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DNA molecular dynamics

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https://www.readbyqxmd.com/read/29047414/histone-isoform-h2a1h-promotes-attainment-of-distinct-physiological-states-by-altering-chromatin-dynamics
#1
Saikat Bhattacharya, Divya Reddy, Vinod Jani, Nikhil Gadewal, Sanket Shah, Raja Reddy, Kakoli Bose, Uddhavesh Sonavane, Rajendra Joshi, Sanjay Gupta
BACKGROUND: The distinct functional effects of the replication-dependent histone H2A isoforms have been demonstrated; however, the mechanistic basis of the non-redundancy remains unclear. Here, we have investigated the specific functional contribution of the histone H2A isoform H2A1H, which differs from another isoform H2A2A3 in the identity of only three amino acids. RESULTS: H2A1H exhibits varied expression levels in different normal tissues and human cancer cell lines (H2A1C in humans)...
October 18, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29047347/the-dynamics-of-smoking-related-disturbed-methylation-a-two-time-point-study-of-methylation-change-in-smokers-non-smokers-and-former-smokers
#2
Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger, Melanie Waldenberger
BACKGROUND: The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29045141/internal-motions-of-basic-side-chains-of-the-antennapedia-homeodomain-in-the-free-and-dna-bound-states
#3
Dan Nguyen, Zoe A Hoffpauir, Junji Iwahara
Basic side chains play crucial roles in protein-DNA interactions. In this study, using NMR spectroscopy, we investigated the dynamics of Arg and Lys side chains of the fruit fly Antennapedia homeodomain in the free state and in the complex with target DNA. We measured (15)N relaxation for Arg and Lys side chains at two magnetic fields, from which generalized order parameters for the cationic groups were determined. Mobility of the R5 side chain, which makes hydrogen bonds with a thymine base in the DNA minor groove, was greatly dampened...
October 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/29044822/first-structure-of-a-designed-minor-groove-binding-heterocyclic-cation-that-specifically-recognizes-mixed-dna-base-pair-sequences
#4
Narinder Kaur Harika, Markus W Germann, W David Wilson
The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition...
October 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29044635/development-and-application-of-a-real-time-polymerase-chain-reaction-assay-for-detection-of-a-novel-gut-bacteriophage-crassphage
#5
Yuying Liang, Xin Jin, Yuan Huang, Shuiping Chen
BACKGROUND: crAssphage is a novel and by far the most abundant bacteriophage in human gut. This bacteriophage might modulate gut microbiota balance so as to be involved in some diseases like obesity, diabetes, metabolic disorders, hypertension, and cancer. Therefore, a rapid and reliable detection and quantification method for crAssphage is essential for studying its molecular epidemiology and pathogenicity in human diseases. MATERIALS AND METHODS: The primers-probes set for the quantitative real-time PCR assay was designed based on the DNA polymerase gene (ORF00018) of crAssphage...
October 16, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29043635/detection-of-dna-rna-hybrids-in-vivo
#6
María García-Rubio, Sonia I Barroso, Andrés Aguilera
DNA-RNA hybrids form naturally during essential cellular functions such as transcription and replication. However, they may be an important source of genome instability, a hallmark of cancer and genetic diseases. Detection of DNA-RNA hybrids in cells is becoming crucial to understand an increasing number of molecular biology processes in genome dynamics and function and to identify new factors and mechanisms responsible for disease in biomedical research. Here, we describe two different procedures for the reliable detection of DNA-RNA hybrids in the yeast Saccharomyces cerevisiae and in human cells: DNA-RNA Immunoprecipitation (DRIP) and Immunofluorescence...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043366/distance-dependent-photoacoustics-revealed-through-dna-nanostructures
#7
James Joseph, Kevin N Baumann, Philipp Koehler, Tim J Zuehlsdorff, Daniel J Cole, Judith Weber, Sarah E Bohndiek, Silvia Hernández-Ainsa
Molecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality for in vivo imaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths...
