keyword
MENU ▼
Read by QxMD icon Read
search

single-molecule

keyword
https://www.readbyqxmd.com/read/28335237/dna-sequencing-by-hexagonal-boron-nitride-nanopore-a-computational-study
#1
Liuyang Zhang, Xianqiao Wang
The single molecule detection associated with DNA sequencing has motivated intensive efforts to identify single DNA bases. However, little research has been reported utilizing single-layer hexagonal boron nitride (hBN) for DNA sequencing. Here we employ molecular dynamics simulations to explore pathways for single-strand DNA (ssDNA) sequencing by nanopore on the hBN sheet. We first investigate the adhesive strength between nucleobases and the hBN sheet, which provides the foundation for the hBN-base interaction and nanopore sequencing mechanism...
June 6, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#2
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334870/annealing-helicase-harp-closes-rpa-stabilized-dna-bubbles-non-processively
#3
Daniel R Burnham, Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, Cees Dekker
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334864/coordination-among-tertiary-base-pairs-results-in-an-efficient-frameshift-stimulating-rna-pseudoknot
#4
Yu-Ting Chen, Kai-Chun Chang, Hao-Teng Hu, Yi-Lan Chen, You-Hsin Lin, Chiung-Fang Hsu, Cheng-Fu Chang, Kung-Yao Chang, Jin-Der Wen
Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334781/auf1-facilitates-microrna-mediated-gene-silencing
#5
Kyung-Won Min, Myung Hyun Jo, Soochul Shin, Sylvia Davila, Richard W Zealy, Soo Im Kang, Lawson T Lloyd, Sungchul Hohng, Je-Hyun Yoon
Eukaryotic mRNA decay is tightly modulated by RNA-binding proteins (RBPs) and microRNAs (miRNAs). RBP AU-binding factor 1 (AUF1) has four isoforms resulting from alternative splicing and is critical for miRNA-mediated gene silencing with a distinct preference of target miRNAs. Previously, we have shown that AUF1 facilitates miRNA loading to Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex. Here, we further demonstrate that depletion of AUF1 abolishes the global interaction of miRNAs and AGO2...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334160/aqua-duct-a-ligands-tracking-tool
#6
Tomasz Magdziarz, Karolina Mitusinska, Sandra Goldowska, Alicja Pluciennik, Michal Stolarczyk, Magdalena Lugowska, Artur Góra
Motivation: The identification and tracking of molecules which enter active site cavity requires screening the positions of thousands of single molecules along several thousand molecular dynamic steps. To fill the existing gap between tools searching for tunnels and pathways and advanced tools employed for accelerated water flux investigations, we have developed AQUA-DUCT. Results: AQUA-DUCT is an easy-to-use tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28332923/different-types-of-pausing-modes-during-transcription-initiation
#7
Eitan Lerner, Antonino Ingargiola, Jookyung J Lee, Sergei Borukhov, Xavier Michalet, Shimon Weiss
In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. (1) and from Lerner, Chung et al. (2) In both studies, pausing is attributed to lack of forward translocation of the nascent transcript during initiation...
March 23, 2017: Transcription
https://www.readbyqxmd.com/read/28332666/direct-observation-of-breathing-dynamics-at-the-mismatch-induced-dna-bubble-with-nanometre-accuracy-a-smfret-study
#8
Tapas Paul, Subhas C Bera, Padmaja P Mishra
The detailed conformational dynamics of the melted region in double-stranded DNA has been studied using a combination of ensemble and single-molecule FRET techniques. We monitored the millisecond time scale fluctuation kinetics of the two strands at the bubble region that varies with the size of the bubble. As the individual strands at the melting bubble behave as single-stranded DNA, and hence fluctuate dynamically to attain energetically favored configurations, the rates of these fluctuations increase with increase in the bubble size...
