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Non canonical DNA

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https://www.readbyqxmd.com/read/27933115/effects-of-trimethylamine-n-oxide-and-urea-on-dna-duplex-and-g-quadruplex
#1
Yu-Mi Ueda, Yu-Ki Zouzumi, Atsushi Maruyama, Shu-Ichi Nakano, Naoki Sugimoto, Daisuke Miyoshi
We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex...
2016: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27923713/when-transcription-goes-on-holliday-double-holliday-junctions-block-rna-polymerase-ii-transcription-in-vitro
#2
Anne Pipathsouk, Boris P Belotserkovskii, Philip C Hanawalt
Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJ), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact...
December 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27915381/regulation-of-non-homologous-end-joining-via-post-translational-modifications-of-components-of-the-ligation-step
#3
REVIEW
Kristína Durdíková, Miroslav Chovanec
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals...
December 3, 2016: Current Genetics
https://www.readbyqxmd.com/read/27915287/light-induced-oxidation-of-the-telomeric-g4-dna-in-complex-with-zn-ii-tetracarboxymethyl-porphyrin
#4
Artemy D Beniaminov, Roman A Novikov, Olga K Mamaeva, Vladimir A Mitkevich, Igor P Smirnov, Mikhail A Livshits, Anna K Shchyolkina, Dmitry N Kaluzhny
Structure-specific ligands are convenient tools for the recognition, targeting or probing of non-canonical DNA structures. Porphyrin derivatives exhibit a preference for interaction with G-quadruplex (G4) structures over canonical duplex DNA and are able to cause photoinducible damage to nucleic acids. Here, we show that Zn(II) 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium)porphyrin ( ZNP1: ) interacts with different conformations of the telomeric sequence d(TAGGG(TTAGGG)3) at submicromolar concentrations without any detectible disturbance of the particular fold...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#5
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27902403/the-non-canonical-tomato-yellow-leaf-curl-virus-recombinant-that-displaced-its-parental-viruses-in-southern-morocco-exhibits-a-high-selective-advantage-in-experimental-conditions
#6
Zineb Belabess, Michel Peterschmitt, Martine Granier, Abdessalem Tahiri, Abdelali Blenzar, Cica Urbino
Recombination events are frequently inferred from the increasing number of sequenced viral genomes, but their impact on natural viral populations has rarely been evidenced. TYLCV-IS76 is a recombinant (Begomovirus, Geminiviridae) between the Israel strain of Tomato yellow leaf curl virus (TYLCV-IL) and the Spanish strain of Tomato yellow leaf curl Sardinia virus (TYLCSV-ES) that was generated most probably in the late 1990s in Southern Morocco (Souss). Its emergence in the 2000s coincided with the increasing use of resistant tomato cultivars bearing the Ty-1 gene, and led eventually to the entire displacement of both parental viruses in the Souss...
October 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27898568/whole-exome-sequencing-to-identify-novel-biological-pathways-associated-with-infertility-after-pelvic-inflammatory-disease
#7
Brandie D Taylor, Xiaojing Zheng, Toni Darville, Wujuan Zhong, Kranti Konganti, Olayinka Abiodun-Ojo, Roberta B Ness, Catherine M O'Connell, Catherine L Haggerty
BACKGROUND: Ideal management of sexually transmitted infections (STI) may require risk markers for pathology or vaccine development. Previously, we identified common genetic variants associated with chlamydial pelvic inflammatory disease (PID) and reduced fecundity. As this explains only a proportion of the long-term morbidity risk, we used whole-exome sequencing to identify biological pathways that may be associated with STI-related infertility. METHODS: We obtained stored DNA from 43 non-Hispanic black women with PID from the PID Evaluation and Clinical Health Study...
January 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/27894815/the-histone-variant-h3-3-in-transcriptional-regulation-and-human-disease
#8
REVIEW
Leilei Shi, Hong Wen, Xiaobing Shi
Histone proteins wrap around DNA to form nucleosomes, which further compact into higher order structure of chromatin. In addition to the canonical histones, there are also variant histones that often have pivotal roles in regulating chromatin dynamics and the accessibility of the underlying DNA. H3.3 is the most common non-centromeric variant of histone H3 that differs from the canonical H3 by just 4-5 amino acids. Here we discuss the current knowledge of H3.3 in transcriptional regulation and the recent discoveries and molecular mechanisms of H3...