October 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/29042652/computational-analysis-of-the-molecular-mechanism-of-ramr-mutations-contributing-to-antimicrobial-resistance-in-salmonella-enterica
#8
Yen-Yi Liu, Chih-Chieh Chen
Antimicrobial resistance (AMR) in pathogenic microorganisms with multidrug resistance (MDR) constitutes a severe threat to human health. A major causative mechanism of AMR is mediated through the multidrug efflux pump (MEP). The resistance-nodulation-division superfamily (RND family) of Gram-negative bacteria is usually the major cause of MDR in clinical studies. In Salmonella enterica, the RND pump is translated from the arcAB gene, which is regulated by the activator RamA. Many MEP-caused AMR strains have high ramA gene expression due to mutations in RamR, which has a homodimeric structure comprising the dimerization domain and DNA-binding domain (DBD)...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042576/knot-energy-complexity-and-mobility-of-knotted-polymers
#9
Fernando Vargas-Lara, Ahmed M Hassan, Marc L Mansfield, Jack F Douglas
The Coulomb energy E C is defined by the energy required to charge a conductive object and scales inversely to the self-capacity C, a basic measure of object size and shape. It is known that C is minimized for a sphere for all objects having the same volume, and that C increases as the symmetry of an object is reduced at fixed volume. Mathematically similar energy functionals have been related to the average knot crossing number 〈m〉, a natural measure of knot complexity and, correspondingly, we find E C to be directly related to 〈m〉 of knotted DNA...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#10
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29038501/effects-of-charge-modifying-mutations-in-histone-h2a-%C3%AE-3-domain-on-nucleosome-stability-assessed-by-single-pair-fret-and-md-simulations
#11
Kathrin Lehmann, Ruihan Zhang, Nathalie Schwarz, Alexander Gansen, Norbert Mücke, Jörg Langowski, Katalin Toth
Nucleosomes are important for chromatin compaction and gene regulation; their integrity depends crucially on the structural properties of the histone tails. Recent all-atom molecular dynamics simulations revealed that removal of the N-terminal tails of histone H3, known to destabilize nucleosomes, causes a rearrangement of two arginines of histone H2A, namely R81 and R88 by altering the electrostatic environment of the H2A α3 domain. Whether this rearrangement is the cause or the effect of decreased stability, is unclear...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036584/cgheliparm-analysis-of-dsdna-helical-parameters-for-coarse-grained-martini-molecular-dynamics-simulations
#12
Ignacio Faustino, S J Marrink
Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. Availability and implementation: This package works with Python 2.7 on MacOS and Linux...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036419/an-accurate-algorithm-for-the-detection-of-dna-fragments-from-dilution-pool-sequencing-experiments
#13
Vikas Bansal
Motivation: The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention...
July 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29031260/aggregation-of-flexible-polyelectrolytes-phase-diagram-and-dynamics
#14
Anvy Moly Tom, R Rajesh, Satyavani Vemparala
Similarly charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the process of aggregation on parameters such as backbone flexibility and charge density of such polymers is crucial for insights into various biological processes which involve biological polyelectrolytes such as protein, DNA, etc. Here, we use large-scale coarse-grained molecular dynamics simulations to obtain the phase diagram of the aggregated structures of flexible charged polymers and characterize the morphology of the aggregates as well as the aggregation dynamics, in the presence of trivalent counterions...
October 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29028340/probing-the-binding-pathway-of-braco19-to-a-parallel-stranded-human-telomeric-g-quadruplex-using-molecular-dynamics-binding-simulation-with-amber-dna-ol15-and-ligand-gaff2-force-fields
#15
Babitha Machireddy, Gurmannat Kalra, Subash Chandra Jonnalagadda, Kandalam V Ramanujachary, Chun Wu
Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in cancer treatment. G-quadruplex specific ligands that stabilize the G-quadruplex, have great potential to be developed as anticancer agents. Two crystal structures (an apo form of parallel stranded human telomeric G-quadruplex and its holo form in complex with BRACO19, a potent G-quadruple ligand) have been solved, yet the binding mechanism and pathway remains to be elusive. In this study, we simulated the binding of a free BRACO19 molecule to the apo form of the G-quadruplex using the latest AMBER DNA (OL15) and ligand GAFF2 force field...
