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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28634398/mutations-in-human-aid-differentially-affect-its-ability-to-deaminate-cytidine-and-5-methylcytidine-in-ssdna-substrates-in-vitro
#1
Lucyna Budzko, Paulina Jackowiak, Karol Kamel, Joanna Sarzynska, Janusz M Bujnicki, Marek Figlerowicz
Activation-induced cytidine deaminase (AID) is known for its established role in antibody production. AID induces the diversification of antibodies by deaminating deoxycytidine (C) within immunoglobulin genes. The capacity of AID to deaminate 5-methyldeoxycytidine (5 mC) and/or 5-hydroxymethyldeoxycytidine (5 hmC), and consequently AID involvement in active DNA demethylation, is not fully resolved. For instance, structural determinants of AID activity on different substrates remain to be identified. To better understand the latter issue, we tested how mutations in human AID (hAID) influence its ability to deaminate C, 5 mC, and 5 hmC in vitro...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634376/structural-basis-to-stabilize-the-domain-motion-of-bard1-ard-brct-by-cstf50
#2
Rajan Kumar Choudhary, Mohd Quadir Siddiqui, Pankaj S Thapa, Nikhil Gadewal, Senthil Kumar Nachimuthu, Ashok K Varma
BRCA1 associated ring domain protein 1(BARD1) is a tumor suppressor protein having a wide role in cellular processes like cell-cycle checkpoint, DNA damage repair and maintenance of genomic integrity. Germ-line mutation Gln 564 His discovered in linker region of BARD1 leads to loss of binding to Cleavage stimulating factor (CstF50), which in turn instigates the premature mRNA transcript formation and apoptosis. We have studied the dynamics of ARD domain present in the BARD1 wild-type and mutant protein in association with CstF50 using biophysical, biochemical and molecular dynamics simulations...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634300/understanding-the-mechanical-response-of-double-stranded-dna-and-rna-under-constant-stretching-forces-using-all-atom-molecular-dynamics
#3
Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28633759/martini-coarse-grained-force-field-extension-to-rna
#4
Jaakko J Uusitalo, Helgi I Ingólfsson, Siewert J Marrink, Ignacio Faustino
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network...
June 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28630277/t-cell-intracellular-antigens-and-hu-antigen-r-antagonistically-modulate-mitochondrial-activity-and-dynamics-by-regulating-optic-atrophy-1-gene-expression
#5
Isabel Carrascoso, José Alcalde, Carmen Sánchez-Jiménez, Paloma González-Sánchez, José M Izquierdo
Mitochondria undergo frequent morphological changes to control their function. We show here that T-cell intracellular antigens (TIA1b/TIARb) and Hu antigen R (HuR) have antagonistic roles in mitochondrial function by modulating the expression of mitochondrial shaping proteins. Expression of TIA1b/TIARb alters the mitochondrial dynamic network by enhancing fission and clustering, which is accompanied by a decrease in respiration. By contrast, HuR expression promotes fusion and cristae remodeling and increases respiratory activity...
June 19, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28629130/optimization-of-polyplex-formation-between-dna-oligonucleotide-and-poly-%C3%AA-lysine-experimental-study-and-modeling-approach
#6
Tudor Vasiliu, Corneliu Cojocaru, Alexandru Rotaru, Gabriela Pricope, Mariana Pinteala, Lilia Clima
The polyplexes formed by nucleic acids and polycations have received a great attention owing to their potential application in gene therapy. In our study, we report experimental results and modeling outcomes regarding the optimization of polyplex formation between the double-stranded DNA (dsDNA) and poly(ʟ-Lysine) (PLL). The quantification of the binding efficiency during polyplex formation was performed by processing of the images captured from the gel electrophoresis assays. The design of experiments (DoE) and response surface methodology (RSM) were employed to investigate the coupling effect of key factors (pH and N/P ratio) affecting the binding efficiency...
