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DNA structure review

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https://www.readbyqxmd.com/read/28445713/deregulation-of-%C3%AE-synuclein-in-parkinson-s-disease-insight-from-epigenetic-structure-and-transcriptional-regulation-of-snca
#1
REVIEW
Subhrangshu Guhathakurta, Eugene Bok, Baggio A Evangelista, Yoon-Seong Kim
Understanding regulation of α-synuclein has long been a central focus for Parkinson's disease (PD) researchers. Accumulation of this protein in the Lewy body or neurites, mutations in the coding region of the gene and strong association of α-synuclein encoding gene multiplication (duplication/triplication) with familial form of PD have indicated the importance of this molecule in pathogenesis of the disease. Several years of research identified many potential faulty pathways associated with accumulation of α-synuclein inside dopaminergic neurons and its transmission to neighboring ones...
April 23, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28444822/triplex-dna-nanostructures-from-basic-properties-to-applications
#2
Yuwei Hu, Alessandro Cecconello, Andrea Idili, Francesco Ricci, Itamar Willner
Triplex nucleic acids attract recent interest as part of the rich "tool-box" of structures used to develop DNA-based nanostructures and materials. This review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles and the reversible oligomerization of "origami" tiles or DNA circles are described. Also, the use of triplex-DNA structures as functional units to assemble pH-responsive systems and materials are presented...
April 26, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28442432/fibre-diffraction-studies-of-biological-macromolecules
#3
REVIEW
D A Marvin
Two fundamental structures in molecular biology, DNA and the α-helix, were determined using X-ray fibre diffraction data, and yet fibre diffraction occupies an obscure niche in structural biology. Relatively few structures are appropriate for the technique, and it seldom supplies data of the quality common in protein crystallography; however, it has proven indispensable in some cases. Here we outline some aspects of helix diffraction mathematics, and then illustrate the application of fibre diffraction by three case studies: DNA, filamentous bacterial viruses, and bacterial pili...
April 22, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28439266/a-novel-regulator-of-activation-induced-cytidine-deaminase-apobecs-in-immunity-and-cancer-schr%C3%A3-dinger-s-catalytic-pocket
#4
REVIEW
Justin J King, Mani Larijani
Activation-induced cytidine deaminase (AID) and its relative APOBEC3 cytidine deaminases boost immune response by mutating immune or viral genes. Because of their genome-mutating activities, AID/APOBECs are also drivers of tumorigenesis. Due to highly charged surfaces, extensive non-specific protein-protein/nucleic acid interactions, formation of polydisperse oligomers, and general insolubility, structure elucidation of these proteins by X-ray crystallography and NMR has been challenging. Hence, almost all available AID/APOBEC structures are of mutated and/or truncated versions...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28428957/coordinating-regulation-of-gene-expression-in-cardiovascular-disease-interactions-between-chromatin-modifiers-and-transcription-factors
#5
REVIEW
Ashley J Bauer, Kathleen A Martin
Cardiovascular disease is a leading cause of death with increasing economic burden. The pathogenesis of cardiovascular diseases is complex, but can arise from genetic and/or environmental risk factors. This can lead to dysregulated gene expression in numerous cell types including cardiomyocytes, endothelial cells, vascular smooth muscle cells, and inflammatory cells. While initial studies addressed transcriptional control of gene expression, epigenetics has been increasingly appreciated to also play an important role in this process through alterations in chromatin structure and gene accessibility...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28426282/emerging-roles-of-macrosatellite-repeats-in-genome-organization-and-disease-development
#6
Gabrijela Dumbovic, Sonia-V Forcales, Manuel Perucho
Abundant repetitive DNA sequences are an enigmatic part of the human genome. Despite increasing evidence on the functionality of DNA repeats, their biological role is still elusive and under frequent debate. Macrosatellites are the largest of the tandem DNA repeats, located on one or multiple chromosomes. The contribution of macrosatellites to genome regulation and human health was demonstrated for the D4Z4 macrosatellite repeat array on chromosome 4q35. Reduced copy number of D4Z4 repeats is associated with local euchromatinization and the onset of facioscapulohumeral muscular dystrophy...
April 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28423958/strategies-and-perspectives-of-assembling-multi-enzyme-systems
#7
Shi-Zhen Wang, Yong-Hui Zhang, Hong Ren, Ya-Li Wang, Wei Jiang, Bai-Shan Fang
Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein...
April 20, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28423228/targeting-dna-pk-for-cancer-therapy
#8
Céline Cano, Suzannah J Harnor
The catalytic activity of DNA-dependent protein kinase (DNA-PK) is critical to its ability to repair lethal DNA-double strand breaks (DSBs). This includes repair of DSB lesions resulting from oxidative stress, oncogene-induced transcription, or following therapeutic treatment of cancer cells. Armed with this knowledge, many attempts have been made to identify small molecule inhibitors of DNA-PK activity as an approach to induce tumour chemo- and radio-sensitisation. This review examines the structures of known reversible and irreversible inhibitors, including those based upon chromen-4-one, arylmorpholine, and benzaldehyde scaffolds...
April 19, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28420154/mechanisms-of-ltr-retroelement-transposition-lessons-from-drosophila-melanogaster
#9
REVIEW
Lidia Nefedova, Alexander Kim
Long terminal repeat (LTR) retrotransposons occupy a special place among all mobile genetic element families. The structure of LTR retrotransposons that have three open reading frames is identical to DNA forms of retroviruses that are integrated into the host genome. Several lines of evidence suggest that LTR retrotransposons share a common ancestry with retroviruses and thus are highly relevant to understanding mechanisms of transposition. Drosophila melanogaster is an exceptionally convenient model for studying the mechanisms of retrotransposon movement because many such elements in its genome are transpositionally active...
