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Kijun Kim, Trung Duc Nguyen, Shaohua Li, Tuan Anh Nguyen
The Microprocessor complex, consisting of an RNase III DROSHA and the DGCR8 dimer, cleaves primary microRNA transcripts (pri-miRNAs) to initiate microRNA (miRNA) maturation. Pri-miRNAs are stem-loop RNAs, and ~79% of them contain at least one of the three major and conserved RNA motifs, UG, UGU, and CNNC. We recently demonstrated that the basal UG and apical UGU motifs of pri-miRNAs interact with DROSHA and DGCR8, respectively. They help orient Microprocessor on the pri-miRNA in a proper direction in which DROSHA and DGCR8 localize to the basal and apical pri-miRNA junctions, respectively...
April 3, 2018: RNA
Jieyan V Chen, Rebecca A Buchwalter, Ling-Rong Kao, Timothy L Megraw
Non-centrosomal microtubule organizing centers (MTOCs) direct microtubule (MT) organization to exert diverse cell-type-specific functions. In Drosophila spermatids, the giant mitochondria provide structural platforms for MT reorganization to support elongation of the extremely long sperm. However, the molecular basis for this mitochondrial MTOC and other non-centrosomal MTOCs has not been discerned. Here we report that Drosophila centrosomin (cnn) expresses two major protein variants: the centrosomal form (CnnC) and a non-centrosomal form in testes (CnnT)...
July 10, 2017: Current Biology: CB
Wei Feng, Huimin Lei, Jiarui Si, Tao Zhang
Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer's disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides...
2017: PloS One
Hai-Jie Liu, Marcos Gil-Sepulcre, Laia Francàs, Pau Nolis, Teodor Parella, Jordi Benet-Buchholz, Xavier Fontrodona, Jordi García-Antón, Nuria Romero, Antoni Llobet, Lluís Escriche, Roger Bofill, Xavier Sala
A new CNNC carbene-phthalazine tetradentate ligand has been synthesised, which in the reaction with [Ru(T)Cl3 ] (T = trpy, tpm, bpea; trpy = 2,2';6',2''-terpyridine; tpm = tris(pyrazol-1-yl)methane; bpea = N,N-bis(pyridin-2-ylmethyl)ethanamine) in MeOH or iPrOH undergoes a C-N bond scission due to the nucleophilic attack of a solvent molecule, with the subsequent formation of the mononuclear complexes cis-[Ru(PhthaPz-OR)(trpy)X]n+ , [Ru(PhthaPz-OMe)(tpm)X]n+ and trans,fac-[Ru(PhthaPz-OMe)(bpea)X]n+ (X = Cl, n = 1; X = H2 O, n = 2; PhthaPz-OR = 1-(4-alkoxyphthalazin-1-yl)-3-methyl-1H-imidazol-3-ium), named 1a+ /2a2+ (R = Me), 1b+ /2b2+ (R = iPr), 3+ /42+ and 5+ /62+ , respectively...
February 28, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Christine Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing...
March 2017: Genome Research
Luís Duarte, Leonid Khriachtchev, Rui Fausto, Igor Reva
2,2'-Dihydroxyazobenzene (DAB), 2,2'-azotoluene (AT) and azobenzene (AB) were isolated in argon and xenon matrices and their molecular structures and photochemical transformations were characterized by infrared spectroscopy and theoretical calculations. All these compounds can adopt the E and Z isomeric forms around the central CNNC moiety, which can be enriched by several conformational and tautomeric modifications for DAB and AT. A number of DAB and AT isomeric forms were identified for the first time. For DAB, the E azo-enol isomer with two intramolecular six-membered quasi-rings formed via OHN hydrogen bonds was found after deposition...
June 22, 2016: Physical Chemistry Chemical Physics: PCCP
Géraldine Féraud, Claude Dedonder-Lardeux, Christophe Jouvet, Ernesto Marceca
Gas phase photodissociation electronic spectra of protonated azobenzene (ABH(+)) and 4-(dimethylamino)azobenzene (dmaABH(+)) were measured in a cryogenically cooled ion trap at temperatures of a few tens of Kelvin. Experimental results were complemented with electronic structure calculations in the ground state at the MP2/cc-pVDZ level of theory, and in the low lying excited states using the RI-CC2 method. Calculated energies revealed that only the trans isomers of the azonium molecular ions (protonation site on the azo group) will likely exist in the trap at the temperatures achieved in the experiment...
