keyword
MENU ▼
Read by QxMD icon Read
search

Duplex systems

keyword
https://www.readbyqxmd.com/read/28731353/altering-dna-programmable-colloidal-crystallization-paths-by-modulating-particle-repulsion
#1
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/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#2
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28724605/heterozygous-loss-of-function-mutation-in-odd-skipped-related-1-osr1-is-associated-with-vesico-ureteric-reflux-duplex-systems-and-hydronephrosis
#3
Marie-Lyne Fillion, Jasmine El Andalousi, Fatima Tokhmafshan, Vasikar Murugapoopathy, Christine L Watt, Inga J Murawski, John-Paul Capolicchio, Mohamed El-Sherbiny, Roman Jednak, Indra Rani Gupta
Osr1 is a transcriptional repressor that plays critical roles in maintaining the mesenchymal stem cell population within the developing kidney. Here, we report that newborn pups with a heterozygous null mutation in Osr1 exhibit a 21% incidence of vesico-ureteric reflux and have hydronephrosis and urinary tract duplications. Newborn pups have a short intravesical ureter resulting in a less competent uretero-vesical junction which arises from a delay in urinary tract development. We describe a new domain of Osr1 expression in the ureteral mesenchyme and within the developing bladder in the mouse...
July 19, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#4
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28717350/properties-of-native-high-density-lipoproteins-inspire-synthesis-of-actively-targeted-in-vivo-sirna-delivery-vehicles
#5
Kaylin M McMahon, Michael P Plebanek, C Shad Thaxton
Efficient systemic administration of therapeutic short interfering RNA (siRNA) is challenging. High-density lipoproteins (HDL) are natural in vivo RNA delivery vehicles. Specifically, native HDLs: 1) Load single-stranded RNA; 2) Are anionic, which requires charge reconciliation between the RNA and HDL, and 3) Actively target scavenger receptor type B-1 (SR-B1) to deliver RNA. Emphasizing these particular parameters, we employed templated lipoprotein particles (TLP), mimics of spherical HDLs, and self-assembled them with single-stranded complements of, presumably, any highly unmodified siRNA duplex pair after formulation with a cationic lipid...
November 15, 2016: Advanced Functional Materials
https://www.readbyqxmd.com/read/28706243/target-guided-synthesis-using-dna-nano-templates-for-selectively-assembling-a-g-quadruplex-binding-c-myc-inhibitor
#6
Deepanjan Panda, Puja Saha, Tania Das, Jyotirmayee Dash
The development of small molecules is essential to modulate the cellular functions of biological targets in living system. Target Guided Synthesis (TGS) approaches have been used for the identification of potent small molecules for biological targets. We herein demonstrate an innovative example of TGS using DNA nano-templates that promote Huisgen cycloaddition from an array of azide and alkyne fragments. A G-quadruplex and a control duplex DNA nano-template have been prepared by assembling the DNA structures on gold-coated magnetic nanoparticles...
July 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28704609/hydrophilic-and-cell-penetrable-pyrrolidinyl-peptide-nucleic-acid-pna-via-post-synthetic-modification-with-hydrophilic-side-chains
#7
Chaturong Suparpprom, Thanesuan Nuanyai, Haruthai Pansuwan, Tirayut Vilaivan, Supason Wanichwecharungruang, Boonsong Ditmangklo, Tanapat Palaga, Porntip Pan-In, Banphot Jiangchareon, Chotima Vilaivan
Peptide Nucleic Acid (PNA) is a nucleic acid mimic in which the deoxyribose-phosphate was replaced by a peptide-like backbone. The absence of negative charge in the PNA backbone leads to several unique behaviors including a stronger binding and salt-independency of the PNA-DNA duplex stability. However, PNA possesses poor aqueous solubility and cannot directly penetrate cell membranes. These are major obstacles that limited in vivo applications of PNA. In previous strategies, the PNA can be conjugated to macromolecular carrier, or modified with positively charged side chains such as guanidinium groups to improve the aqueous solubility and/or cell permeability...
