, M., Hideharu Shimizu, Kunio Funami, and H. Mori. "Biaxial Tensile Deformation Behavior and Microstructural Evolutions of Superplasticity in AZ31 Magnesium Alloy." Materials Science Forum 551-552 (July 2007): 225–30. http://dx.doi.org/10.4028/www.scientific.net/msf.551-552.225.

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Magnesium alloys show promise in meeting the demand for materials of lighter weight and higher rigidity. Mg alloys are hard to process and normally require grain refining for improved formability and mechanical properties. To process these fine-grained Mg alloys effectively, it is important to relate their load stress and mechanical properties to changes in their microstructures. Using a biaxial tensile machine and cruciform specimens, to evaluate the mechanical properties, microstructure, and plasticity, in a high temperature biaxial stress state, used of AZ31 Mg alloy sheet. With biaxial deformation, grain boundary slide occurred more frequently than with uniaxial deformation, causing grain boundary separation and formation of micro-voids between the grains. In the vicinity of the cracks and at the locations of grain boundary separation, although deformation temperature at higher than the recrystallization temperature, fine grains (about 2 )m) showing in duplex grain structures were formed locally. The formation of duplex grain structures as a result of local formation of fine grains during the deformation process is a major issue to be solved from the viewpoint of plasticity processing.

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