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DNA molecular dynamics

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https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#1
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27905522/circulating-cell-free-dna-telomere-length-and-bilirubin-in-the-vienna-active-ageing-study-exploratory-analysis-of-a-randomized-controlled-trial
#2
Anela Tosevska, Bernhard Franzke, Marlene Hofmann, Immina Vierheilig, Barbara Schober-Halper, Stefan Oesen, Oliver Neubauer, Barbara Wessner, Karl-Heinz Wagner
Telomere length (TL) in blood cells is widely used in human studies as a molecular marker of ageing. Circulating cell-free DNA (cfDNA) as well as unconjugated bilirubin (UCB) are dynamic blood constituents whose involvement in age-associated diseases is largely unexplored. To our knowledge, there are no published studies integrating all three parameters, especially in individuals of advanced age. Here we present a secondary analysis from the Vienna Active Aging Study (VAAS), a randomized controlled intervention trial in institutionalized elderly individuals (n = 101)...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903910/structural-insights-into-dynamics-of-recu-hj-complex-formation-elucidates-key-role-of-ntr-and-stalk-region-toward-formation-of-reactive-state
#3
Sagar Khavnekar, Sarath Chandra Dantu, Svetlana Sedelnikova, Sylvia Ayora, John Rafferty, Avinash Kale
Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900730/understanding-the-interactions-of-high-mobility-group-of-protein-domain-b1-with-dna-adducts-generated-by-platinum-anticancer-molecules-using-in-silico-approaches
#4
Gauri Misra, Shipra Gupta, Neetu Jabalia
Platinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins...
November 30, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27899598/kinetics-of-transcription-initiation-directed-by-multiple-cis-regulatory-elements-on-the-glnap2-promoter
#5
Yaolai Wang, Feng Liu, Wei Wang
Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three low-affinity sequences (sites III-V), to which the transcriptional activator NtrC binds. By structure reconstruction, we analyze all possible organization architectures of the transcription apparatus (TA)...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27894815/the-histone-variant-h3-3-in-transcriptional-regulation-and-human-disease
#6
REVIEW
Leilei Shi, Hong Wen, Xiaobing Shi
Histone proteins wrap around DNA to form nucleosomes, which further compact into higher order structure of chromatin. In addition to the canonical histones, there are also variant histones that often have pivotal roles in regulating chromatin dynamics and the accessibility of the underlying DNA. H3.3 is the most common non-centromeric variant of histone H3 that differs from the canonical H3 by just 4-5 amino acids. Here we discuss the current knowledge of H3.3 in transcriptional regulation and the recent discoveries and molecular mechanisms of H3...
November 25, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27894195/accelerated-placental-aging-in-early-onset-preeclampsia-pregnancies-identified-by-dna-methylation
#7
Benjamin T Mayne, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, Tina Bianco-Miotto
AIM: To determine whether dynamic DNA methylation changes in the human placenta can be used to predict gestational age. MATERIALS & METHODS: Publicly available placental DNA methylation data from 12 studies, together with our own dataset, using Illumina Infinium Human Methylation BeadChip arrays. RESULTS & CONCLUSION: We developed an accurate tool for predicting gestational age of placentas using 62 CpG sites. There was a higher predicted gestational age for placentas from early onset preeclampsia cases, but not term preeclampsia, compared with their chronological age...
November 29, 2016: Epigenomics
https://www.readbyqxmd.com/read/27892573/thermodynamics-of-dna-sensitizer-recognition-characterizing-binding-motifs-with-all-atom-simulations
#8
Hugo Gattuso, Elise Dumont, Christophe Chipot, Antonio Monari, François Dehez
We report the investigation of the thermochemical properties of benzophenone interacting with B-DNA studied by all-atom molecular dynamic simulations. In particular, we determine the binding free energy for two competitive binding modes, minor groove binding and double insertion. Our results allow us to quantitatively resolve for the first time the mode of binding of this paradigmatic photosensitizer, indicating a marked preference for minor groove binding. Furthermore, we have settled a protocol allowing for the determination of binding energies in the case of non-covalent interaction with DNA, in particular, tackling the non-trivial problem of the strong reorganization of the DNA imposing extended statistical sampling...
November 28, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27889454/the-use-of-molecular-dynamics-simulations-to-evaluate-the-dna-sequence-selectivity-of-g-a-cross-linking-pbd-duocarmycin-dimers
#9
Paul J M Jackson, Khondaker M Rahman, David E Thurston
The pyrrolobenzodiazepine (PBD) and duocarmycin families are DNA-interactive agents that covalently bond to guanine (G) and adenine (A) bases, respectively, and that have been joined together to create synthetic dimers capable of cross-linking G-G, A-A, and G-A bases. Three G-A alkylating dimers have been reported in publications to date, with defined DNA-binding sites proposed for two of them. In this study we have used molecular dynamics simulations to elucidate preferred DNA-binding sites for the three published molecular types...