June 9, 2016: Journal of Physical Chemistry. A
M H Le, R Warotayanont, J Stahl, P K Den Besten, Y Nakano
Amelogenins constitute the major portion of secretory enamel matrix proteins and are known to be highly alternative spliced. Of all the alternatively spliced forms of amelogenins, exon4 is most commonly spliced out. Our analyses of the exon4 sequence led us to hypothesize that when spliced out, exon4 may generate a novel mature miRNA. To explore this possibility, we used in vivo mouse models (wild-type and Amel knockout mice) and in vitro cell culture to investigate the presence and function of a mature miRNA derived from exon4 (miR-exon4)...
April 2016: Journal of Dental Research
Xujun Liu, Leilei Guan, Xiaoniu Fu, Yu Zhao, Jiada Wu, Ning Xu
Light-absorbing and electrically conductive binary CNx nanocone (CNNC) arrays have been fabricated using a glow discharge plasma-assisted reaction deposition method. The intact CNNCs with amorphous structure and central nickel-filled pipelines could be vertically and neatly grown on nickel-covered substrates according to the catalyst-leading mode. The morphologies and composition of the as-grown CNNC arrays can be well controlled by regulating the methane/nitrogen mixture inlet ratio, and their optical absorption and resistivity strongly depend on their morphologies and composition...
2014: Nanoscale Research Letters
Vincent C Auyeung, Igor Ulitsky, Sean E McGeary, David P Bartel
To use microRNAs to downregulate mRNA targets, cells must first process these ~22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants...
February 14, 2013: Cell
Robert L Kerby, Gary P Roberts
The single-component RcoM transcription factor couples an N-terminally bound heme cofactor with a C-terminal "LytTR" DNA-binding domain. Here the RcoM(Bx)-1 protein from Burkholderia xenovorans LB400 was heterologously expressed and then purified in a form with minimal bound CO (~10%) and was found to stably bind this effector with a nanomolar affinity. DNase I protection assays demonstrated that the CO-associated form binds with a micromolar affinity to two ~60-bp DNA regions, each comprised of a novel set of three direct-repeat binding sites spaced 21 bp apart on center...
November 2012: Journal of Bacteriology
Sayak Roy, Biprajit Sarkar, Hans-Georg Imrich, Jan Fiedler, Stanislav Záliš, Reyes Jimenez-Aparicio, Francisco A Urbanos, Shaikh M Mobin, Goutam Kumar Lahiri, Wolfgang Kaim
Neutral diastereoisomeric diruthenium(III) complexes, meso- and rac-[(acac)(2)Ru(μ-adc-OR)Ru(acac)(2)] (acac(-) = 2,4-pentanedionato and adc-OR(2-) = dialkylazodicarboxylato = [RO(O)CNNC(O)OR](2-), R = tert-butyl or isopropyl), were obtained from electron transfer reactions between Ru(acac)(2)(CH(3)CN)(2) and azodicarboxylic acid dialkyl esters (adc-OR). The meso isomer 3 with R = isopropyl was structurally characterized, revealing two deprotonated and N-N coupled carbamate functions in a reduced dianionic bridge with d(N-N) = 1...
September 3, 2012: Inorganic Chemistry
David P Hoffman, Richard A Mathies
Azobenzenes are used in many applications because of their robust and reversible light induced trans⇋cis isomerization about the N=N bond, but the mechanism of this ultrafast reaction has not been conclusively defined. Addressing this problem we have used Femtosecond Stimulated Raman Spectroscopy (FSRS) to determine the structural transients in the trans→cis photoisomerization of the azobenzene derivative, 4-nitro-4'-dimethylamino-azobenzene (NDAB). Key marker modes, such as the 1570/1590 cm(-1) NO(2) stretch and the 1630 cm(-1) C-N(Me)(2) stretch, enable the separation and analysis of distinct trans and cis photoproduct dynamics revealing the 400 fs Frank-Condon relaxation, the 800 fs timescale of the cis product formation and the 2 ps emergence and 8 ps relaxation of the unsuccessful ground state trans species...
