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DNA molecular dynamics

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https://www.readbyqxmd.com/read/29244866/molecular-dynamics-simulations-of-the-glucocorticoid-receptor-dna-binding-domain-suggest-a-role-of-the-lever-arm-mobility-in-transcriptional-output
#1
Lautaro Damián Álvarez, Diego Martín Presman, Adalí Pecci
One of the first and essential steps in gene expression regulation involves the recruitment of transcription factors (TFs) to specific response elements located at enhancers and/or promoters of targeted genes. These DNA elements have a certain variability in both sequence and length, which may affect the final transcriptional output. The molecular mechanisms in which TFs integrate the subtle differences within specific recognition sequences to offer different transcriptional responses is still largely unknown...
2017: PloS One
https://www.readbyqxmd.com/read/29244022/the-structural-basis-for-dynamic-dna-binding-and-bridging-interactions-which-condense-the-bacterial-centromere
#2
Gemma Lm Fisher, César L Pastrana, Victoria A Higman, Alan Koh, James A Taylor, Annika Butterer, Timothy Craggs, Frank Sobott, Heath Murray, Matthew P Crump, Fernando Moreno-Herrero, Mark S Dillingham
The ParB protein forms DNA bridging interactions around parS to condense DNA and earmark the bacterial chromosome for segregation. The molecular mechanism underlying the formation of these ParB networks is unclear. We show here that while the central DNA binding domain is essential for anchoring at parS, this interaction is not required for DNA condensation. Structural analysis of the C-terminal domain reveals a dimer with a lysine-rich surface that binds DNA non-specifically and is essential for DNA condensation in vitro...
December 15, 2017: ELife
https://www.readbyqxmd.com/read/29243048/spectroscopic-evidence-of-phosphorous-heterocycle-dna-interaction-and-its-verification-by-docking-approach
#3
Swarup Roy, Shailendra K Saxena, Suryakant Mishra, Priyanka Yogi, P R Sagdeo, Rajesh Kumar
In the present work, the interaction of phosphorous heterocycle (PH) with calf thymus DNA (CTDNA) has been studied using spectroscopy and verified by molecular modeling which is found to be in consonance with each other. Apparent association constant (Kapp = 4.77 × 103 M- 1), calculated using UV-Vis spectra indicating an adequate complex formation between CTDNA and PH. A dynamic mode of the fluorescence quenching mechanism in case of ethidium bromide (EB) + CTDNA by PH has been observed confirming formation of DNA-PH complex...
December 14, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/29242317/enzyme-free-nucleic-acid-dynamical-systems
#4
Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik
Chemistries exhibiting complex dynamics-from inorganic oscillators to gene regulatory networks-have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process...
December 15, 2017: Science
https://www.readbyqxmd.com/read/29241299/nmr-elucidation-of-monomer-dimer-transition-and-conformational-heterogeneity-in-histone-like-dna-binding-protein-of-helicobacter-pylori-hup
#5
Nancy Jaiswal, Nisha Raikwal, Himanshu Pandey, Nipanshu Agarwal, Ashish Arora, Krishna Mohan Poluri, Dinesh Kumar
Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is Histone like DNA binding protein (Hup) which in its homo-dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation...
December 14, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/29237070/rolling-circle-amplification-shows-a-sinusoidal-template-length-dependent-amplification-bias
#6
Bastian Joffroy, Yavuz O Uca, Domen Prešern, Jonathan P K Doye, Thorsten L Schmidt
Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with integer helical turns circularize much more efficiently than those with odd helical half turns due to stronger stacking of duplex ends. Small DNA circles can serve as templates for rolling circle amplification (RCA), which is a common and extremely robust amplification mechanism for nucleic acids...
December 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29235008/oncological-assessment-of-stent-placement-for-obstructive-colorectal-cancer-from-circulating-cell-free-dna-and-circulating-tumor-dna-dynamics
#7
Goro Takahashi, Takeshi Yamada, Takuma Iwai, Kohki Takeda, Michihiro Koizumi, Seiichi Shinji, Eiji Uchida
BACKGROUND: The self-expanding metallic stent (SEMS) provides effective decompression for patients with malignant large bowel obstruction (MLBO); however, mechanical damage to malignant cells from insertion may negatively affect prognosis, similar to surgical manipulation, and its oncological safety is unclear. We examined mechanical damage from SEMS placement using circulating cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA). METHODS: Between 1 November 2014 and 30 June 2017, 35 MLBO patients were analyzed, comprising 25 SEMS patients and 10 transanal decompression tube (TDT) patients (control)...
