keyword
MENU ▼
Read by QxMD icon Read
search

Duplex

keyword
https://www.readbyqxmd.com/read/28097429/early-and-noninvasive-evaluation-using-superficial-temporal-artery-duplex-ultrasonography-after-indirect-bypass-for-adult-ischemic-moyamoya-disease
#1
Sayaka Ogawa, Hiroshi Abe, Toshiro Katsuta, Kenji Fukuda, Toshiyasu Ogata, Koichi Miki, Tooru Inoue
BACKGROUND: The validity of indirect bypass for adult patients with moyamoya disease is still debatable. Some patients are poor responders to indirect bypass, and additive intervention is occasionally required in these cases. Therefore, it is necessary to evaluate the development of collateral circulation as early as possible postoperatively. METHODS: Fifteen adult patients (>17 years old) with moyamoya disease (22 affected sides) who underwent encephalo-duro-arterio-synangiosis (EDAS) at Fukuoka University Hospital from April 2008 to August 2014 were included...
January 17, 2017: Acta Neurochirurgica
https://www.readbyqxmd.com/read/28096349/structure-of-eukaryotic-cmg-helicase-at-a-replication-fork-and-implications-to-replisome-architecture-and-origin-initiation
#2
Roxana Georgescu, Zuanning Yuan, Lin Bai, Ruda de Luna Almeida Santos, Jingchuan Sun, Dan Zhang, Olga Yurieva, Huilin Li, Michael E O'Donnell
The eukaryotic CMG (Cdc45, Mcm2-7, GINS) helicase consists of the Mcm2-7 hexameric ring along with five accessory factors. The Mcm2-7 heterohexamer, like other hexameric helicases, is shaped like a ring with two tiers, an N-tier ring composed of the N-terminal domains, and a C-tier of C-terminal domains; the C-tier contains the motor. In principle, either tier could translocate ahead of the other during movement on DNA. We have used cryo-EM single-particle 3D reconstruction to solve the structure of CMG in complex with a DNA fork...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095445/cytosolic-rna-dna-duplexes-generated-by-endogenous-reverse-transcriptase-activity-as-autonomous-inducers-of-skin-inflammation-in-psoriasis
#3
Jean-Pierre Molès, Anthony Griez, Jean-Jacques Guilhou, Céline Girard, Nicolas Nagot, Philippe Van de Perre, Pierre Dujols
Psoriasis is a chronic skin disease of unknown ætiology. Recent studies suggested that a large amount of cytosolic DNA (cyDNA) in keratinocytes is breaking keratinocytes DNA tolerance and promotes self-sustained inflammation in the psoriatic lesion. We investigated the origin of this cyDNA. We show that, amongst all the possible DNA structures, the cyDNA could be present as RNA:DNA duplexes in keratinocytes. We further show that endogenous reverse transcriptase activities generate such duplexes and consequently activate the production of Th1-inflammatory cytokines...
2017: PloS One
https://www.readbyqxmd.com/read/28094993/the-biophysics-of-artificially-expanded-genetic-information-systems-thermodynamics-of-dna-duplexes-containing-matches-and-mismatches-involving-2-amino-3-nitropyridin-6-one-z-and-imidazo-1-2-a-1-3-5-triazin-4-8h-one-p
#4
Xiaoyu Wang, Shuichi Hoshika, Raymond J Peterson, Myong-Jung Kim, Steven A Benner, Jason D Kahn
Synthetic nucleobases presenting non-Watson Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2'-deoxyriboside (presenting a {donor-donor-acceptor} hydrogen bonding pattern on the Watson-Crick face of the small component, trivially designated Z) and imidazo[1,2-a]-1,3,5-triazin-4(8H)one 2'-deoxyriboside (presenting an {acceptor-acceptor-donor} hydrogen bonding pattern on the large component, trivially designated P) is one of these extra pairs for which a substantial amount of molecular biology has been developed...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28094979/photo-induced-cross-linking-of-short-furan-modified-dna-on-surfaces
#5
Cinthya Yamila Véliz Montes, Henry Memczak, Ellen Gyssels, Tomas Torres, Annemieke Madder, Rudolf J Schneider
We report for the first time the formation of site-specifically interstrand cross-linked (ICL) surface-immobilized furan-modified DNA duplexes via singlet oxygen. 1O2, necessary for effecting furan-mediated ICL formation, was produced in situ using methylene blue or a zinc phthalocyanine derivative (TT1) as photosensitizers. Via surface plasmon resonance spectroscopy we show that surface ICL was achieved and established a robust link which enhances the stability of the 12-mer duplex even after surface regeneration...
January 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28094928/efficient-charge-transport-via-dna-g-quadruplexes
#6
Arun K Thazhathveetil, Michelle A Harris, Ryan M Young, Michael R Wasielewski, Frederick D Lewis
The dynamics and efficiency of photoinduced charge transport has been investigated in DNA capped hairpins possessing a stilbenedicarboxamide (Sa) hole donor and stilbenediether (Sd) hole acceptor separated by DNA G-quadruplex structures possessing 2-to-4 tetrads by means of femtosecond and nanosecond transient absorption spectroscopy with global analysis. The results for the quadruplex structures are compared with those for the corresponding duplex structures having G-C base pairs in place of the G-tetrads...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28094588/mechanisms-and-regulation-of-dna-replication-initiation-in-eukaryotes
#7
Matthew W Parker, Michael R Botchan, James M Berger
Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG...
