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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28731702/drude-polarizable-force-field-for-molecular-dynamics-simulations-of-saturated-and-unsaturated-zwitterionic-lipids
#1
Hui Li, Janamejaya Chowdhary, Lei Huang, Xibing He, Alexander D MacKerell, Benoît Roux
Additive force fields are designed to account for induced electronic polarization in a mean-field average way using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28731353/altering-dna-programmable-colloidal-crystallization-paths-by-modulating-particle-repulsion
#2
Mary X Wang, Jeffrey D Brodin, Jaime A Millan, Soyoung E Seo, Martin Girard, Monica Olvera de la Cruz, Byeongdu Lee, Chad A Mirkin
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior...
July 21, 2017: Nano Letters
https://www.readbyqxmd.com/read/28730229/molecular-analysis-of-brca1-and-brca2-genes-by-next-generation-sequencing-and-ultrastructural-aspects-of-breast-tumor-tissue
#3
Corina Elena Mihalcea, Ana Maria Moroşanu, Daniela Murăraşu, Liliana Puiu, Sabin Aurel Cinca, Silviu Cristian Voinea, Nicolae Mirancea
In this paper, we focus our interest on the dynamics alterations of the tumor-stroma interface at the ultrastructural level and to detect BRCA1 and BRCA2 mutations using next generation sequencing (NGS) of breast tumor tissue. Electron microscopic investigation revealed some peculiar infrastructural alterations of the tumor cells per se as well as of the tumor-stroma interface: invadopodia, shedding microvesicles, altered morphology and reduced number of telocytes, different abnormalities of the microvasculature...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28728523/structural-insights-into-the-binding-of-small-ligand-molecules-to-a-g-quadruplex-dna-located-in-the-hiv-1-promoter
#4
Petar M Mitrasinovic
Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinities for such a sequence (5'-T(1)G(2)G(3)C(4)C(5)T(6)G(7)G(8)G(9)C(10)G(11)G(12)G(13)A(14)C(15)T(16)G(17)G(18)G(19)-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28723206/evaluating-dye-labeled-dna-dendrimers-for-potential-applications-in-molecular-biosensing
#5
Carl W Brown, Susan Buckhout-White, Sebastián A Díaz, Joseph S Melinger, Mario G Ancona, Ellen R Goldman, Igor L Medintz
DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28722675/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#6
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28719910/correlating-the-genetic-and-physical-map-of-barley-chromosome-3h-revealed-limitations-of-the-fish-based-mapping-of-nearby-single-copy-probes-caused-by-the-dynamic-structure-of-metaphase-chromosomes
#7
Fernanda O Bustamante, Lala Aliyeva-Schnorr, Jörg Fuchs, Sebastian Beier, Andreas Houben
Genetic maps are based on the recombination frequency of molecular markers which often show different positions in comparison to the corresponding physical maps. To decipher the position and order of DNA sequences genetically mapped to terminal and interstitial regions of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes was performed with 16 genomic single-copy probes derived from fingerprinted BAC contigs. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H...
July 19, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28719294/molecular-markers-for-sensitive-detection-of-plasmodium-falciparum-asexual-stage-parasites-and-their-application-in-a-malaria-clinical-trial
#8
Fitsum G Tadesse, Kjerstin Lanke, Issa Nebie, Jodie A Schildkraut, Bronner P Gonçalves, Alfred B Tiono, Robert Sauerwein, Chris Drakeley, Teun Bousema, Sanna R Rijpma
Plasmodium falciparum parasite life stages respond differently to antimalarial drugs. Sensitive stage-specific molecular assays may help to examine parasite dynamics at microscopically detectable and submicroscopic parasite densities in epidemiological and clinical studies. In this study, we compared the performance of skeleton-binding protein 1 (SBP1), ring-infected erythrocyte surface antigen, Hyp8, ring-exported protein 1 (REX1), and PHISTb mRNA for detecting ring-stage trophozoite-specific transcripts using quantitative reverse transcriptase polymerase chain reaction...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719194/molecular-modeling-of-the-major-dna-adduct-formed-from-the-food-mutagen-ochratoxin-a-in-nari-2-base-deletion-duplexes-impact-of-sequence-context-and-adduct-ionization-on-conformational-preference-and-mutagenicity
#9
Preetleen Kathuria, Purshotam Sharma, Richard A Manderville, Stacey D Wetmore
Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C(8)-dG aromatic amine adducts to analyze the conformational features of post-replication 2-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C(8) position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens...