June 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28629023/heparin-dna-aptamer-co-assembled-multifunctional-catecholamine-coating-for-epc-capture-and-improved-hemocompatibility-of-vascular-devices
#7
Jinchuan Deng, Shuheng Yuan, Xin Li, Kebing Wang, Lingxia Xie, Na Li, Jin Wang, Nan Huang
Good hemocompatibility and rapid endothelialization are two key factors in the success of stent interventional therapy. In this study, aptamers with the ability to capture endothelial progenitors and anticoagulant molecular heparin were successfully immobilized on the surface of dopamine/polyethylenimine (PDA/PEI) copolymer coating via electrostatic interaction. The results of X-ray spectroscopy (XPS), water contact angle (WCA), and immunofluorescence staining tests confirmed the successful introduction of heparin and aptamers...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28628667/characterization-of-hiv-1-crf90_bf1-and-putative-novel-crfs_bf1-in-central-west-north-and-northeast-brazilian-regions
#8
Mônica Nogueira da Guarda Reis, Gonzalo Bello, Monick Lindenmeyer Guimarães, Mariane Martins Araújo Stefani
The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates...
2017: PloS One
https://www.readbyqxmd.com/read/28627755/labeling-dna-replication-foci-to-visualize-chromosome-territories-in-vivo
#9
Apolinar Maya-Mendoza, Dean A Jackson
While a detailed understanding of chromatin dynamics is needed to explain how higher-order chromatin organization influences nuclear function, the molecular principles that regulate chromatin mobility in mammalian nuclei remain largely unknown. Here we describe experimental tools to follow chromatin dynamics by labeling DNA during S phase. Using these methods, we have found that foci labeled during early and mid/late S phase have significantly different dynamic behavior. Spatially constrained heterochromatic foci restrict long-range transformations of the chromosome territory (CT) structure while providing a structural framework on which highly mobile euchromatic foci undergo positional oscillations that drive local changes in the chromosome shape...
June 19, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28625643/sequential-liquid-biopsies-reveal-dynamic-alterations-of-egfr-driver-mutations-and-indicate-egfr-amplification-as-a-new-mechanism-of-resistance-to-osimertinib-in-nsclc
#10
Franciele H Knebel, Fabiana Bettoni, Andrea K Shimada, Manoel Cruz, João Victor Alessi, Marcelo V Negrão, Luiz Fernando L Reis, Artur Katz, Anamaria A Camargo
Osimertinib is an EGFR-T790M-specific TKI, which has demonstrated impressive response rates in NSCLC, after failure to first-line anti-EGFR TKIs. However, acquired resistance to osimertinib is also observed and the molecular mechanisms of resistance are not yet fully understood. Monitoring and managing NSCLC patients who progressed on osimertinib is, therefore, emerging as an important clinical challenge. Sequential liquid biopsies were used to monitor a patient with EGFR-exon19del positive NSCLC, who received erlotinib and progressed through the acquisition of the EGFR-T790M mutation...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28623258/chromatin-organization-regulates-viral-egress-dynamics
#11
Vesa Aho, Markko Myllys, Visa Ruokolainen, Satu Hakanen, Elina Mäntylä, Jori Virtanen, Veijo Hukkanen, Thomas Kühn, Jussi Timonen, Keijo Mattila, Carolyn A Larabell, Maija Vihinen-Ranta
Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28623092/ctip-ctp1-sae2-molecular-form-fit-for-function
#12
REVIEW
Sara N Andres, R Scott Williams
Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of the Mre11/Rad50/Nbs1 (MRN) DSB repair processing and signaling complex, CtIP/Ctp1/Sae2/Com1 is integral to the channeling of DNA double strand breaks through DSB repair by homologous recombination (HR). Nearly two decades since its discovery, emerging new data are defining the molecular underpinnings for CtIP DSB repair regulatory activities...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28621576/tethering-of-lsh-at-the-oct4-locus-promotes-gene-repression-associated-with-epigenetic-changes
#13
Jianke Ren, Nathaniel A Hathaway, Gerald R Crabtree, Kathrin Muegge
Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered Oct4 locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation...