December 12, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/29234169/characterization-of-hybridization-within-a-secondary-contact-region-of-the-inshore-fish-bostrychus-sinensis-in-the-east-china-sea
#8
Shaoxiong Ding, Mrinal Mishra, Haohao Wu, Shuang Liang, Michael M Miyamoto
The northwest Pacific marginal seas are a primary center of phylogeographic and evolutionary research, because of their dynamic geographic history of falling and rising sea levels during the glaciations and interglaciations of the last one million years. Here we present new molecular and morphological data for geographic samples of the four-eyed sleeper (Bostrychus sinensis), which reinforce the evidence for secondary contact and hybridization between two phylogeographic lineages in the East China Sea. Specifically, we find that the secondary contact region is characterized by a low frequency of hybridization, where mitochondrial DNA introgression is relatively common, whereas F1 hybrids are correspondingly scarce...
January 2018: Heredity
https://www.readbyqxmd.com/read/29234107/bulky-lesion-bypass-requires-dpo4-binding-in-distinct-conformations
#9
Pramodha S Liyanage, Alice R Walker, Alfonso Brenlla, G Andrés Cisneros, Louis J Romano, David Rueda
Translesion DNA synthesis is an essential process that helps resume DNA replication at forks stalled near bulky adducts on the DNA. Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon (PAH) that can be metabolically activated to benzo[a]pyrene diol epoxide (BPDE), which then can react with DNA to form carcinogenic DNA adducts. Here, we have used single-molecule florescence resonance energy transfer (smFRET) experiments, classical molecular dynamics simulations, and nucleotide incorporation assays to investigate the mechanism by which the model Y-family polymerase, Dpo4, bypasses a (+)-cis-B[a]P-N 2-dG adduct in DNA...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29234087/conformational-switch-regulates-the-dna-cytosine-deaminase-activity-of-human-apobec3b
#10
Ke Shi, Özlem Demir, Michael A Carpenter, Jeff Wagner, Kayo Kurahashi, Reuben S Harris, Rommie E Amaro, Hideki Aihara
The APOBEC3B (A3B) single-stranded DNA (ssDNA) cytosine deaminase has important roles in innate immunity but is also a major endogenous source of mutations in cancer. Previous structural studies showed that the C-terminal catalytic domain of human A3B has a tightly closed active site, and rearrangement of the surrounding loops is required for binding to substrate ssDNA. Here we report structures of the A3B catalytic domain in a new crystal form that show alternative, yet still closed, conformations of active site loops...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233992/global-unleashing-of-transcription-elongation-waves-in-response-to-genotoxic-stress-restricts-somatic-mutation-rate
#11
Matthieu D Lavigne, Dimitris Konstantopoulos, Katerina Z Ntakou-Zamplara, Anastasios Liakos, Maria Fousteri
Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233477/molecular-anatomy-of-the-developing-human-retina
#12
Akina Hoshino, Rinki Ratnapriya, Matthew J Brooks, Vijender Chaitankar, Matthew S Wilken, Chi Zhang, Margaret R Starostik, Linn Gieser, Anna La Torre, Mario Nishio, Olivia Bates, Ashley Walton, Olivia Bermingham-McDonogh, Ian A Glass, Rachel O L Wong, Anand Swaroop, Thomas A Reh
Clinical and genetic heterogeneity associated with retinal diseases makes stem-cell-based therapies an attractive strategy for personalized medicine. However, we have limited understanding of the timing of key events in the developing human retina, and in particular the factors critical for generating the unique architecture of the fovea and surrounding macula. Here we define three key epochs in the transcriptome dynamics of human retina from fetal day (D) 52 to 136. Coincident histological analyses confirmed the cellular basis of transcriptional changes and highlighted the dramatic acceleration of development in the fovea compared with peripheral retina...
December 1, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29229758/the-stress-sigma-factor-of-rna-polymerase-rpos-%C3%AF-s-is-a-solvent-exposed-open-molecule-in-solution
#13
Paola Cavaliere, Sébastien Brier, Petr Filipenko, Christina Sizun, Bertrand Raynal, Françoise Bonneté, Fabienne Levi-Acobas, Jacques Bellalou, Patrick England, Julia Chamot-Rooke, Claudine Mayer, Françoise Norel
In bacteria, one primary and multiple alternative σ factors associate with the RNA polymerase core enzyme (E) to form holoenzymes (Eσ) with different promoter recognition specificities. The alternative σ factor RpoS/σS is produced in stationary phase and under stress conditions and reprograms global gene expression to promote bacterial survival. To date, the three-dimensional structure of a full-length free σ factor remains elusive. The current model suggests that extensive interdomain contacts in a free σ factor result in a compact conformation that masks the DNA-binding determinants of σ, explaining why a free σ factor does not bind double stranded promoter DNA efficiently...