April 16, 2017: Viruses
https://www.readbyqxmd.com/read/28420141/coordinated-actions-of-micrornas-with-other-epigenetic-factors-regulate-skeletal-muscle-development-and-adaptation
#10
REVIEW
Marzia Bianchi, Alessandra Renzini, Sergio Adamo, Viviana Moresi
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally...
April 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28419345/dehydration-responsive-element-binding-transcription-factors-and-their-applications-for-the-engineering-of-stress-tolerance
#11
Pradeep K Agarwal, Kapil Gupta, Sergiy Lopato, Parinita Agarwal
Dehydration responsive element binding (DREB) factors or CRT element binding factors (CBFs) are members of the AP2/ERF family, which comprises a large number of stress-responsive regulatory genes. This review traverses almost two decades of research, from the discovery of DREB/CBF factors to their optimization for application in plant biotechnology. In this review, we describe (i) the discovery, classification, structure, and evolution of DREB genes and proteins; (ii) induction of DREB genes by abiotic stresses and involvement of their products in stress responses; (iii) protein structure and DNA binding selectivity of different groups of DREB proteins; (iv) post-transcriptional and post-translational mechanisms of DREB transcription factor (TF) regulation; and (v) physical and/or functional interaction of DREB TFs with other proteins during plant stress responses...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28412585/the-promise-of-epigenetic-therapy-reprogramming-the-cancer-epigenome
#12
REVIEW
Andrew D Kelly, Jean-Pierre J Issa
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics...
April 13, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28410597/the-role-of-nuclear-localization-signal-in-parvovirus-life-cycle
#13
REVIEW
Peng Liu, Shun Chen, Mingshu Wang, Anchun Cheng
Parvoviruses are small, non-enveloped viruses with an approximately 5.0 kb, single-stranded DNA genome. Usually, the parvovirus capsid gene contains one or more nuclear localization signals (NLSs), which are required for guiding the virus particle into the nucleus through the nuclear pore. However, several classical NLSs (cNLSs) and non-classical NLSs (ncNLSs) have been identified in non-structural genes, and the ncNLSs can also target non-structural proteins into the nucleus. In this review, we have summarized recent research findings on parvovirus NLSs...
April 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/28410129/epigenetics-of-reproductive-infertility
#14
Laxmidhar Das, Sabnam Parbin, Nibedita Pradhan, Chahat Kausar, Samir K Patra
Infertility is a complex pathophysiological condition. It may caused by specific or multiple physical and physiological factors, including abnormalities in homeostasis, hormonal imbalances and genetic alterations. In recent times various studies implicated that, aberrant epigenetic mechanisms are associated with reproductive infertility. There might be transgenerational effects associated with epigenetic modifications of gametes and studies suggest the importance of alterations in epigenetic modification at early and late stages of gametogenesis...
June 1, 2017: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28407294/altered-tert-promoter-and-other-genomic-regulatory-elements-occurrence-and-impact
#15
Barbara Heidenreich, Rajiv Kumar
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome...
April 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28403676/an-overview-application-of-silver-nanoparticles-in-inhibition-of-herpes-simplex-virus
#16
Abolfazl Akbarzadeh, Leila Kafshdooz, Zohre Razban, Ali Dastranj Tbrizi, Shadi Rasoulpour, Rovshan Khalilov, Taras Kavetskyy, Siamak Saghfi, Aygun N Nasibova, Sharif Kaamyabi, Taiebeh Kafshdooz
Nanoscale particles and molecules are a potential different for the treatment of disease because they have distinctive biologic property based on their structure and size, which is different from traditional small-molecule drugs. The antimicrobial mechanisms of silver nanoparticles include the formation of free radicals damaging the bacterial membranes, interactions with DNA, adhesion to cell surface altering the membrane properties, and enzyme damage. In this review, we focus on applications of silver nanoparticles in inhibition of herpes simplex virus...
April 12, 2017: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/28399655/cyclic-gmp-amp-as-an-endogenous-second-messenger-in-innate-immune-signaling-by-cytosolic-dna
#17
Kazuki Kato, Hiroki Omura, Ryuichiro Ishitani, Osamu Nureki
The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/ STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclicGMP-AMP(2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3)...
April 7, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28394347/new-factors-in-mammalian-dna-repair-the-chromatin-connection
#18
REVIEW
G Raschellà, G Melino, M Malewicz
In response to DNA damage mammalian cells activate a complex network of stress response pathways collectively termed DNA damage response (DDR). DDR involves a temporary arrest of the cell cycle to allow for the repair of the damage. DDR also attenuates gene expression by silencing global transcription and translation. Main function of DDR is, however, to prevent the fixation of debilitating changes to DNA by activation of various DNA repair pathways. Proper execution of DDR requires careful coordination between these interdependent cellular responses...
April 10, 2017: Oncogene
https://www.readbyqxmd.com/read/28392403/matrix-metalloproteinases-outside-vertebrates
#19
Laura Marino-Puertas, Theodoros Goulas, F Xavier Gomis-Rüth
The matrix metalloproteinase (MMP) family belongs to the metzincin clan of zinc-dependent metallopeptidases. Due to their enormous implications in physiology and disease, MMPs have mainly been studied in vertebrates. They are engaged in extracellular protein processing and degradation, and present extensive paralogy, with 23 forms in humans. One characteristic of MMPs is a~165-residue catalytic domain (CD), which has been structurally studied for 14 MMPs from human, mouse, rat, pig and the oral-microbiome bacterium Tannerella forsythia...
April 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28390838/super-resolution-microscopy-approaches-to-nuclear-nanostructure-imaging
#20
Christoph Cremer, Aleksander Szczurek, Florian Schock, Amine Gourram, Udo Birk
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca...
April 5, 2017: Methods: a Companion to Methods in Enzymology
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