March 23, 2017: Nanoscale
https://www.readbyqxmd.com/read/28332209/quantitation-and-mapping-of-the-epigenetic-marker-5-hydroxymethylcytosine
#9
Ying Qing, Zhiqi Tian, Ying Bi, Yongyao Wang, Jiangang Long, Chun-Xiao Song, Jiajie Diao
We here review primary methods used in quantifying and mapping 5-hydroxymethylcytosine (5hmC), including global quantification, restriction enzyme-based detection, and methods involving DNA-enrichment strategies and the genome-wide sequencing of 5hmC. As discovered in the mammalian genome in 2009, 5hmC, oxidized from 5-methylcytosine (5mC) by ten-eleven translocation (TET) dioxygenases, is increasingly being recognized as a biomarker in biological processes from development to pathogenesis, as its various detection methods have shown...
March 23, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28329910/nucleosome-mobility-and-the-regulation-of-gene-expression-insights-from-single-molecule-studies
#10
REVIEW
Sergei Rudnizky, Omri Malik, Adaiah Bavly, Lilach Pnueli, Philippa Melamed, Ariel Kaplan
Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA, and function as a basic layer in the complex regulation of gene expression. Our understanding of the role of the nucleosome's spontaneous, thermally driven position changes in modulating expression is lacking. This is the result of the paucity of experimental data on these dynamics, at high-resolution, and for DNA sequences that belong to real, transcribed genes. We have developed an assay that uses partial, reversible unzipping of nucleosomes with optical tweezers to repeatedly probe a nucleosome's position over time...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28328539/polarization-sensitive-localization-based-super-resolution-microscopy-with-a-birefringent-wedge
#11
József Sinkó, Tamás Gajdos, Elvira Czvik, Gábor Szabó, Miklós Erdélyi
A practical method has been presented for polarization sensitive localization based super-resolution microscopy using a birefringent dual wedge. The measurement of the polarization degree at the single molecule level can reveal the chemical and physical properties of the local environment of the fluorescent dye molecule and can hence provide information about the sub-diffraction sized structure of biological samples. Polarization sensitive STORM imaging of the F-Actins proved correlation between the orientation of fluorescent dipoles and the axis of the fibril...
March 22, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#12
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#13
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327774/huge-magnetoresistance-induced-by-half-metal-semiconductor-phase-transition-in-a-one-dimensional-spin-chain-a-first-principles-study
#14
Jing Zeng, Ke-Qiu Chen
In experimental studies, magnetoresistance (MR) values of 10(3) are hard to reach for conventional single-molecule spin-valves. Motivated by a recent experiment [Nano Lett., 2016, 16, 577-582], where tailored Co-salophene-based all-spin molecular devices are successfully realized, we demonstrate the functionality of a Co-salophene-based spin chain without magnetic electrodes. By using nonequilibrium Green's functions in combination with density functional theory, we find that the maximum MR ratio of this spin chain can reach 10(6) by manipulating its spins in a controlled way, which is several orders of magnitude higher than previously reported experimental values...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327758/a-dy4-single-molecule-magnet-and-its-gd-iii-tb-iii-ho-iii-and-er-iii-analogues-encapsulated-by-an-8-hydroxyquinoline-schiff-base-derivative-and-%C3%AE-diketonate-coligand
#15
Hong-Ling Gao, Xiao-Pu Zhou, Yan-Xia Bi, Hai-Yun Shen, Wen-Min Wang, Ni-Ni Wang, Yi-Xin Chang, Ru-Xia Zhang, Jian-Zhong Cui
Five new tetranuclear complexes based on an 8-hydroxyquinoline Schiff base derivative and the β-diketone coligand, [Ln4(acac)4L6(μ3-OH)2]·CH3CN·0.5CH2Cl2 (Ln = Gd (1), Tb (2), Dy (3), Ho (4) and Er (5); HL = 5-(benzylidene)amino-8-hydroxyquinoline; acac = acetylacetonate) have been synthesized, and structurally and magnetically characterized. Complexes 1-5 have similar tetranuclear structures. Each Ln(III) ion is eight coordinated and its coordination polyhedra can be described as being in a distorted square-antiprismatic geometry...
