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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
Viet Hoang Man, Feng Pan, Celeste Sagui, Christopher Roland
We explore the use of a fast laser melting simulation approach combined with atomistic molecular dynamics simulations in order to determine the melting and healing responses of B-DNA and Z-DNA dodecamers with the same d(5'-CGCGCGCGCGCG-3')2 sequence. The frequency of the laser pulse is specifically tuned to disrupt Watson-Crick hydrogen bonds, thus inducing melting of the DNA duplexes. Subsequently, the structures relax and partially refold, depending on the field strength. In addition to the inherent interest of the nonequilibrium melting process, we propose that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent...
April 14, 2016: Journal of Chemical Physics
Fengqiu Zhang, Qing Huang, Jingwen Yan, Zhu Chen
A nucleosome is made up of DNA and histones, and acetylation of histones perturbs the interaction of DNA and histones and thus affects the chromatin conformation and function. However, whether or how acetylation induces DNA conformation changes is still elusive. In this work, we applied FT-IR spectroscopy to monitor the DNA signals in cells as the histone acetylation was regulated by trichostatin A (TSA), a reversible inhibitor to histone deacetylases (HDACs). Our results unambiguously demonstrate the significant transformation of B-DNA to Z-DNA upon histone acetylation in the TSA treated HeLa cells...
April 19, 2016: Analytical Chemistry
Ah-Young Kwon, Gi-Moon Nam, Albert Johner, Seyong Kim, Seok-Cheol Hong, Nam-Kyung Lee
Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions...
February 2016: Physical Review. E
Farid Semsarha, Gholamreza Raisali, Bahram Goliaei, Hossein Khalafi
In order to obtain the energy deposition pattern of ionizing radiation in the nanometric scale of genetic material and to investigate the different sensitivities of the DNA conformations, direct effects of (60)Co gamma rays on the three A, B and Z conformations of DNA have been studied. For this purpose, single-strand breaks (SSB), double-strand breaks (DSB), base damage (BD), hit probabilities and three microdosimetry quantities (imparted energy, mean chord length and lineal energy) in the mentioned DNA conformations have been calculated and compared by using GEometry ANd Tracking 4 (Geant4) toolkit...
May 2016: Radiation and Environmental Biophysics
Maurice Guéron, Pierre Plateau, Marcel Filoche
It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution...
July 2016: Biopolymers
Ae-Ree Lee, Chin-Ju Park, Hae-Kap Cheong, Kyoung-Seok Ryu, Jin-Wan Park, Mun-Young Kwon, Janghyun Lee, Kyeong Kyu Kim, Byong-Seok Choi, Joon-Hwa Lee
Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B-Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B-Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ)...
April 7, 2016: Nucleic Acids Research
Qiwang Jin, Tingting Li, Xiaobing He, Huaijie Jia, Guohua Chen, Shuang Zeng, Yongxiang Fang, Zhizhong Jing, Xiaopu Yang
OBJECTIVE: To study the structural characteristics of the mouse DNA-dependent activator of interferon-regulatory factors (DAI) and its related molecular mechanism in anti-viral innate immune responses and signal transduction. METHODS: The coding sequence of mouse DAI gene was amplified from splenic mononuclear cells by reverse transcription-PCR, and the genetic evolution and molecular structure of the mouse DAI gene were analyzed by bioinformatics softwares. After mouse DAI was stimulated by poly(dA-dT) and poly(dG-dC), the nuclear factor κB (NF-κB) and interferon-beta (IFN-β) promoter-driven luciferase activity were detected by dual-luciferase reporter assay system...
December 2015: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
Chuxin Wu, Yousheng Hu, Lihua Fan, Haizhou Wang, Zhicheng Sun, Shoulong Deng, Yong Liu, Chengyu Hu
PKZ, protein kinase containing Z-DNA binding domains, is a novel member of eIF2α kinase in fish. PKZ can be up-regulated in response to Poly I:C or heat stress, and it has a typical eIF2α kinase activity. However, the relationship between fish PKZ and apoptosis remains unclear. In the present study, effects of PKZ on apoptosis were explored. Initially, we found that PKZ and PKR were up-regulated by poly I:C in a time-dependent manner. Q-PCR analysis showed that the change of Caspase-3 mRNA was consistent with that of PKZ under the stimulation of poly I:C or transfection with PKZ siRNA in CIK cells...
January 2016: Molecular Immunology
Marie Zgarbová, Jiří Šponer, Michal Otyepka, Thomas E Cheatham, Rodrigo Galindo-Murillo, Petr Jurečka
Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β...
December 8, 2015: Journal of Chemical Theory and Computation
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