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Kensuke Kawara, Genichiro Tsuji, Yosuke Taniguchi, Shigeki Sasaki
The 2,13-dimethoxy[5]helicene-spermine ligand 8 b possesses an axial chirality. The racemic 8 b was bound to B-DNA by the accompanying induction of its (P)-chirality together with the B-to-Z helicity change of the duplex DNA, [(dC-dG)3 ]2 . The (P)-chirality of the bound 8 b, in turn, transitioned to the (M)-chirality according to the Z-helicity of the DNA. These results illustrate the chirality synchronization between the DNA and the ligand.
December 11, 2016: Chemistry: a European Journal
Debayan Chakraborty, David J Wales
The complex conformational change from B-DNA to Z-DNA requires inversion of helix-handedness. Multiple degrees of freedom are intricately coupled during this transition, and formulating an appropriate reaction coordinate that captures the underlying complexity would be problematic. In this contribution, we adopt an alternative approach, based on the potential energy landscape perspective, to construct a kinetic transition network. Microscopic insight into the B → Z transition is provided in terms of geometrically defined discrete paths consisting of local minima and the transition states that connect them...
December 21, 2016: Physical Chemistry Chemical Physics: PCCP
Teneema Kuriakose, Si Ming Man, R K Subbarao Malireddi, Rajendra Karki, Sannula Kesavardhana, David E Place, Geoffrey Neale, Peter Vogel, Thirumala-Devi Kanneganti
The interferon-inducible protein Z-DNA binding protein 1 (ZBP1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1) was identified as a dsDNA sensor, which instigates innate immune responses. However, this classification has been disputed and whether ZBP1 functions as a pathogen sensor during an infection has remained unknown. Herein, we demonstrated ZBP1-mediated sensing of the influenza A virus (IAV) proteins NP and PB1, triggering cell death and inflammatory responses via the RIPK1-RIPK3-Caspase-8 axis...
August 5, 2016: Science Immunology
Vladislav Kulikov, Naomi A B Johnson, Andrew J Surman, Marie Hutin, Sharon M Kelly, Mohammed Hezwani, De-Liang Long, Gerd Meyer, Leroy Cronin
Herein, we report a hybrid polyoxometalate organic-inorganic compound, Na2 [(HGMP)2 Mo5 O15 ]⋅7 H2 O (1; where GMP=guanosine monophosphate), which spontaneously assembles into a structure with dimensions that are strikingly similar to those of the naturally occurring left-handed Z-form of DNA. The helical parameters in the crystal structure of the new compound, such as rise per turn and helical twist per dimer, are nearly identical to this DNA conformation, allowing a close comparison of the two structures...
November 30, 2016: Angewandte Chemie
Madhabi M Bhanjadeo, Ashok K Nayak, Umakanta Subudhi
DNA adopts different conformation not only because of novel base pairs but also while interacting with inorganic or organic compounds. Self-assembled branched DNA (bDNA) structures or DNA origami that change conformation in response to environmental cues hold great promises in sensing and actuation at the nanoscale. Recently, the B-Z transition in DNA is being explored to design various nanomechanical devices. In this communication we have demonstrated that Cerium chloride binds to the phosphate backbone of self-assembled bDNA structure and induce B-to-Z transition at physiological concentration...
January 22, 2017: Biochemical and Biophysical Research Communications
Ae-Ree Lee, Yeo-Jin Seo, Seo-Ree Choi, Kyoung-Seok Ryu, Hae-Kap Cheong, Shim Sung Lee, Masato Katahira, Chin-Ju Park, Joon-Hwa Lee
A Z-DNA binding protein (ZBP)-containing protein kinase (PKZ) in fish species has an important role in the innate immune response. Previous structural studies of the Zα domain of the PKZ from Carassius auratus (caZαPKZ) showed that the protein initially binds to B-DNA and induces B-Z transition of double stranded DNA in a salt concentration-dependent manner. However, the significantly reduced B-Z transition activity of caZαPKZ at high salt concentration was not fully understood. In this study, we present the binding affinity of the protein for B-DNA and Z-DNA and characterize its extremely low B-Z transition activity at 250 mM NaCl...
January 8, 2017: Biochemical and Biophysical Research Communications
Kim Newton, Katherine E Wickliffe, Allie Maltzman, Debra L Dugger, Andreas Strasser, Victoria C Pham, Jennie R Lill, Merone Roose-Girma, Søren Warming, Margaret Solon, Hai Ngu, Joshua D Webster, Vishva M Dixit
Receptor-interacting protein kinase 1 (RIPK1) promotes cell survival-mice lacking RIPK1 die perinatally, exhibiting aberrant caspase-8-dependent apoptosis and mixed lineage kinase-like (MLKL)-dependent necroptosis. However, mice expressing catalytically inactive RIPK1 are viable, and an ill-defined pro-survival function for the RIPK1 scaffold has therefore been proposed. Here we show that the RIP homotypic interaction motif (RHIM) in RIPK1 prevents the RHIM-containing adaptor protein ZBP1 (Z-DNA binding protein 1; also known as DAI or DLM1) from activating RIPK3 upstream of MLKL...
December 1, 2016: Nature
Juan Lin, Snehlata Kumari, Chun Kim, Trieu-My Van, Laurens Wachsmuth, Apostolos Polykratis, Manolis Pasparakis
Receptor-interacting protein kinase 1 (RIPK1) regulates cell death and inflammation through kinase-dependent and -independent functions. RIPK1 kinase activity induces caspase-8-dependent apoptosis and RIPK3 and mixed lineage kinase like (MLKL)-dependent necroptosis. In addition, RIPK1 inhibits apoptosis and necroptosis through kinase-independent functions, which are important for late embryonic development and the prevention of inflammation in epithelial barriers. The mechanism by which RIPK1 counteracts RIPK3-MLKL-mediated necroptosis has remained unknown...