July 13, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28694612/cerebral-and-coronary-vasculature-in-disease-associations-and-dissociations-in-the-south-indian-population
#8
Krishnan Srinivasan, Srinivasan Ravikumar, Sadanandavalli Retnaswami Chandra, Selva Ganapathy, G S Ravi
INTRODUCTION: Cerebrovascular accidents constitute the most common cause of disability all over the world. In India prevalence rate is 545 per 100000 and mortality rate is around 7.5 per thousand. Therefore the authors undertook a study on patients who underwent coronary artery bypass surgery (CABG). They were investigated for clinical and/or radiological evidence of cerebrovascular disease (CVD) with the aim to decide on early neurological intervention. PATIENTS AND METHODS: 210 patients who had undergone CABG were evaluated with neck vessel Doppler using high resolution duplex scanner system and computed tomography (CT) scan as well as MR angiogram (MRA) in addition to assessment of co morbid risk factors...
July 2017: Journal of Neurosciences in Rural Practice
https://www.readbyqxmd.com/read/28682373/fluorescent-mirna-analysis-enhanced-by-mesopore-effects-of-polydopamine-nanoquenchers
#9
Zhenqiang Wang, Jixi Zhang, Feng Chen, Kaiyong Cai
The combination of fluorophore-labelled single-strand DNA probes and nanomaterial quenchers has shown great potential in miRNA detection. The development of advanced detection systems by understanding and controlling the fluorescence quenching/recovery via nanoquenchers' microstructures and local morphologies is an attractive area warranting further investigations. Inspired by nanopore sequencing, we present a novel miRNA sensing strategy using fluorophore-labeled DNA as probes and a type of large-pore-sized mesoporous polydopamine nanoparticles (MPDA-L, 70 nm in diameter) as fluorescence quenchers...
July 6, 2017: Analyst
https://www.readbyqxmd.com/read/28672111/analyzing-spin-selectivity-in-dna-mediated-charge-transfer-via-fluorescence-microscopy
#10
John M Abendroth, Nako Nakatsuka, Matthew Ye, Dokyun Kim, Eric E Fullerton, Anne M Andrews, Paul S Weiss
Understanding spin-selective interactions between electrons and chiral molecules is critical to elucidating the significance of electron spin in biological processes and to assessing the potential of chiral assemblies for organic spintronics applications. Here, we use fluorescence microscopy to visualize the effects of spin-dependent charge transport in self-assembled monolayers of double-stranded DNA on ferromagnetic substrates. Patterned DNA arrays provide background regions for every measurement to enable quantification of substrate magnetization-dependent fluorescence due to the chiral-induced spin selectivity effect...
July 3, 2017: ACS Nano
https://www.readbyqxmd.com/read/28668638/crystal-structure-and-dna-binding-property-of-the-atpase-domain-of-bacterial-mismatch-repair-endonuclease-mutl-from-aquifex-aeolicus
#11
Kenji Fukui, Hitoshi Iino, Seiki Baba, Takashi Kumasaka, Seiki Kuramitsu, Takato Yano
DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus...
June 29, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28666002/hopping-into-a-hot-seat-role-of-dna-structural-features-on-is5-mediated-gene-activation-and-inactivation-under-stress
#12
M Zafri Humayun, Zhongge Zhang, Anna M Butcher, Aref Moshayedi, Milton H Saier
Insertion sequence elements (IS elements) are proposed to play major roles in shaping the genetic and phenotypic landscapes of prokaryotic cells. Recent evidence has raised the possibility that environmental stress conditions increase IS hopping into new sites, and often such hopping has the phenotypic effect of relieving the stress. Although stress-induced targeted mutations have been reported for a number of E. coli genes, the glpFK (glycerol utilization) and the cryptic bglGFB (β-glucoside utilization) systems are among the best characterized where the effects of IS insertion-mediated gene activation are well-characterized at the molecular level...
2017: PloS One
https://www.readbyqxmd.com/read/28656928/dynamic-and-morphologic-evaluation-of-erectile-dysfunction-on-penile-doppler-sonography-and-contrast-cavernosography
#13
A Ismail, A M Tabari, S U Alhasan, A Abdullahi
BACKGROUND: Penile erection is a complex phenomenon that involves coordinated interaction of the psychologic, hormonal, nervous, arterial, venous, and sinusoidal systems. Erectile dysfunction (ED) is the persistent inability to attain or maintain penile erection sufficient for sexual intercourse. This study aims to determine the real-time morphologic vascular abnormalities in men with ED using penile Doppler sonography in Kano, Nigeria. MATERIALS AND METHODS: Twenty-one patients who were referred from urology clinics on account of suspected vasculogenic ED were reviewed...