October 12, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27889453/simultaneous-real-time-imaging-of-leading-and-lagging-strand-synthesis-reveals-the-coordination-dynamics-of-single-replisomes
#10
Karl E Duderstadt, Hylkje J Geertsema, Sarah A Stratmann, Christiaan M Punter, Arkadiusz W Kulczyk, Charles C Richardson, Antoine M van Oijen
The molecular machinery responsible for DNA replication, the replisome, must efficiently coordinate DNA unwinding with priming and synthesis to complete duplication of both strands. Due to the anti-parallel nature of DNA, the leading strand is copied continuously, while the lagging strand is produced by repeated cycles of priming, DNA looping, and Okazaki-fragment synthesis. Here, we report a multidimensional single-molecule approach to visualize this coordination in the bacteriophage T7 replisome by simultaneously monitoring the kinetics of loop growth and leading-strand synthesis...
November 15, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27889303/pgla-h-tandem-repeat-peptides-active-against-multidrug-resistant-clinical-bacterial-isolates
#11
Tomislav Rončević, Goran Gajski, Nada Ilić, Ivana Goić-Barišić, Marija Tonkić, Larisa Zoranić, Juraj Simunić, Monica Benincasa, Marijana Mijaković, Alessandro Tossi, Davor Juretić
Antimicrobial peptides (AMPs) are promising candidates for new antibiotic classes but often display an unacceptably high toxicity towards human cells. A naturally produced C-terminal fragment of PGLa, named PGLa-H, has been reported to have a very low haemolytic activity while maintaining a moderate antibacterial activity. A sequential tandem repeat of this fragment, diPGLa-H, was designed, as well as an analogue with a Val to Gly substitution at a key position. These peptides showed markedly improved in vitro bacteriostatic and bactericidal activity against both reference strains and multidrug resistant clinical isolates of Gram-negative and Gram-positive pathogens, with generally low toxicity for human cells as assessed by haemolysis, cell viability, and DNA damage assays...
November 23, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27886174/5-hydroxymethylcytosine-localizes-to-enhancer-elements-and-is-associated-with-survival-in-glioblastoma-patients
#12
Kevin C Johnson, E Andres Houseman, Jessica E King, Katharine M von Herrmann, Camilo E Fadul, Brock C Christensen
Glioblastomas exhibit widespread molecular alterations including a highly distorted epigenome. Here, we resolve genome-wide 5-methylcytosine and 5-hydroxymethylcytosine in glioblastoma through parallel processing of DNA with bisulfite and oxidative bisulfite treatments. We apply a statistical algorithm to estimate 5-methylcytosine, 5-hydroxymethylcytosine and unmethylated proportions from methylation array data. We show that 5-hydroxymethylcytosine is depleted in glioblastoma compared with prefrontal cortex tissue...
November 25, 2016: Nature Communications
https://www.readbyqxmd.com/read/27885845/dna-methylation-in-systemic-lupus-erythematosus
#13
Christian M Hedrich, Katrin Mäbert, Thomas Rauen, George C Tsokos
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease facilitated by aberrant immune responses directed against cells and tissues, resulting in inflammation and organ damage. In the majority of patients, genetic predisposition is accompanied by additional factors conferring disease expression. While the exact molecular mechanisms remain elusive, epigenetic alterations in immune cells have been demonstrated to play a key role in disease pathogenesis through the dysregulation of gene expression...