March 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28327642/surface-chemistry-of-rare-earth-oxide-surfaces-at-ambient-conditions-reactions-with-water-and-hydrocarbons
#16
Elçin Külah, Laurent Marot, Roland Steiner, Andriy Romanyuk, Thomas A Jung, Aneliia Wäckerlin, Ernst Meyer
Rare-earth (RE) oxide surfaces are of significant importance for catalysis and were recently reported to possess intrinsic hydrophobicity. The surface chemistry of these oxides in the low temperature regime, however, remains to a large extent unexplored. The reactions occurring at RE surfaces at room temperature (RT) in real air environment, in particular, in presence of polycyclic aromatic hydrocarbons (PAHs), were not addressed until now. Discovering these reactions would shed light onto intermediate steps occurring in automotive exhaust catalysts before reaching the final high operational temperature and full conversion of organics...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28324628/linear-trinuclear-cobalt-complexes-with-o-phenylene-bis-silylamido-ligands
#17
Kirill Yu Monakhov, Jan van Leusen, Paul Koegerler, Emilie-Laure Zins, Esmaïl Alikhani, Moniek Tromp, Andreas Danopoulos, Pierre Braunstein
Transamination of [Co{N(SiMe3)2}2]2 with C6H4(NHSiiPr3)2 gave the linear trinuclear [(Coter{N(SiMe3)2}{μ-η-(o-C6H4(κNSiiPr3)2)2}Coint)] (1) (Coter, Coint = terminal, internal Co, respectively), with 3-coordinate Coter, and Coint 'sandwiched' between the o-phenylenes of the two ligands; experimental and computational data support CoII centres and ditopic o-amido-imino-cyclohexen-allyl ligands; magnetic studies reveal intermetallic ferromagnetic interactions and single-molecule magnet (SMM) character. One-electron reduction of 1 gave the salt 4 with the anion isostructural to 1...
March 21, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28324612/quantitative-image-analysis-of-single-molecule-mrna-dynamics-in-living-cells
#18
José Rino, Ana C de Jesus, Maria Carmo-Fonseca
Single mRNA molecules can be imaged in living cells by a method that consists in genetically inserting binding sites for a bacteriophage protein in the gene of interest. The resulting reporter transgene is then integrated in the genome of cells that express the phage protein fused to a fluorescent tag. Upon transcription, binding of the fluorescent protein to its target sequence makes the RNA visible. With this approach it is possible to track, in real time, the life cycle of a precursor mRNA at the site of transcription in the nucleus and transport of mature mRNA to the cytoplasm...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324598/introduction-to-modern-methods-in-light-microscopy
#19
Joel Ryan, Abby R Gerhold, Vincent Boudreau, Lydia Smith, Paul S Maddox
For centuries, light microscopy has been a key method in biological research, from the early work of Robert Hooke describing biological organisms as cells, to the latest in live-cell and single-molecule systems. Here, we introduce some of the key concepts related to the development and implementation of modern microscopy techniques. We briefly discuss the basics of optics in the microscope, super-resolution imaging, quantitative image analysis, live-cell imaging, and provide an outlook on active research areas pertaining to light microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28322800/single-molecule-mtdna-fiber-fish-for-analyzing-numtogenesis
#20
Dal-Hoe Koo, Bhupendra Singh, Jiming Jiang, Bernd Friebe, Bikarm S Gill, Paul D Chastain, Upender Manne, Hemant K Tiwari, Keshav K Singh
Somatic human cells contains thousands of copies of mitochondrial DNA (mtDNA). In eukaryotes, natural transfer of mtDNA into the nucleus generates nuclear mitochondrial DNA (NUMT) copies in eukaryotes. We name this phenomenon as "numtogenesis". Numtogenesis is a well-established evolutionary process reported in various sequenced eukaryotic genomes. We have established a molecular tool to rapidly detect and analyze NUMT insertions in whole genomes. To date, NUMT analyses depend on deep genome sequencing combined with comprehensive computational analyses of the whole genome...
March 17, 2017: Analytical Biochemistry
keyword
keyword
67788
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"