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https://www.readbyqxmd.com/read/28397312/3lessons-from-the-cagi-4-hopkins-clinical-panel-challenge
#1
John-Marc Chandonia, Aashish Adhikari, Marco Carraro, Aparna Chhibber, Garry R Cutting, Yao Fu, Alessandra Gasparini, David T Jones, Andreas Kramer, Kunal Kundu, Hugo Y K Lam, Emanuela Leonardi, John Moult, Lipika R Pal, David B Searls, Sohela Shah, Shamil Sunyaev, Silvio C E Tosatto, Yizhou Yin, Bethany A Buckley
The CAGI-4 Hopkins clinical panel challenge was an attempt to assess state of the art methods for clinical phenotype prediction from DNA sequence. Participants were provided with exonic sequences of 83 genes for 106 patients from the Johns Hopkins DNA Diagnostic Laboratory. Five groups participated in the challenge, predicting both the probability that each patient had each of fourteen possible classes of disease, as well as one or more causal variants. In cases where the Hopkins laboratory reported a variant, at least one predictor correctly identified the disease class in 36 of 43 patients (84%)...
April 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28335274/metallic-nanostructures-based-on-dna-nanoshapes
#2
REVIEW
Boxuan Shen, Kosti Tapio, Veikko Linko, Mauri A Kostiainen, Jari Jussi Toppari
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds...
August 10, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28319084/structural-and-mechanistic-insights-into-an-archaeal-dna-guided-argonaute-protein
#3
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/28306508/prokaryotic-argonaute-uses-an-all-in-one-mechanism-to-provide-host-defense
#4
Dipali G Sashital
In this issue, Swarts et al. (2017) discover that prokaryotic Argonaute proteins generate their own DNA guide strands through a newly characterized, unguided "chopping" activity. Double-stranded chopping products are selectively loaded onto Argonaute, enabling DNA-guided defense against foreign DNA.
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28287704/orientational-binding-of-dna-guided-by-the-c2n-template
#5
Zonglin Gu, Lin Zhao, Shengtang Liu, Guangxin Duan, Jose Manuel Perez-Aguilar, Judong Luo, Weifeng Li, Ruhong Zhou
A detailed understanding of the interactions between biomolecules and nanomaterial surfaces is critical for the development of biomedical applications of these nanomaterials. Here, we characterized the binding patterns and dynamics of a double stranded DNA (dsDNA) segment on the recently synthesized nitrogenized graphene (C2N) with both theoretical (including classical and quantum calculations) and experimental approaches. Our results show that the dsDNA repeatedly exhibits a strong preference in its binding mode on the C2N substrate, displaying an upright orientation that is independent of its initial configurations...
March 28, 2017: ACS Nano
https://www.readbyqxmd.com/read/28262506/autonomous-generation-and-loading-of-dna-guides-by-bacterial-argonaute
#6
Daan C Swarts, Malwina Szczepaniak, Gang Sheng, Stanley D Chandradoss, Yifan Zhu, Elizabeth M Timmers, Yong Zhang, Hongtu Zhao, Jizhong Lou, Yanli Wang, Chirlmin Joo, John van der Oost
Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#7
REVIEW
Eugene V Koonin
Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28165224/programmable-dna-guided-artificial-restriction-enzymes
#8
Behnam Enghiad, Huimin Zhao
Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs...
February 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28105837/hrp-mimicking-dnazyme-catalyzed-in-situ-generation-of-polyaniline-to-assist-signal-amplification-for-ultrasensitive-surface-plasmon-resonance-biosensing
#9
Haiyin Li, Jiafu Chang, Ting Hou, Feng Li
It is well-known that the horseradish peroxidase- (HRP-) mimicking DNAzyme, namely, hemin/G-quadruplex, can effectively catalyze the polymerization of aniline to form DNA-guided polyaniline. Meanwhile, polyaniline exhibits extraordinary electrical, electrochemical, and redox properties, as well as excellent SPR signal-enhancing ability. Herein, we report a novel ultrasensitive surface plasmon resonance (SPR) biosensor based on HRP-mimicking DNAzyme-catalyzed in situ formation of polyaniline for signal amplification, using bleomycin (BLM) as the proof-of-concept analyte...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28066798/an-ngago-tool-for-genome-editing-did-crispr-cas9-just-find-a-competitor
#10
Qiang Wei, Junyi Liao, Xinyi Yu, Eric J Wang, Claire Wang, Hue H Luu, Rex C Haydon, Michael J Lee, Tong-Chuan He
While CRISPR/Cas9-mediated genome editing technology has been experiencing a rapid transformation during the past few years, a recent report on NgAgo-mediated single-stranded DNA-guided genome editing may offer an attractive alternative for genome manipulation. While it's too early to predict whether NgAgo will be able to compete with or be superior to CRISPR/Cas9, the scientific community is anxiously waiting for further optimization and broader applications of the NgAgo genome editing technology.
September 2016: Genes & Diseases
https://www.readbyqxmd.com/read/28053232/directional-emission-from-dye-functionalized-plasmonic-dna-superlattice-microcavities
#11
Daniel J Park, Jessie C Ku, Lin Sun, Clotilde M Lethiec, Nathaniel P Stern, George C Schatz, Chad A Mirkin
Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a testbed to study directional light emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal body-centered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27893702/failure-to-detect-dna-guided-genome-editing-using-natronobacterium-gregoryi-argonaute
#12
Seung Hwan Lee, Giandomenico Turchiano, Hirotaka Ata, Somaira Nowsheen, Marianna Romito, Zhenkun Lou, Seuk-Min Ryu, Stephen C Ekker, Toni Cathomen, Jin-Soo Kim
No abstract text is available yet for this article.