October 13, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29028325/dna-aptamer-based-activatable-probes-for-photoacoustic-imaging-in-living-mice
#16
Jing-Jing Zhang, Lukas P Smaga, Nitya Sai Reddy Satyavolu, Jefferson Chan, Yi Lu
DNA aptamers have been demonstrated to be a powerful class of molecules for sensing a wide range of targets, but have so far been quite limited when applied to imaging in living animals, because most aptamer probes are fluorescence- based, which has limited imaging penetration depth. Photoacoustic (PA) imaging has emerged as a promising alternative to MRI and X-ray tomography in biomedical imaging, due to its ability to afford high-resolution images at depths in the cm range. Despite its promise, PA imaging is still limited by the lack of a general strategy to design selective and activatable probes for a wide range of targets...
October 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29027751/the-emerging-role-of-mrna-methylation-in-normal-and-pathological-behavior
#17
REVIEW
Mareen Engel, Alon Chen
Covalent RNA modifications were recently rediscovered as abundant RNA chemical tags. Similarly to DNA epigenetic modifications, they have been proposed as essential regulators of gene expression. Here we focus on two of the most abundant adenosine methylations: N6-methyladenosine (m(6) A), N6,2'-O-dimethyladenosine (m(6) Am) and N1-methyladenosine (m(1) A). We review the potential role of these modifications on mature mRNA in regulating gene expression within the adult brain, nervous system function and normal and pathological behavior...
October 13, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29027501/anticancer-activity-of-new-imidazole-derivative-of-1r-2r-diaminocyclohexane-palladium-and-platinum-complexes-as-dna-fluorescent-probes
#18
Sara Hadian Rasanani, Mahboube Eslami Moghadam, Esmaeil Soleimani, Adeleh Divsalar, Davood Ajloo, Aliakbar Tarlani, Majid Amiri
The aim of this study was synthesis of two new water-soluble fluorescent palladium and platinumcomplexes with formulas of [Pt(DACH)(FIP)](NO3)2 and [Pd(DACH)(FIP)](NO3)2, respectively, where FIP is 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10] phenanthroline and DACH is 1R,2R-diaminocyclohexane. Fluorescence spectroscopy, circular dichroism (CD), thermal denaturation measurement, ionic strength, and kinetic study displayed groove binding of Pt complex on DNA, while due to binding of Pd complex,B form of DNA convert to Z form...
October 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29026072/dynamic-regulation-of-canonical-tgf%C3%AE-signalling-by-endothelial-transcription-factor-erg-protects-from-liver-fibrogenesis
#19
Neil P Dufton, Claire R Peghaire, Lourdes Osuna-Almagro, Claudio Raimondi, Viktoria Kalna, Abhishek Chuahan, Gwilym Webb, Youwen Yang, Graeme M Birdsey, Patricia Lalor, Justin C Mason, David H Adams, Anna M Randi
The role of the endothelium in protecting from chronic liver disease and TGFβ-mediated fibrosis remains unclear. Here we describe how the endothelial transcription factor ETS-related gene (ERG) promotes liver homoeostasis by controlling canonical TGFβ-SMAD signalling, driving the SMAD1 pathway while repressing SMAD3 activity. Molecular analysis shows that ERG binds to SMAD3, restricting its access to DNA. Ablation of ERG expression results in endothelial-to-mesenchymal transition (EndMT) and spontaneous liver fibrogenesis in EC-specific constitutive hemi-deficient (Erg (cEC-Het) ) and inducible homozygous deficient mice (Erg (iEC-KO) ), in a SMAD3-dependent manner...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29025412/dynamic-transcriptome-and-dna-methylome-analyses-on-longissimus-dorsi-to-identify-genes-underlying-intramuscular-fat-content-in-pigs
#20
Yuding Wang, Cai Ma, Yi Sun, Yi Li, Li Kang, Yunliang Jiang
BACKGROUND: The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations...
October 12, 2017: BMC Genomics
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