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DNA structure review

Marvin V Dilworth, Mathilde S Piel, Kim E Bettaney, Pikyee Ma, Ji Luo, David Sharples, David R Poyner, Stephane R Gross, Karine Moncoq, Peter J F Henderson, Bruno Miroux, Roslyn M Bill
Despite many high-profile successes, recombinant membrane protein production remains a technical challenge; it is still the case that many fewer membrane protein structures have been published than those of soluble proteins. However, progress is being made because empirical methods have been developed to produce the required quantity and quality of these challenging targets. This review focuses on the microbial expression systems that are a key source of recombinant prokaryotic and eukaryotic membrane proteins for structural studies...
April 12, 2018: Methods: a Companion to Methods in Enzymology
Ada Soler-Ventura, Judit Castillo, Alberto de la Iglesia, Meritxell Jodar, Ferran Barrachina, Josep Lluis Ballesca, Rafael Oliva
Protamines are the most abundant sperm nuclear proteins and pack approximately the 92-98% of the mammalian sperm DNA. In mammals, two types of protamines have been described, the protamine 1 (P1) and the protamine 2 (P2) family, whose relative ratio has been related to the proper sperm chromatin maturity and the normality/abnormality of the male gamete. Specifically, the deregulation of the P1/P2 ratio has been correlated to DNA damage, alterations in seminal parameters, and low success rate of assisted reproduction techniques...
April 12, 2018: Protein and Peptide Letters
Tiphanie Faïs, Julien Delmas, Nicolas Barnich, Richard Bonnet, Guillaume Dalmasso
Cyclomodulins are bacterial toxins that interfere with the eukaryotic cell cycle. A new cyclomodulin called colibactin, which is synthetized by the pks genomic island, was discovered in 2006. Despite many efforts, colibactin has not yet been purified, and its structure remains elusive. Interestingly, the pks island is found in members of the family Enterobacteriaceae (mainly Escherichia coli and Klebsiella pneumoniae ) isolated from different origins, including from intestinal microbiota, septicaemia, newborn meningitis, and urinary tract infections...
April 10, 2018: Toxins
Adrián Montaño, Maribel Forero-Castro, Darnel Marchena-Mendoza, Rocío Benito, Jesús María Hernández-Rivas
The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures...
April 7, 2018: Cancers
Koichi Ogami, Yaqiong Chen, James L Manley
The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation and cell differentiation...
2018: Non-Coding RNA
Răzvan V Chereji, David J Clark
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair...
April 5, 2018: Biophysical Journal
O I Podgornaya, D I Ostromyshenskii, N I Enukashvily
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC)...
April 2018: Biochemistry. Biokhimii︠a︡
S V Razin, A A Gavrilov
It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains...
April 2018: Biochemistry. Biokhimii︠a︡
Masae Ohno, David G Priest, Yuichi Taniguchi
Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms...
April 6, 2018: Biochemical Society Transactions
Mihai Ciubotaru, Mihaela Georgiana Musat, Marius Surleac, Elena Ionita, Andrei Jose Petrescu, Edgars Abele, Ramona Abele
Currently used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes, changes these viral enzymes which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations...
April 5, 2018: Current Medicinal Chemistry
Subhajit Dutta, Mehali Mitra, Puja Agarwal, Kalyan Mahapatra, Sayanti De, Upasana Sett, Sujit Roy
Plants, being sessile in nature, are constantly exposed to various environmental stresses, such as solar UV radiations, soil salinity, drought and desiccation, rehydration, low and high temperatures and other vast array of air and soil borne chemicals, industrial waste products, metals and metalloids. These agents, either directly or indirectly via the induction of oxidative stress and overproduction of reactive oxygen species (ROS), frequently perturb the chemical or physical structures of DNA and induce both cytotoxic or genotoxic stresses...
April 5, 2018: Plant Signaling & Behavior
Xinyu Liao, Aliyu Idris Muhammad, Shiguo Chen, Yaqin Hu, Xingqian Ye, Donghong Liu, Tian Ding
Cold plasma has emerged as a non-thermal technology for microbial inactivation in the food industry over the last decade. Spore-forming microorganisms pose challenges for microbiological safety and for the prevention of food spoilage. Inactivation of spores induced by cold plasma has been reported by several studies. However, the exact mechanism of spore deactivation by cold plasma is poorly understood; therefore, it is difficult to control this process and to optimize cold plasma processing for efficient spore inactivation...
April 5, 2018: Critical Reviews in Food Science and Nutrition
Yonggang Ke, Carlos Castro, Jong Hyun Choi
Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli...
April 4, 2018: Annual Review of Biomedical Engineering
Juan S Ramirez-Prado, Sophie J M Piquerez, Abdelhafid Bendahmane, Heribert Hirt, Cécile Raynaud, Moussa Benhamed
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses...
2018: Frontiers in Plant Science
Emanuela Stampone, Ilaria Caldarelli, Alberto Zullo, Debora Bencivenga, Francesco Paolo Mancini, Fulvio Della Ragione, Adriana Borriello
The CDKN1C gene encodes the p57Kip2 protein which has been identified as the third member of the CIP/Kip family, also including p27Kip1 and p21Cip1 . In analogy with these proteins, p57Kip2 is able to bind tightly and inhibit cyclin/cyclin-dependent kinase complexes and, in turn, modulate cell division cycle progression. For a long time, the main function of p57Kip2 has been associated only to correct embryogenesis, since CDKN1C -ablated mice are not vital. Accordingly, it has been demonstrated that CDKN1C alterations cause three human hereditary syndromes, characterized by altered growth rate...
April 2, 2018: International Journal of Molecular Sciences
Zhaowei Chen, Chaoqun Liu, Fangfang Cao, Jinsong Ren, Xiaogang Qu
DNA metallization has witnessed tremendous growth and development, from the initial simple synthesis aimed at manufacturing conductive metal nanowires to the current fabrication of various nanostructures for applications in areas as diverse as nanolithography, energy conversion and storage, catalysis, sensing, and biomedical engineering. To this, our aim here was to present a comprehensive review to summarize the research activities on DNA metallization that have appeared since the concept was first proposed in 1998...
April 3, 2018: Chemical Society Reviews
Ewa Anna Oprzeska-Zingrebe, Jens Smiatek
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes...
April 2, 2018: Biophysical Reviews
Brianna D Griffin, Hank W Bass
DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined...
April 2018: Plant Science: An International Journal of Experimental Plant Biology
Shruti Aggarwal, Travis Peck, Jeffrey Golen, Zeynel A Karcioglu
Macular corneal dystrophy (MCD) is a corneal stromal dystrophy which leads to progressive vision loss. MCD is an autosomal recessive condition in which there is abnormality of proteoglycan synthesis. Mutations in the carbohydrate sulphotransferase gene (CHST6) prevent normal sulfation of corneal keratan. Different immunophenotypes have been described depending on the presence of keratan sulfate in cornea and or serum. The deposition of abnormal proteoglycans leads to loss of corneal transparency and decreased vision...
March 28, 2018: Survey of Ophthalmology
Ryan P Barnes, Elise Fouquerel, Patricia L Opresko
Telomeres are dynamic nucleoprotein-DNA structures that cap and protect linear chromosome ends. Because telomeres shorten progressively with each replication, they impose a functional limit on the number of times a cell can divide. Critically short telomeres trigger cellular senescence in normal cells, or genomic instability in pre-malignant cells, which contribute to numerous degenerative and aging-related diseases including cancer. Therefore, a detailed understanding of the mechanisms of telomere loss and preservation is important for human health...
March 28, 2018: Mechanisms of Ageing and Development
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