keyword
MENU ▼
Read by QxMD icon Read
search

nucleic acids

keyword
https://www.readbyqxmd.com/read/28106879/bacterial-community-segmentation-facilitates-the-prediction-of-ecosystem-function-along-the-coast-of-the-western-antarctic-peninsula
#1
Jeff S Bowman, Linda A Amaral-Zettler, Jeremy J Rich, Catherine M Luria, Hugh W Ducklow
Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106804/ultrafast-electronic-deactivation-dynamics-of-xanthosine-monophosphate
#2
Katharina Röttger, Rebecca Stellmacher, Mayra C Stuhldreier, Friedrich Temps
Ultrafast energy dissipation is a crucial factor for the photostability of DNA and RNA, but even some of the key electronic deactivation pathways in monomeric nucleic acid building stones are still controversial. Here, we report on the excited-state dynamics of the rare nucleotide xanthosine monophosphate as a function of deprotonation state (XMP vs. XMP - ) and excitation wavelength ( λ pump = 278-243 nm) by femtosecond time-resolved fluorescence and absorption spectroscopy. We show that the predominating relaxation channel leads to a return of the photo-excited molecules to the electronic ground state in τ∼1 ps...
January 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28106202/a-colorimetric-sensing-platform-based-upon-recognizing-hybridization-chain-reaction-products-with-oligonucleotide-modified-gold-nanoparticles-through-triplex-formation
#3
Li Zou, Ruimin Li, Manjun Zhang, Yanwei Luo, Nian Zhou, Jing Wang, Liansheng Ling
A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal...
January 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28105843/adaptive-pcr-based-on-hybridization-sensing-of-mirror-image-l-dna
#4
Nicholas M Adams, William E Gabella, Austin N Hardcastle, Frederick R Haselton
Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that these hybridization events occur, current PCR approaches rely on temperature set points and reaction contents that are optimized and maintained using rigid thermal cycling programs and stringent sample preparation procedures. This report describes a fundamentally simpler and more robust PCR design that dynamically controls thermal cycling by more directly monitoring the two key hybridization events during the reaction...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28105831/nucleic-acid-biosensors-recent-advances-and-perspectives
#5
Yan Du, Shaojun Dong
No abstract text is available yet for this article.
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28105473/recent-applications-of-the-combination-of-mesoporous-silica-nanoparticles-with-nucleic-acids-development-of-bioresponsive-devices-carriers-and-sensors
#6
REVIEW
Rafael R Castillo, Alejandro Baeza, María Vallet-Regí
The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Such is the importance of these gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples reporting the use of combination of nanoparticles with nucleic acids, so boundaries are demanded. Following this premise, this review will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles...
January 20, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28104913/exosome-derived-micrornas-in-cancer-metabolism-possible-implications-in-cancer-diagnostics-and-therapy
#7
REVIEW
Marco Tomasetti, Wan Lee, Lory Santarelli, Jiri Neuzil
Malignant progression is greatly affected by dynamic cross-talk between stromal and cancer cells. Exosomes are secreted nanovesicles that have key roles in cell-cell communication by transferring nucleic acids and proteins to target cells and tissues. Recently, MicroRNAs (miRs) and their delivery in exosomes have been implicated in physiological and pathological processes. Tumor-delivered miRs, interacting with stromal cells in the tumor microenvironment, modulate tumor progression, angiogenesis, metastasis and immune escape...
January 20, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28104433/micrornas-in-the-pathophysiology-of-epilepsy
#8
REVIEW
Gary P Brennan, David C Henshall
Temporal lobe epilepsy is a common and often drug-resistant seizure disorder. The underlying pathological processes which give rise to the development of spontaneous seizures include neuroinflammation, cell loss, neurogenesis and dendritic abnormalities and many of these are driven by insult-induced changes in gene expression and gene expression regulation. MicroRNAs are powerful modulators of post-transcriptional gene expression which are dysregulated during epileptogenesis. The advent of locked nucleic acid (LNA) based inhibitory methods and mimic technology has facilitated in vivo functional assessment of these molecules in epilepsy...
January 16, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28103530/an-anti-oxidant-%C3%AE-lipoic-acid-conjugated-oleoyl-sn-phosphatidylcholineas-a-helper-lipid-in-cationic-liposomal-formulations
#9
Priya Dharmalingam, