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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28340381/studying-the-adsorption-of-dna-nanostructures-on-graphene-in-the-aqueous-phase-using-molecular-dynamic-simulations
#1
Jixue Sun, Yang Li, Jianping Lin
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene...
March 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28337900/the-fingerprint-of-the-human-gastrointestinal-tract-microbiota-a-hypothesis-of-molecular-mapping
#2
G Tomasello, M Mazzola, A Jurjus, F Cappello, F Carini, P Damiani, A Gerges Geagea, M N Zeenny, A Leone
The precise etiology of Inflammatory Bowel Disease (IDB) remains unclear and several factors are believed to play a role in its development and progression, including the composition of microbial communities resident in the gastrointestinal tract. Human intestinal microbiota are extensive with at least 15,000-36,000 bacterial species. However, thanks to the new development in sequencing and molecular taxonomic methodologies, our understanding of the microbiota population composition, dynamics, and ecology has greatly increased...
January 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28335237/dna-sequencing-by-hexagonal-boron-nitride-nanopore-a-computational-study
#3
Liuyang Zhang, Xianqiao Wang
The single molecule detection associated with DNA sequencing has motivated intensive efforts to identify single DNA bases. However, little research has been reported utilizing single-layer hexagonal boron nitride (hBN) for DNA sequencing. Here we employ molecular dynamics simulations to explore pathways for single-strand DNA (ssDNA) sequencing by nanopore on the hBN sheet. We first investigate the adhesive strength between nucleobases and the hBN sheet, which provides the foundation for the hBN-base interaction and nanopore sequencing mechanism...
June 6, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334863/consecutive-non-natural-pz-nucleobase-pairs-in-dna-impact-helical-structure-as-seen-in-50-%C3%AE-s-molecular-dynamics-simulations
#4
Robert W Molt, Millie M Georgiadis, Nigel G J Richards
Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334816/dynamic-changes-in-chromatin-states-during-specification-and-differentiation-of-adult-intestinal-stem-cells
#5
Juri Kazakevych, Sergi Sayols, Berith Messner, Christina Krienke, Natalia Soshnikova
Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331161/isolation-of-cyanobacterial-mutants-exhibiting-growth-defects-under-microoxic-conditions-by-transposon-tagging-mutagenesis-of-synechocystis-sp-pcc-6803
#6
Kazuki Terauchi, Riho Sobue, Yuho Furutani, Rina Aoki, Yuichi Fujita
Cyanobacteria are photosynthetic prokaryotes that perform oxygenic photosynthesis by extracting electrons from water, with the generation of oxygen as a byproduct. Cyanobacteria use oxygen not only for respiration to produce energy in the dark but also for biosynthesis of various metabolites, such as heme and chlorophyll. Oxygen levels dynamically fluctuate in the field environments, from hyperoxic at daytime to almost anaerobic at night. Thus, adaptation to anaerobiosis should be important for cyanobacteria to survive in low-oxygen and anaerobic environments...
March 22, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/28330758/regulation-of-type-i-interferon-signaling-in-immunity-and-inflammation-a-comprehensive-review
#7
REVIEW
Kun Chen, Juan Liu, Xuetao Cao
Type I interferons (IFNs) play essential roles in establishing and modulating host defense against microbial infection via induction of IFN-stimulated genes (ISGs) through Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. However, dysregulation of IFNs production and function could also mediate immune pathogenesis such as inflammatory autoimmune diseases and infectious diseases via aberrantly activating inflammatory responses or improperly suppressing microbial controls...
March 19, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28330421/the-proteinopathy-of-d169g-and-k263e-mutants-at-the-rna-recognition-motif-rrm-domain-of-tar-dna-binding-protein-tdp43-causing-neurological-disorders-a-computational-study
#8
Vishwambhar Vishnu Bhandare, Amutha Ramaswamy
One of the multitasking proteins, transactive response DNA-binding protein 43 (tdp43) plays a key role in RNA regulation and the two pathogenic mutations such as D169G and K263E, located at the RNA Recognition Motif (RRM) of tdp43, are reported to cause neurological disorders such as Amyotrophic Lateral Sclerosis (ALS) and Fronto Temporal Lobar Degeneration (FTLD). As the exploration of the proteinopathy demands both structural and functional characterization of mutants, a comparative analysis on the wild type and mutant tdp43 (D169G and K263E) and their complexes with RNA have been performed using computational approaches...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28330413/molecular-dynamic-simulation-and-dft-study-on-the-drug-dna-interaction-crocetin-as-an-anticancer-and-dna-nanostructure-model
#9
Ebrahim Azarhazin, Mohammad Izadyar, Mohammad Reza Housaindokht
In this research, the interaction of Crocetin as an anticancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of twelve base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28329017/navigating-in-foldonia-using-accelerated-molecular-dynamics-to-explore-stability-unfolding-and-self-healing-of-the-%C3%AE-solenoid-structure-formed-by-a-silk-like-polypeptide
#10
Binwu Zhao, Martien A Cohen Stuart, Carol K Hall
The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#11
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28322855/reconstitutions-of-plasmid-partition-systems-and-their-mechanisms
#12
REVIEW
Adam C Brooks, Ling Chin Hwang
Bacterial plasmid and chromosome segregation systems ensure that genetic material is efficiently transmitted to progeny cells. Cell-based studies have shed light on the dynamic nature and the molecular basis of plasmid partition systems. In vitro reconstitutions, on the other hand, have proved to be an invaluable tool for studying the minimal components required to elucidate the mechanism of DNA segregation. This allows us to gain insight into the biological and biophysical processes that enable bacterial cells to move and position DNA...