November 28, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27813013/dna-directed-self-assembly-of-highly-ordered-and-dense-single-walled-carbon-nanotube-arrays
#13
Hareem Maune, Si-Ping Han
Single-walled carbon nanotubes (SWNT or CNT) have unique and well-known high-performance material properties that can enable revolutionary increases in the performance of electronic devices and architectures. However, fabrication of large-scale SWNT-based ICs is an enormously challenging, unsolved problem, and self-assembly is likely needed for critical steps. Over the past several years, methods have been introduced to created ordered carbon nanotube structures using DNA guided self-assembly. In this chapter, we briefly review the challenges involved in using DNA to assemble SWNT nanostructures, and then give detailed methods to assemble dense, aligned SWNT arrays...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27741323/mechanistic-insights-into-archaeal-and-human-argonaute-substrate-binding-and-cleavage-properties
#14
Sarah Willkomm, Adrian Zander, Dina Grohmann, Tobias Restle
Argonaute (Ago) proteins from all three domains of life are key players in processes that specifically regulate cellular nucleic acid levels. Some of these Ago proteins, among them human Argonaute2 (hAgo2) and Ago from the archaeal organism Methanocaldococcus jannaschii (MjAgo), are able to cleave nucleic acid target strands that are recognised via an Ago-associated complementary guide strand. Here we present an in-depth kinetic side-by-side analysis of hAgo2 and MjAgo guide and target substrate binding as well as target strand cleavage, which enabled us to disclose similarities and differences in the mechanistic pathways as a function of the chemical nature of the substrate...
2016: PloS One
https://www.readbyqxmd.com/read/27730722/dry-sintering-meets-wet-silver-ion-soldering-charge-transfer-plasmon-engineering-of-solution-assembled-gold-nanodimers-from-visible-to-near-infrared%C3%A2-i-and-ii%C3%A2-regions
#15
Lingling Fang, Yueliang Wang, Miao Liu, Ming Gong, An Xu, Zhaoxiang Deng
Achieving highly tunable and localized surface plasmon resonance up to near infrared (NIR) regions is a key target in nanoplasmonics. In particular, a self-assembly process capable of producing highly uniform and solution-processable nanomaterials with tailor-made plasmonic properties is lacking. We herein address this problem through a conjunctive use of wet Ag(+) soldering and dry thermal sintering to produce nanodimer-derived structures with precisely engineered charge-transfer plasmon (CTP). The sintered dimers are water soluble, featuring gradually shifted CTP spanning an 800 nm wavelength range (up to NIR II)...
October 12, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27640875/dna-guided-genome-editing-using-structure-guided-endonucleases
#16
Gaurav K Varshney, Shawn M Burgess
The search for novel ways to target and alter the genomes of living organisms accelerated rapidly this decade with the discovery of CRISPR/Cas9. Since the initial discovery, efforts to find alternative methods for altering the genome have expanded. A new study presenting an alternative approach has been demonstrated that utilizes flap endonuclease 1 (FEN-1) fused to the Fok1 endonuclease, which shows potential for DNA-guided genome targeting in vivo.
2016: Genome Biology
https://www.readbyqxmd.com/read/27571968/crispr-cas9-a-promising-way-to-exploit%C3%A2-genetic-variation-in-plants
#17
REVIEW
Reema Rani, Prashant Yadav, Kalyani M Barbadikar, Nikita Baliyan, Era Vaidya Malhotra, Binay Kumar Singh, Arun Kumar, Dhiraj Singh
Creation of variation in existing gene pool of crop plants is the foremost requirement in crop improvement programmes. Genome editing is a tool to produce knock out of target genes either by introduction of insertion or by deletion that disrupts the function of a specific gene. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system is the most recent addition to the toolbox of sequence-specific nucleases that includes ZFNs and TALENs. The CRISPR/Cas9 system allows targeted cleavage of genomic DNA guided by a small noncoding RNA, resulting in gene modifications by both non-homologous end joining and homology-directed repair mechanisms...
December 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27514463/laboratory-medicine-in-the-clinical-decision-support-for-treatment-of-hypercholesterolemia-pharmacogenetics-of-statins
#18
REVIEW
Gualberto Ruaño, Richard Seip, Andreas Windemuth, Alan H B Wu, Paul D Thompson
Statin responsiveness is an area of great research interest given the success of the drug class in the treatment of hypercholesterolemia and in primary and secondary prevention of cardiovascular disease. Interrogation of the patient's genome for gene variants will eventually guide anti-hyperlipidemic intervention. In this review, we discuss methodological approaches to discover genetic markers predictive of class-wide and drug-specific statin efficacy and safety. Notable pharmacogenetic findings are summarized from hypothesis-free genome wide and hypothesis-led candidate gene association studies...
September 2016: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/27428505/dna-scaffolds-for-the-dictated-assembly-of-left-right-handed-plasmonic-au-np-helices-with-programmed-chiro-optical-properties
#19
Alessandro Cecconello, Jason S Kahn, Chun-Hua Lu, Larousse Khosravi Khorashad, Alexander O Govorov, Itamar Willner
Within the broad interest of assembling chiral left- and right-handed helices of plasmonic nanoparticles (NPs), we introduce the DNA-guided organization of left- or right-handed plasmonic Au NPs on DNA scaffolds. The method involves the self-assembly of stacked 12 DNA quasi-rings interlinked by 30 staple-strands. By the functionalization of one group of staple units with programmed tether-nucleic acid strands and additional staple elements with long nucleic acid chains, acting as promoter strands, the promoter-guided assembly of barrels modified with 12 left- or right-handed tethers is achieved...
August 10, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27207137/dna-guided-genome-editing-tool
#20
Dandan Zhang, Jian-Feng Li
No abstract text is available yet for this article.
July 2016: Science China. Life Sciences
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