June 2017: Nigerian Journal of Clinical Practice
https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#14
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611213/spacer-capture-and-integration-by-a-type-i-f-cas1-cas2-3-crispr-adaptation-complex
#15
Robert D Fagerlund, Max E Wilkinson, Oleg Klykov, Arjan Barendregt, F Grant Pearce, Sebastian N Kieper, Howard W R Maxwell, Angela Capolupo, Albert J R Heck, Kurt L Krause, Mihnea Bostina, Richard A Scheltema, Raymond H J Staals, Peter C Fineran
CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA...
June 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28611171/pitfalls-of-the-duplex-system-the-mystery-of-the-missing-stone
#16
Donald Kudakwashe Nyanhongo, Satpal Antil, Syed Nasir
A duplex ureter constitutes about 1% of the renal tract anomalies.A 39-year-old man presented with a 4-week history of left loin pain and microscopic haematuria. Investigation with a non-contrast CT KUB revealed a 6 mm non-obstructing calculus in the left distal ureter.Left ureteroscopy and lithotripsy was planned. However, ureteroscopy failed to identify the calculus. A double J ureteric stent was left in situ and the procedure abandoned in favour of further assessment with a CT urogram. Imaging surprisingly showed a left duplex ureter with the calculus in the non-stented ureter...
June 13, 2017: BMJ Case Reports
https://www.readbyqxmd.com/read/28608333/in-vitro-formation-of-plant-rna-induced-silencing-complexes-using-an-extract-of-evacuolated-tobacco-protoplasts
#17
Taichiro Iki, Masayuki Ishikawa, Manabu Yoshikawa
Small RNA-mediated gene silencing is involved in a variety of biological processes among many eukaryotic organisms. The silencing effector, generally referred to as RNA-induced silencing complex (RISC), comprises an ARGONAUTE (AGO) protein and a small single-stranded guide RNA in its core. RISCs recognize target genes containing sequences complementary to the guide RNA and repress their expression transcriptionally or posttranscriptionally. In vitro systems that recapitulate RISC assembly are useful not only to decipher the molecular mechanisms underlying the assembly process itself but also to dissect the downstream silencing pathways mediated by RISCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28603040/a-real-time-control-system-of-gene-expression-using-ligand-bound-nucleic-acid-aptamer-for-metabolic-engineering
#18
Jing Wang, Xun Cui, Le Yang, Zhe Zhang, Liping Lv, Haoyuan Wang, Zhenmin Zhao, Ningzi Guan, Lichun Dong, Rachel Chen
Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS...
June 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28602637/inhibition-mechanism-of-an-anti-crispr-suppressor-acriia4-targeting-spycas9
#19
Hui Yang, Dinshaw J Patel
Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to overcome the CRISPR-Cas-mediated defense of the host. Recently, AcrIIA2 and AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity of type II-A Streptococcus pyogene Cas9 (SpyCas9). We now report the crystal structure of AcrIIA4 in complex with single-guide RNA-bound SpyCas9, thereby establishing that AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access to key catalytic residues lining the RuvC pocket...
July 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28602578/femoral-arterial-haemostasis-using-an-anchored-collagen-plug-after-percutaneous-evar-with-an-ultra-low-profile-device-prospective-audit-of-an-evolving-post-close-technique
#20
A Chaudhuri
OBJECTIVE: To present an audit of a successful "post-close" haemostatic technique using the Angio-Seal VIP vascular closure device (VCD) after percutaneous endovascular aneurysm repair (p-EVAR) using an ultra-low profile (ULP) device. METHODS: Thirty patients underwent EVAR using the Ovation device, of which 26 procedures were totally percutaneous. Data including patient habitus, procedural details, number of VCDs deployed including use of the double wire approach, and technical success/complications were prospectively recorded...
June 8, 2017: European Journal of Vascular and Endovascular Surgery
keyword
keyword
33637
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"