November 25, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27884082/enhanced-conformational-flexibility-of-the-histone-like-hu-protein-from-mycoplasma-gallisepticum
#9
Dmitry A Altukhov, Anna A Talyzina, Yulia K Agapova, Anna V Vlaskina, Dmitry A Korzhenevskiy, Eduard V Bocharov, Tatiana V Rakitina, Vladimir I Timofeev, Vladimir O Popov
The histone-like (HU) protein is one of the major nucleoid-associated proteins involved in DNA supercoiling and compaction into bacterial nucleoid as well as in all DNA-dependent transactions. This small positively charged dimeric protein binds DNA in a non-sequence specific manner promoting DNA super-structures. The majority of HU proteins are highly conserved among bacteria; however, HU protein from Mycoplasma gallisepticum (HUMgal) has multiple amino acid substitutions in the most conserved regions, which are believed to contribute to its specificity to DNA targets unusual for canonical HU proteins...
November 24, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27875688/morphological-identification-and-single-cell-genomics-of-marine-diplonemids
#10
Ryan M R Gawryluk, Javier Del Campo, Noriko Okamoto, Jürgen F H Strassert, Julius Lukeš, Thomas A Richards, Alexandra Z Worden, Alyson E Santoro, Patrick J Keeling
Recent global surveys of marine biodiversity have revealed that a group of organisms known as "marine diplonemids" constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2, 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean...
November 21, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27862996/tannic-acid-inhibits-egfr-stat1-3-and-enhances-p38-stat1-signalling-axis-in-breast-cancer-cells
#11
Pramod Darvin, Youn Hee Joung, Dong Young Kang, Nipin Sp, Hyo Joo Byun, Tae Sook Hwang, Hema Sasidharakurup, Chi Ho Lee, Kwang Hyun Cho, Kyung Do Park, Hak Kyo Lee, Young Mok Yang
Tannic acid (TA), a naturally occurring polyphenol, is a potent anti-oxidant with anti-proliferative effects on multiple cancers. However, its ability to modulate gene-specific expression of tumour suppressor genes and oncogenes has not been assessed. This work investigates the mechanism of TA to regulate canonical and non-canonical STAT pathways to impose the gene-specific induction of G1-arrest and apoptosis. Regardless of the p53 status and membrane receptors, TA induced G1-arrest and apoptosis in breast cancer cells...
November 15, 2016: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/27861975/convergence-of-the-nobel-fields-of-telomere-biology-and-dna-repair
#12
Elise Fouquerel, Patricia Opresko
The fields of telomere biology and DNA repair have enjoyed a great deal of cross-fertilization and convergence in recent years. Telomeres function at chromosome ends to prevent them from being falsely recognized as chromosome breaks by the DNA damage response and repair machineries. Conversely, both canonical and non-conical functions of numerous DNA repair proteins have been found to be critical for preserving telomere structure and function. In 2009 Elizabeth Blackburn, Carol Greider, and Jack Szostak were awarded the Nobel prize in Physiology or Medicine for the discovery of telomeres and telomerase...
November 18, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27856299/als-and-ftd-linked-ggggcc-repeat-containing-dna-oligonucleotide-folds-into-two-distinct-g-quadruplexes
#13
Jasna Brčić, Janez Plavec
BACKGROUND: The most common genetic cause of neurological disorders ALS and FTD is a largely increased number of GGGGCC repeats in C9orf72 gene. Non-canonical structures including G-quadruplexes adopted by expanded repeats are hypothesized to be crucial in pathogenesis. Recently, we have shown that structural polymorphism of oligonucleotide d(G4C2)3G4 is reduced by dG to 8Br-dG substitution. High-resolution structure of one of the two major G-quadruplexes adopts antiparallel topology comprising of four G-quartets...
November 14, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27855634/identification-of-novel-targets-of-diabetic-nephropathy-and-pedf-peptide-treatment-using-rna-seq
#14
Ana Rubin, Anna C Salzberg, Yuka Imamura, Anzor Grivitishvilli, Joyce Tombran-Tink
BACKGROUND: Diabetic nephropathy (DN) is a major complication of type1 and type 2 diabetes. Understanding how diabetes regulate transcriptome dynamics in DN is important for understanding the biology of the disease and for guiding development of new treatments. RESULTS: We analyzed the kidney transcriptome of a DN mouse model, D2.B6-Ins2 (Akita) /MatbJ, before/after treatment with P78-PEDF. Age, weight, and gender-matched mice and wild-type (wt) littermates were treated at 6 weeks (early treatment) or 12 weeks (late treatment) of age for the duration of 6 weeks...