November 25, 2016: Epigenomics
https://www.readbyqxmd.com/read/27883072/non-rvd-mutations-that-enhance-the-dynamics-of-the-tal-repeat-array-along-the-superhelical-axis-improve-talen-genome-editing-efficacy
#14
Naoya Tochio, Kohei Umehara, Jun-Ichi Uewaki, Holger Flechsig, Masaharu Kondo, Takehisa Dewa, Tetsushi Sakuma, Takashi Yamamoto, Takashi Saitoh, Yuichi Togashi, Shin-Ichi Tate
Transcription activator-like effector (TALE) nuclease (TALEN) is widely used as a tool in genome editing. The DNA binding part of TALEN consists of a tandem array of TAL-repeats that form a right-handed superhelix. Each TAL-repeat recognises a specific base by the repeat variable diresidue (RVD) at positions 12 and 13. TALEN comprising the TAL-repeats with periodic mutations to residues at positions 4 and 32 (non-RVD sites) in each repeat (VT-TALE) exhibits increased efficacy in genome editing compared with a counterpart without the mutations (CT-TALE)...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882317/bacterial-rna-polymerase-dna-interaction-the-driving-force-of-gene-expression-and-the-target-for-drug-action
#15
REVIEW
Jookyung Lee, Sergei Borukhov
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27882060/simple-and-reliable-method-to-quantify-the-hepatitis-b-viral-load-and-replicative-capacity-in-liver-tissue-and-blood-leukocytes
#16
Claudia Minosse, Sabrina Coen, Ubaldo Visco Comandini, Raffaella Lionetti, Marzia Montalbano, Stefano Cerilli, Donatella Vincenti, Andrea Baiocchini, Maria R Capobianchi, Stefano Menzo
BACKGROUND: A functional cure of chronic hepatitis B (CHB) is feasible, but a clear view of the intrahepatic viral dynamics in each patient is needed. Intrahepatic covalently closed circular DNA (cccDNA) is the stable form of the viral genome in infected cells, and represents the ideal marker of parenchymal colonization. Its relationships with easily accessible peripheral parameters need to be elucidated in order to avoid invasive procedures in patients. OBJECTIVES: The goal of this study was to design, set up, and validate a reliable and straightforward method for the quantification of the cccDNA and total DNA of the hepatitis B virus (HBV) in a variety of clinical samples...
October 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27881238/rational-identification-of-natural-organic-compounds-to-target-the-intermolecular-interaction-between-foxm-and-dna-in-colorectal-cancer
#17
Chunling Dong, Peng Yan, Juxun Wang, Hailian Mu, Shuli Wang, Fangchun Guo
The oncogenic transcription factor forkhead box M (Foxm) is overexpressed in human colorectal cancer (CRC). Targeting the protein interaction with its cognate DNA has been established as an attractive approach to anti-CRC chemotherapy. State-of-the-art molecular dynamics (MD) simulations revealed that the Foxm adopts considerably different conformations to interact with and without its DNA partner; the holo conformation is tightly packed as a typical globulin configuration, whereas the apo form is locally unstructured that exhibits intrinsic disorder in DNA recognition helix, indicating that DNA binding can help the Foxm refolding...
November 9, 2016: Bioorganic Chemistry
https://www.readbyqxmd.com/read/27880935/evolutionary-biologic-changes-of-gut-microbiota-in-an-adenoma-carcinoma-sequence-mouse-colorectal-cancer-model-induced-by-1-2-dimethylhydrazine
#18
Teng Sun, Shanglong Liu, Yanbing Zhou, Zengwu Yao, Dongfeng Zhang, Shougen Cao, Zhiliang Wei, Bin Tan, Yi Li, Zheng Lian, Song Wang
The molecular biological mechanisms underlying the evolutionary biologic changes leading to carcinogenesis remain unclear. The main objective of our study was to explore the evolution of the microbiota community and molecules related with CRC in the dynamic transition from normal colon epithelium to premalignant adenoma with the aid of an 'adenoma-carcinoma sequence' mouse CRC model induced by DMH. We generated a modified mouse CRC model induced by DMH for DNA sequences, and characterized the molecular networks...
November 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27875979/self-assembled-nucleic-acid-nanostructures-for-cancer-theranostic-medicines
#19
Jinglin Fu, Gabriele Stankeviciute, Sung Won Oh, John Collins, Yinghui Zhong, Ting Zhang
Theranostic medicine has become more promising in cancer treatment, where the cancer diagnosis and chemotherapy are combined for early diagnosis and precise treatment with improved efficacy and reduced side effects. Nanotechnology has played a critical role in developing various nanomaterials with engendered smart functions and targeted delivery. The rapid development of structural DNA nanotechnology has enabled the design and fabrication of complex nanostructures with prescribed 1D, 2D and 3D patterns in vitro and in vivo...
November 22, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27874316/extra-views-on-structure-and-dynamics-of-dna-loops-on-nucleosomes-studied-with-molecular-simulations
#20
Marco Pasi, Dimitar Angelov, Jan Bednar, Stefan Dimitrov, Richard Lavery
It has been shown experimentally that the action of the RSC chromatin remodeler leads to the formation of an irregular, partially remodeled nucleosome, termed a remosome. The remosome contains an extra 30-40 base pairs of DNA compared to a canonical nucleosome. Large-scale molecular simulations have provided information on the probable structure of remosomes and have explained why they remain stable in the absence of RSC. Here we explain how these simulations were carried out and what the resulting remosome models imply in terms of the mechanism of action of RSC...
November 22, 2016: Nucleus
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