March 16, 2017: Plasmid
https://www.readbyqxmd.com/read/28320905/insights-into-the-deactivation-of-5-bromouracil-after-ultraviolet-excitation
#13
Francesca Peccati, Sebastian Mai, Leticia González
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28319896/a-dynamic-sandwich-assay-on-magnetic-beads-for-selective-detection-of-single-nucleotide-mutations-at-room-temperature
#14
Junxiu Wang, Guoliang Xiong, Liang Ma, Shihui Wang, Xu Zhou, Lei Wang, Lehui Xiao, Xin Su, Changyuan Yu
Single-nucleotide mutation (SNM) has proven to be associated with a variety of human diseases. Development of reliable methods for the detection of SNM is crucial for molecular diagnosis and personalized medicine. The sandwich assays are widely used tools for detecting nucleic acid biomarkers due to their low cost and rapid signaling. However, the poor hybridization specificity of signal probe at room temperature hampers the discrimination of mutant and wild type. Here, we demonstrate a dynamic sandwich assay on magnetic beads for SNM detection based on the transient binding between signal probe and target...
March 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28319616/dna-probes-for-monitoring-dynamic-and-transient-molecular-encounters-on-live-cell-membranes
#15
Mingxu You, Yifan Lyu, Da Han, Liping Qiu, Qiaoling Liu, Tao Chen, Cuichen Sam Wu, Lu Peng, Liqin Zhang, Gang Bao, Weihong Tan
Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals...
March 20, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28319084/structural-and-mechanistic-insights-into-an-archaeal-dna-guided-argonaute-protein
#16
Sarah Willkomm, Christine A Oellig, Adrian Zander, Tobias Restle, Ronan Keegan, Dina Grohmann, Sabine Schneider
Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing(1), while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA(2,3). Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process(4-6)...
March 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28317903/stability-and-dynamics-of-membrane-spanning-dna-nanopores
#17
Vishal Maingi, Jonathan R Burns, Jaakko J Uusitalo, Stefan Howorka, Siewert J Marrink, Mark S P Sansom
Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28317184/self-assembled-multivalent-samul-polyanion-binding-impact-of-hydrophobic-modifications-in-the-micellar-core-on-dna-and-heparin-binding-at-the-peripheral-cationic-ligands
#18
Buthaina Albanyan, Erik Laurini, Paola Posocco, Sabrina Pricl, David K Smith
This paper reports a small family of cationic surfactants designed to bind polyanions such as DNA and heparin. Each molecule has the same hydrophilic cationic ligand, and a hydrophobic aliphatic group with eighteen carbon atoms with either one, two or three alkene groups within the hydrophobic chain (C18-1, C18-2 and C18-3). Dynamic light scattering indicates that more alkenes lead to geometric distortion, giving rise to larger self-assembled multivalent (SAMul) nanostructures. Mallard Blue and Ethidium Bromide dye displacement assays demonstrate that heparin and DNA have markedly different binding preferences, with heparin binding most effectively to C18-1, and DNA to C18-3, even though the molecular structural differences of these SAMul systems are buried in the hydrophobic core...
March 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28314372/exploring-fluorescent-dyes-at-biomimetic-interfaces-with-second-harmonic-generation-and-molecular-dynamics
#19
Giuseppe Licari, Lukasz Cwiklik, Pavel Jungwirth, Eric Vauthey
The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface-second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption of the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids...
March 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28304160/nucleosome-histone-tail-conformation-and-dynamics-impacts-of-lysine-acetylation-and-a-nearby-minor-groove-benzo-a-pyrene-derived-lesion
#20
Iwen Fu, Yuqin Cai, Nicholas E Geacintov, Yingkai Zhang, Suse Broyde
Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored...
March 22, 2017: Biochemistry
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