May 14, 2012: Physical Chemistry Chemical Physics: PCCP
Marek Pederzoli, Jiří Pittner, Mario Barbatti, Hans Lischka
Ab initio nonadiabatic dynamics simulations of cis-to-trans isomerization of azobenzene upon S(1) (n-π*) excitation are carried out employing the fewest-switches surface hopping method. Azobenzene photoisomerization occurs purely as a rotational motion of the central CNNC moiety. Two nonequivalent rotational pathways corresponding to clockwise or counterclockwise rotation are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via an S(0)/S(1) crossing seam located near the midpoint of both of these rotational pathways...
October 20, 2011: Journal of Physical Chemistry. A
Chen-Wei Jiang, Rui-Hua Xie, Fu-Li Li, Roland E Allen
Using density-functional-based molecular dynamics simulations, we have performed comparative studies of the trans-cis isomerizations of azobenzene and bridged azobenzene (B-Ab) 5,6-dihydrodibenzo[c,g][1,2]diazocine induced by nπ* electronic excitation. The quantum yields found in our calculations, 45% for the bridged azobenzene versus 25% for azobenzene, are consistent with the experiment. Both isomerization processes involve two steps: (1) Starting from the trans structure, each molecule moves on its S(1) excited-state potential energy surface, via rotation around the NN bond, to an avoided crossing near the S(1)/S(0) conical intersection, where de-excitation occurs...
January 27, 2011: Journal of Physical Chemistry. A
Ron Siewertsen, Jan Boyke Schönborn, Bernd Hartke, Falk Renth, Friedrich Temps
The ultrafast Z→E and E→Z photoisomerisation dynamics of 5,6-dihydrodibenzo[c,g][1,2]diazocine (1), the parent compound of a class of bridged azobenzene-based photochromic molecular switches with a severely constrained eight-membered heterocyclic ring as central unit, have been studied by femtosecond time-resolved spectroscopy in n-hexane as solvent and by quantum chemical calculations. The diazocine contrasts with azobenzene (AB) in that its Z rather than E isomer is the energetically more stable form...
January 21, 2011: Physical Chemistry Chemical Physics: PCCP
Matthias Ruckenbauer, Mario Barbatti, Bernhard Sellner, Thomas Muller, Hans Lischka
The nonadiabatic deactivation of trans-azomethane starting from the nπ* state has been investigated in gas phase, water, and n-hexane using an on-the-fly surface-hopping method. A quantum mechanical/molecular mechanics (QM/MM) approach was used employing a flexible quantum chemical level for the description of electronically excited states and bond dissociation (generalized valence bond perfect-pairing complete active space). The solvent effect on the lifetime and structural parameters of azomethane was investigated in detail...
December 9, 2010: Journal of Physical Chemistry. A
Marcus Böckmann, Nikos L Doltsinis, Dominik Marx
A nonadiabatic hybrid quantum and molecular mechanical (na-QM/MM) molecular dynamics scheme has been implemented recently combining the nonadiabatic Car-Parrinello molecular dynamics method by Doltsinis and Marx [Phys. Rev. Lett. 2002, 88, 166402] with the QM/MM coupling approach by Laio et al. [J. Chem. Phys. 2002, 116, 6941]. Here an extensive validation of the underlying, density functional theory based, electronic structure methods by comparison to CASPT2 ab initio data is presented for the case of azobenzene...
January 21, 2010: Journal of Physical Chemistry. A
Jr-Wei Ho, Wei-Kan Chen, Po-Yuan Cheng
We report studies of ultrafast dynamics of azobenzene cation using femtosecond photoionization-photofragmentation spectroscopy. In our experiments, a femtosecond pump pulse first produces an ensemble of azobenzene cations via photoionization of the neutrals. A delayed probe pulse then brings the evolving ionic system to excited states that ultimately undergo ion fragmentation. The dynamics is followed by monitoring either the parent-ion depletion or fragment-ion formation as a function of the pump-probe delay time...
October 7, 2009: Journal of Chemical Physics
J Olazarán, E Navarro, Ml Galiano, A Vaquero, A Guillem, F Villaverde, Y Fernández
INTRODUCTION: The medical conditions shared by hospital emergency services and community-hospital neurology clinics (CHNC) have not been described, and the quality of the medical care received in these conditions has not been evaluated in our environment. METHODS: Over a 2 month period, those patients presenting at any of the seven CHNC in a Health Care Area 1 of Madrid due to previously attended medical conditions in the emergency services were systematically registered...
May 2009: Neurología: Publicación Oficial de la Sociedad Española de Neurología
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