July 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28717992/melting-of-polymeric-dna-double-helix-at-elevated-temperature-a-molecular-dynamics-approach
#10
Sangeeta Kundu, Sanchita Mukherjee, Dhananjay Bhattacharyya
Genomic DNA of higher organisms exists as extremely long polymers, while in bacteria and other lower organisms it is circular with no terminal base pairs. Temperature-induced melting of the DNA double helix by localized strand separation has been unattainable by molecular dynamic simulations due to more rapid fraying of the terminal base pairs in oligomeric DNA. However, local-sequence-dependent unfolding of the DNA double helix is extremely important for understanding various biochemical phenomena, and can be addressed by simulating a model polymeric DNA duplex...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28714285/dynamic-cooperation-of-hydrogen-binding-and-%C3%AF-stacking-in-ssdna-adsorption-on-graphene-oxide
#11
Zhen Xu, Xiaoling Lei, Yusong Tu, Zhi-Jie Tan, Bo Song, Haiping Fang
Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on a GO surface. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and a π-π stacking interaction, with preferential binding to an oxidized region rather than to an unoxidized region of the GO surface...
July 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28714247/-molecular-cytogenetics-to-characterize-mechanisms-of-gene-duplication-in-pesticide-resistance
#12
REVIEW
Mithila Jugulam, Bikram S Gill
Recent advances in molecular cytogenetics empower construction of physical maps to illustrate the precise position of genetic loci on the chromosomes. Such maps provide visible information about the position of DNA sequences, including the distribution of repetitive sequences on the chromosomes. This will be an important step forward toward unraveling the genetic mechanisms implicated in chromosomal aberrations (e.g., gene duplication). In response to stress, such as pesticide selection, the duplicated genes provide an immediate adaptive advantage to organisms that overcome unfavorable conditions...
July 17, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28709320/weak-nanoscale-chaos-and-anomalous-relaxation-in-dna
#13
Alexey K Mazur
Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28708456/mosquito-borne-diseases-and-omics-tissue-restricted-expression-and-alternative-splicing-revealed-by-transcriptome-profiling-of-anopheles-stephensi
#14
Sreelakshmi K Sreenivasamurthy, Anil K Madugundu, Arun H Patil, Gourav Dey, Ajeet Kumar Mohanty, Manish Kumar, Krishna Patel, Charles Wang, Ashwani Kumar, Akhilesh Pandey, Thottethodi Subrahmanya Keshava Prasad
Malaria is one of the most debilitating mosquito-borne diseases with high global health burdens. While much of the research on malaria and mosquito-borne diseases is focused on Africa, Southeast Asia accounts for a sizable portion of the global burden of malaria. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. A promising development in this context is that the completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, including the progress in deciphering the vectorial ability of this mosquito species at a molecular level...
July 14, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28704776/structural-dynamics-of-wild-type-and-mutated-forms-of-human-l1-endonuclease-and-insights-into-its-sequence-specific-nucleic-acid-binding-mechanism-a-molecular-dynamics-study
#15
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Amutha Ramaswamy
Biomolecular recognition of proteins and nucleic acids is mainly mediated by their structural features and the molecular dynamics simulations approach has been used to explore this recognition processes at the atomic level. L1-Endonuclease, an enzyme involved in L1 retrotransposition, cleaves the TA junction DNA (5'-TTTT/AA-3') and expresses high specificity for target site recognition. The present study highlights the structural features of L1-endonuclease as well as DNA responsible for such specific recognition...