December 1, 2016: Nature
Tomoo Miyahara, Hiroshi Nakatsuji, Hiroshi Sugiyama
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA...
November 17, 2016: Journal of Physical Chemistry. A
Marcin Kowiel, Dariusz Brzezinski, Mariusz Jaskolski
The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries. In this paper, we analyze the bonding deformations of the phosphodiester groups in the Cambridge Structural Database, cluster the studied fragments into six conformation-related categories and propose a revised set of restraints for the O-P-O bond angles and distances...
September 30, 2016: Nucleic Acids Research
So-I Shin, Seokjin Ham, Jihwan Park, Seong Hye Seo, Chae Hyun Lim, Hyeongrin Jeon, Jounghyun Huh, Tae-Young Roh
Z-DNA, a left-handed double helical DNA is structurally different from the most abundant B-DNA. Z-DNA has been known to play a significant role in transcription and genome stability but the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. To obtain genome-wide map of ZFSs, Zaa with two Z-DNA-binding domains was used for ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examined in vivo A large portion of ZFSs was enriched in the promoter regions and contain sequences with high potential to form Z-DNA...
July 3, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Yves Dondelinger, Paco Hulpiau, Yvan Saeys, Mathieu J M Bertrand, Peter Vandenabeele
Throughout the animal kingdom, innate immune receptors protect the organism from microbial intruders by activating pathways that mediate inflammation and pathogen clearance. Necroptosis contributes to the innate immune response by killing pathogen-infected cells and by alerting the immune system through the release of danger signals. Components of the necroptotic signaling axis - TIR-domain-containing adapter-inducing interferon-β (TRIF), Z-DNA sensor DAI, receptor-interacting kinase (RIPK)1, RIPK3 and mixed-lineage kinase domain-like protein (MLKL) - are therefore expected to be found in all animals...
October 2016: Trends in Cell Biology
Galina Gulis, Izabel Cristina Rodrigues Silva, Herdson Renney Sousa, Isabel Garcia Sousa, Maryani Andressa Gomes Bezerra, Luana Salgado Quilici, Andrea Queiroz Maranhao, Marcelo Macedo Brigido
Left-handed Z-DNA is a physiologically unstable DNA conformation, and its existence in vivo can be attributed to localized torsional distress. Despite evidence for the existence of Z-DNA in vivo, its precise role in the control of gene expression is not fully understood. Here, an in vivo probe based on an anti-Z-DNA intrabody is proposed for native Z-DNA detection. The probe was used for chromatin immunoprecipitation of potential Z-DNA-forming sequences in the human genome. One of the isolated putative Z-DNA-forming sequences was cloned upstream of a reporter gene expression cassette under control of the CMV promoter...
September 2016: Molecular Biotechnology
Maura Malinska, Zbigniew Dauter
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin...
June 2016: Acta Crystallographica. Section D, Structural Biology
Melanie Rohner, Alfredo Medina-Molner, Bernhard Spingler
Many research groups study the generation of supramolecular n-dimensional arrays by combining metals with DNA building blocks. Most of the time, the natural nucleobases are modified to obtain higher-affinity metal binding sites. Using unmodified nucleobases avoids a potentially difficult synthesis; however, they have the possible disadvantage of a less defined and/or weaker coordination mode of the metal. Structural studies on the behavior of copper(II) as a linking metal and guanine as the natural ligand for metals in unmodified DNA are reported...
June 20, 2016: Inorganic Chemistry
Ashok K Nayak, Aseem Mishra, Bhabani S Jena, Barada K Mishra, Umakanta Subudhi
Controlled conversion of right-handed B-DNA to left-handed Z-DNA is one of the greatest conformational transitions in biology. Recently, the B-Z transition has been explored from nanotechnological points of view and used as the driving machinery of many nanomechanical devices. Using a combination of CD spectroscopy, fluorescence spectroscopy, and PAGE, we demonstrate that low concentration of lanthanum chloride can mediate B-to-Z transition in self-assembled Y-shaped branched DNA (bDNA) structure. The transition is sensitive to the sequence and structure of the bDNA...
2016: Scientific Reports
Xiancheng Liu, Keyi Huang, Qunhao Hou, Zhicheng Sun, Binhua Wang, Gang Lin, Dongming Li, Yong Liu, Xiaowen Xu, Chengyu Hu
As one member of ADAR family, ADAR1 (adenosine deaminase acting on RNA 1) can convert adenosine to inosine within dsRNA. There are many ADAR1 splicing isoforms in mammals, including an interferon (IFN) inducible ∼150 kD protein (ADAR1-p150) and a constitutively expressed ∼110 kD protein (ADAR1-p110). The structural diversity of ADAR1 splicing isoforms may reflect their multiple functions. ADAR1 splicing isoforms were also found in fish. In our previous study, we have cloned and identified two different grass carp ADAR1 splicing isoforms, i...
October 2016: Developmental and Comparative Immunology
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger
Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt 'left-handed' conformations in DNA and RNA, in double as well as single stranded contexts. These 'Z-like' steps involve the coexistence of several rare structural features: a C2'-endo puckering, a syn nucleotide and a lone pair-π stacking between a ribose O4' atom and a nucleobase...
July 8, 2016: Nucleic Acids Research
Jiří Černý, Paulína Božíková, Bohdan Schneider
The web service DNATCO ( classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline...
July 8, 2016: Nucleic Acids Research
Albino Bacolla, John A Tainer, Karen M Vasquez, David N Cooper
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e...
July 8, 2016: Nucleic Acids Research
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