January 17, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28094182/dna-duplex-linker-for-afm-selex-of-dna-aptamer-against-human-serum-albumin
#8
Musashi Takenaka, Yuzo Okumura, Tomokazu Amino, Yusuke Miyachi, Chiaki Ogino, Akihiko Kondo
DNA-duplex interactions in thymines and adenins are used as a linker for the novel methodology of Atomic Force Microscope-Systematic Evolution of Ligands by EXpotential enrichment (AFM-SELEX). This study used the hydrogen bonds in 10 mer of both thymines (T10) and adenines (A10). Initially, the interactive force in T10-A10 was measured by AFM, which returned an average interactive force of approximately 350pN. Based on this result, DNA aptamers against human serum albumin could be selected in the 4th round, and 15 different clones could be sequenced...
January 7, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28091673/conformational-and-electronic-effects-on-the-formation-of-anti-cyclobutane-pyrimidine-dimers-in-g-quadruplex-structures
#9
Wook Lee, Spiridoula Matsika
Cyclobutane pyrimidine dimers (CPDs) are the most commonly formed photochemical products when nucleic acids interact with UV radiation. In duplex DNA, the relative inflexible structure allows for only the cis, syn CPD isomer to be formed. G-quadruplex structures, however, have loops that are more flexible and allow for different orientations of the bases to interact. As a result, the highly unusual formation of an anti CPD has been observed in these structures. Due to the close proximity between two opposing loops containing the TTA sequence in two G-quadruplex structures (called "form-3" and "basket"), a high yield of anti CPD formation was expected in these structures...
January 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28090713/nucleotide-independent-copper-ii-based-distance-measurements-in-dna-by-pulsed-esr-spectroscopy
#10
Matthew J Lawless, Jessica L Sarver, Sunil Saxena
A site-specific Cu(2+) binding motif within a DNA duplex for distance measurements by ESR spectroscopy is reported. This motif utilizes a commercially available 2,2'-dipicolylamine (DPA) phosphormadite easily incorporated into any DNA oligonucleotide during initial DNA synthesis. The method only requires the simple post-synthetic addition of Cu(2+) without the need for further chemical modification. Notably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for an accurate measurement of duplex distance...
January 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28090121/redox-signaling-through-dna
#11
Elizabeth O'Brien, Rebekah M B Silva, Jacqueline K Barton
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances...
October 2016: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/28089613/high-frequency-of-hepatitis-e-virus-infection-in-swine-from-south-brazil-and-close-similarity-to-human-hev-isolates
#12
Ana Maria Passos-Castilho, Celso Francisco Hernandes Granato
Hepatitis E virus is responsible for acute and chronic liver infections worldwide. Swine hepatitis E virus has been isolated in Brazil, and a probable zoonotic transmission has been described, although data are still scarce. The aim of this study was to investigate the frequency of hepatitis E virus infection in pigs from a small-scale farm in the rural area of Paraná State, South Brazil. Fecal samples were collected from 170 pigs and screened for hepatitis E virus RNA using a duplex real-time RT-PCR targeting a highly conserved 70nt long sequence within overlapping parts of ORF2 and ORF3 as well as a 113nt sequence of ORF2...
January 3, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28088759/how-accurate-are-accurate-force-fields-for-b-dna
#13
Pablo D Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing 'experimental models', which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of (1)H nuclear magnetic resonance (NMR)...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28087715/sf3b1-hsh155-heat-motif-mutations-affect-interaction-with-the-spliceosomal-atpase-prp5-resulting-in-altered-branch-site-selectivity-in-pre-mrna-splicing
#14
Qing Tang, Susana Rodriguez-Santiago, Jing Wang, Jia Pu, Andrea Yuste, Varun Gupta, Alberto Moldón, Yong-Zhen Xu, Charles C Query
Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28080035/fluorescence-turn-on-sensing-of-dna-duplex-formation-by-a-tricyclic-cytidine-analogue
#15
Dillon D Burns, Kristine L Teppang, Raymond W Lee, Melissa Eleanor Lokensgard, Byron W Purse
Most fluorescent nucleoside analogues are quenched when base stacked and some maintain their brightness, but there has been little progress towards developing nucleoside analogues that markedly increase their fluorescence upon duplex formation. Here, we report on the design and synthesis of a new tricyclic cytidine analogue, 8-diethylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases...
January 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28078722/ssb-and-the-recg-dna-helicase-an-intimate-association-to-rescue-a-stalled-replication-fork
#16
REVIEW
Piero R Bianco, Yuri L Lyubchenko
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28077881/a-pilot-study-of-penile-hemodynamics-in-men-with-penile-curvatures
#17
A A Zaazaa, I Fathy, O Ayman, A Hassanin, H Ghanem
Penile curvature (PC) is bothersome to the patient. PC is either congenital or acquired. In most of the circulatory system, blood flows in a laminar profile with minimal energy expenditure. When a fluid passes in a curved tube, the laminar profile is disturbed and changed into a turbulent flow. It increases the energy expenditure and reduces the flow. Turbulent flow may have a role in the development of an atherosclerotic plaque and in localizing its site. The aim of this research was to study penile hemodynamics before and after correction of PC...
January 12, 2017: International Journal of Impotence Research
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#18
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3' end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28076812/spermine-condenses-dna-but-not-rna-duplexes
#19
Andrea M Katz, Igor S Tolokh, Suzette A Pabit, Nathan Baker, Alexey V Onufriev, Lois Pollack
Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28074973/fluorescence-turn-on-hairpin-probe-pcr
#20
F Takei, K Nakatani
A new fluorescence turn-on type of PCR monitoring system (Hpro-PCR) using a hairpin probe and a primer having a tag sequence at the 5' end with the fluorescent molecule 2,7-diamino-1,8-naphthyridine derivative (DANP) has been developed. The Hpro-PCR exploited the modulation of the equilibrium states between the DANP-bound hairpin structure and probe-tag duplex, and the PCR progress alternated the equilibrium state, resulting in the change of fluorescent intensity.
January 11, 2017: Chemical Communications: Chem Comm
keyword
keyword
4812
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"