November 17, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27846236/disruption-of-higher-order-dna-structures-in-friedreich-s-ataxia-gaa-n-repeats-by-pna-or-lna-targeting
#15
Helen Bergquist, Cristina S J Rocha, Rubén Álvarez-Asencio, Chi-Hung Nguyen, Mark W Rutland, C I Edvard Smith, Liam Good, Peter E Nielsen, Rula Zain
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich's ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions...
2016: PloS One
https://www.readbyqxmd.com/read/27836759/the-effect-of-single-nucleotide-polymorphisms-in-g-rich-regions-of-high-risk-human-papillomaviruses-on-structural-diversity-of-dna
#16
Maja Marušič, Lea Hošnjak, Petra Krafčikova, Mario Poljak, Viktor Viglasky, Janez Plavec
BACKGROUND: Infection with high-risk human papillomaviruses (HPVs) can lead to development of cancer of the head and neck and anogenital regions. G-rich sequences found in genomes of high-risk HPVs can fold into non-canonical secondary structures that could serve as 3D motifs distinct from double-stranded DNA and present recognition sites for ligands and opportunity for gene expression modulation. METHODS: Combination of UV, CD and NMR spectroscopy and PAGE electrophoresis were used as they offer complementary insights into structural changes of G-rich oligonucleotides...
November 9, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27836755/discovery-of-the-first-dual-g-triplex-g-quadruplex-stabilizing-compound-a-new-opportunity-in-the-targeting-of-g-rich-dna-structures
#17
Jussara Amato, Alessia Pagano, Sandro Cosconati, Giorgio Amendola, Iolanda Fotticchia, Nunzia Iaccarino, Jessica Marinello, Alessio De Magis, Giovanni Capranico, Ettore Novellino, Bruno Pagano, Antonio Randazzo
BACKGROUND: Guanine-rich DNA motifs can form non-canonical structures known as G-quadruplexes, whose role in tumorigenic processes makes them attractive drug-target candidates for cancer therapy. Recent studies revealed that the folding and unfolding pathways of G-quadruplexes proceed through a quite stable intermediate named G-triplex. METHODS: Virtual screening was employed to identify a small set of putative G-triplex ligands. The G-triplex stabilizing properties of these compounds were analyzed by CD melting assay...
November 9, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27825959/transcription-and-dna-damage-holding-hands-or-crossing-swords
#18
REVIEW
Giuseppina D'Alessandro, Fabrizio d'Adda di Fagagna
Transcription has classically been considered a potential threat to genome integrity. Collision between transcription and DNA replication machinery, and retention of DNA:RNA hybrids, may result in genome instability. On the other hand, it has been proposed that active genes repair faster and preferentially via homologous recombination. Moreover, while canonical transcription is inhibited in the proximity of DNA double-strand breaks, a growing body of evidence supports active non-canonical transcription at DNA damage sites...
November 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27808230/non-canonical-rna-directed-dna-methylation
#19
REVIEW
Diego Cuerda-Gil, R Keith Slotkin
Small RNA-directed DNA methylation (RdDM) has been extensively studied in plants, resulting in a deep understanding of a major 'canonical RdDM' mechanism. However, current models of canonical RdDM cannot explain how this self-perpetuating mechanism is initiated. Recent investigations into the initiation of epigenetic silencing have determined that there are several alternative 'non-canonical RdDM' pathways that function through distinct mechanisms to modify chromatin. This Review aims to illustrate the diversity of non-canonical RdDM mechanisms described to date, recognize common themes within this dizzying array of interconnected pathways, and identify the key unanswered questions remaining in this field...
November 3, 2016: Nature Plants
https://www.readbyqxmd.com/read/27801425/overview-of-the-rna-g-quadruplex-structures
#20
Magdalena Malgowska, Karolina Czajczynska, Dorota Gudanis, Aleksander Tworak, Zofia Gdaniec
G-quadruplexes are non-canonical secondary structures which may be formed by guanine rich sequences, both in vitro and in living cells. The number of biological functions assigned to these structural motifs has grown rapidly since the discovery of their involvement in the telomere maintenance. Knowledge of the G-quadruplexes' three-dimensional structures plays an important role in understanding of their conformational diversity, physiological functions, and in the design of novel drugs targeting the G-quadruplexes...
November 2, 2016: Acta Biochimica Polonica
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