July 5, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28702663/tuning-phase-and-aging-of-dna-hydrogels-through-molecular-design
#16
Dan T Nguyen, Omar A Saleh
The programmable, sequence-dependent hybridization of DNA has spurred the development of DNA hydrogels, polymer networks that swell in water and are comprised either entirely or partially of DNA. Specific applications require hydrogels of particular structure for optimal functionality. Here, we use self-assembling, multi-valent DNA nanostars to examine how hydrogel structure is influenced by the non-equilibrium dynamics of its interacting components. We show that hydrogel aging kinetics - from an arrested, solid-like percolated network to an equilibrium, phase-separated liquid analogous to coacervates - are modulated by DNA hybridization strength and ion-specific nanostar internal flexibility...
July 12, 2017: Soft Matter
https://www.readbyqxmd.com/read/28700917/structure-and-dynamics-of-dna-and-rna-double-helices-of-cag-and-gac-trinucleotide-repeats
#17
Feng Pan, Viet Hoang Man, Christopher Roland, Celeste Sagui
CAG trinucleotide repeats are known to cause 10 late-onset progressive neurodegenerative disorders as the repeats expand beyond a threshold, whereas GAC repeats are associated with skeletal dysplasias and expand from the normal five to a maximum of seven repeats. The TR secondary structure is believed to play a role in CAG expansions. We have carried out free energy and molecular dynamics studies to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats (n = 1, 4) and the consequent changes in the overall structure of the RNA and DNA duplexes...
July 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28699755/co2-reactive-ionic-liquid-surfactants-for-the-control-of-colloidal-morphology
#18
Paul Brown, Vishnu Sresht, Huseyin Burak Eral, Andrew Fiore, César de la Fuente-Núñez, Marcus O'Mahony, Gabriel P Mendes, William T Heller, Patrick S Doyle, Daniel Blankschtein, T Alan Hatton
This paper reports on a new class of stimuli-responsive surfactant generated from commercially available amphiphiles such as dodecyltrimethylammmonium bromide (DTAB) by substitution of the halide counterion with counterions such as 2-cyanopyrrolide, 1,2,3-triazolide, and L-proline that complex reversibly with CO2. Through a combination of small-angle neutron scattering (SANS), electrical conductivity measurements, thermal gravimetric analysis, and molecular dynamics simulations, we show how small changes in charge reorganization and counterion shape and size induced by complexation with CO2 allow for fine tunability of surfactant properties...
July 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28698591/molecular-dynamics-study-on-the-mechanism-of-polynucleotide-encapsulation-by-chitosan
#19
Jia-Wei Shen, Jiachen Li, Zhennan Zhao, Li Zhang, Guoteng Peng, Lijun Liang
The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene delivery carrier due to its good biocompatibility and biodegradability. Understanding the atomic interaction mechanism between chitosan and DNA is important in the design and application of chitosan-based drug and gene delivery systems. In this work, the interactions between single-stranded polynucleotides and different types of chitosan were systematically investigated by using molecular dynamics (MD) simulation...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698241/longitudinal-characterisation-of-function-and-structure-of-bietti-crystalline-dystrophy-report-on-a-novel-homozygous-mutation-in-cyp4v2
#20
Catherine M Lockhart, Travis B Smith, Paul Yang, Malini Naidu, Allan E Rettie, Abhinav Nath, Richard Weleber, Edward J Kelly
BACKGROUND: Bietti crystalline dystrophy (BCD) is a rare inherited disorder characterised by fine crystalline deposits in the corneal limbus and retinal posterior pole. In 2004, mutations in the CYP4V2 gene were identified as the cause of BCD. Here, we describe the report of a homozygous point mutation in a patient with BCD and provide detailed characterisation of functional and structural changes over 20 years. METHODS: At regular intervals, the patient underwent repeat ophthalmic evaluations...
July 11, 2017: British Journal of Ophthalmology
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