June 16, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28617676/interactions-between-low-energy-electrons-and-dna-a-perspective-from-first-principles-simulations
#14
Jorge Jose Kohanoff, Maeve McAllister, Gareth Tribello, Bin Gu
DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -- either photons or swift ions -- with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals...
June 15, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28616969/ph-driven-actuation-of-dna-origami-via-parallel-i-motif-sequences-in-solution-and-on-surfaces
#15
Jacob M Majikes, Lucas C C Ferraz, Thomas H LaBean
As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures...
June 15, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28614831/liquid-biopsies-for-monitoring-temporal-genomic-heterogeneity-in-breast-and-colon-cancers
#16
Tiziana Venesio, Giulia Siravegna, Alberto Bardelli, Anna Sapino
Cancer is a spatial and temporal dynamic disease where differently evolving genetic clones are responsible for progression. In this landscape, the genomic heterogeneity of the primary tumours can be captured by deep-sequencing representative spatial samples. However, the recognition of genetic alterations responsible for tumour evolution remains a challenging task. Recently, the "liquid biopsy" was recognized as a powerful real-time approach for the molecular monitoring of this dynamic disease. The term "liquid biopsy" generally refers to the use of circulating (cell-free) tumour DNA (ctDNA) and circulating tumour cells (CTCs) as non-invasive biomarkers for the early diagnosis, prognosis, monitoring of clinical progression, and response to treatment in different types of tumours, including the highly genomic heterogeneous breast cancer...
June 15, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28610839/fly-fishing-for-histones-catch-and-release-by-histone-chaperone-intrinsically-disordered-regions-and-acidic-stretches
#17
REVIEW
Christopher Warren, David Shechter
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly, and thus the fluidity of the ever-changing chromatin landscape...
June 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28609787/molecular-structures-guide-the-engineering-of-chromatin
#18
Stefan J Tekel, Karmella A Haynes
Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28608866/a-small-wolbachia-protein-directly-represses-phage-lytic-cycle-genes-in-candidatus-liberibacter-asiaticus-within-psyllids
#19
Mukesh Jain, Laura A Fleites, Dean W Gabriel
Huanglongbing (HLB) is a severe disease of citrus caused by an uncultured alphaproteobacterium "Candidatus Liberibacter asiaticus" and transmitted by Asian citrus psyllids (Diaphorina citri). Two prophage genomes, SC1 and SC2, integrated in "Ca. Liberibacter asiaticus" strain UF506 were described previously, and very similar prophages are found resident in the majority of "Ca. Liberibacter asiaticus" strains described worldwide. The SC1 lytic cycle is marked by upregulation of prophage late genes, including a functional holin (SC1_gp110); these late genes are activated when "Ca...
May 2017: MSphere
https://www.readbyqxmd.com/read/28608578/cantharidin-inhibits-competitively-heme-fe-iii-binding-to-the-fa1-site-of-human-serum-albumin
#20
Fabio Polticelli, Loris Leboffe, Valentina Tortosa, Viviana Trezza, Gabriella Fanali, Mauro Fasano, Paolo Ascenzi
Cantharidin, a monoterpene isolated from the insect blister beetle, has long been used as a medicinal agent in the traditional Chinese medicine. Cantharidin inhibits a subgroup of serine/threonine phosphatases, thus inducing cell growth inhibition and cytotoxicity. Cantharidin has anticancer activity in vitro, since it is able of inducing p53-dependent apoptosis and double-strand breakage of DNA in cancer cells. Although the toxicity of cantharidin to the gastrointestinal and urinary tracts prevents its medical use, it is a promising lead compound for chemical modification to develop new anticancer therapeutics...
June 13, 2017: Journal of Molecular Recognition: JMR
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