December 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29225080/second-shell-basic-residues-expand-the-two-metal-ion-architecture-of-dna-and-rna-processing-enzymes
#14
Vito Genna, Matteo Colombo, Marco De Vivo, Marco Marcia
Synthesis and scission of phosphodiester bonds in DNA and RNA regulate vital processes within the cell. Enzymes that catalyze these reactions operate mostly via the recognized two-metal-ion mechanism. Our analysis reveals that basic amino acids and monovalent cations occupy structurally conserved positions nearby the active site of many two-metal-ion enzymes for which high-resolution (<3 Å) structures are known, including DNA and RNA polymerases, nucleases such as Cas9, and splicing ribozymes. Integrating multiple-sequence and structural alignments with molecular dynamics simulations, electrostatic potential maps, and mutational data, we found that these elements always interact with the substrates, suggesting that they may play an active role for catalysis, in addition to their electrostatic contribution...
December 1, 2017: Structure
https://www.readbyqxmd.com/read/29223917/molecular-dynamics-simulations-suggest-changes-in-electrostatic-interactions-as-a-potential-mechanism-through-which-serine-phosphorylation-inhibits-dna-polymerase-%C3%AE-s-activity
#15
Dirar Homouz, Kwee Hong Joyce-Tan, Mohd Shahir Shamsir, Ibrahim M Moustafa, Haitham Idriss
DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics...
November 7, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29222528/structure-and-dynamics-of-cas9-hnh-domain-catalytic-state
#16
Zhicheng Zuo, Jin Liu
The bacterial CRISPR-Cas9 immune system has been harnessed as a powerful and versatile genome-editing tool and holds immense promise for future therapeutic applications. Despite recent advances in understanding Cas9 structures and its functional mechanism, little is known about the catalytic state of the Cas9 HNH nuclease domain, and identifying how the divalent metal ions affect the HNH domain conformational transition remains elusive. A deeper understanding of Cas9 activation and its cleavage mechanism can enable further optimization of Cas9-based genome-editing specificity and efficiency...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221677/epigenetic-regulation-of-biological-rhythms-an-evolutionary-ancient-molecular-timer
#17
REVIEW
Tyler J Stevenson
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms...
December 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29221382/detailed-balance-internal-consistency-and-energy-conservation-in-fragment-orbital-based-surface-hopping
#18
Antoine Carof, Samuele Giannini, Jochen Blumberger
We have recently introduced an efficient semi-empirical non-adiabatic molecular dynamics method for the simulation of charge transfer/transport in molecules and molecular materials, denoted fragment orbital-based surface hopping (FOB-SH) [J. Spencer et al., J. Chem. Phys. 145, 064102 (2016)]. In this method, the charge carrier wavefunction is expanded in a set of charge localized, diabatic electronic states and propagated in the time-dependent potential due to classical nuclear motion. Here we derive and implement an exact expression for the non-adiabatic coupling vectors between the adiabatic electronic states in terms of nuclear gradients of the diabatic electronic states...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29218268/blood-based-tumor-biomarkers-in-lung-cancer-for-detection-and-treatment
#19
REVIEW
Hirva Mamdani, Shahid Ahmed, Samantha Armstrong, Tony Mok, Shadia I Jalal
The therapeutic landscape of lung cancer has expanded significantly over the past decade. Advancements in molecularly targeted therapies, strategies to discover and treat resistance mutations, and development of personalized cancer treatments in the context of tumor heterogeneity and dynamic tumor biology have made it imperative to obtain tumor samples on several different occasions through the course of patient treatment. While this approach is critical to the delivery of optimal cancer treatment, it is fraught with a number of barriers including the need for invasive procedures with associated complications, access to limited amount of tissue, logistical delays in obtaining the biopsy, high healthcare cost, and in many cases inability to obtain tissue because of technically difficult location of the tumor...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29216580/microfluidic-magnetic-fluidized-bed-for-dna-analysis-in-continuous-flow-mode
#20
Iván Hernández-Neuta, Iago Pereiro, Annika Ahlford, Davide Ferraro, Qiongdi Zhang, Jean-Louis Viovy, Stéphanie Descroix, Mats Nilsson
Magnetic solid phase substrates for biomolecule manipulation have become a valuable tool for simplification and automation of molecular biology protocols. However, the handling of magnetic particles inside microfluidic chips for miniaturized assays is often challenging due to inefficient mixing, aggregation, and the advanced instrumentation required for effective actuation. Here, we describe the use of a microfluidic magnetic fluidized bed approach that enables dynamic, highly efficient and simplified magnetic bead actuation for DNA analysis in a continuous flow platform with minimal technical requirements...
November 26, 2017: Biosensors & Bioelectronics
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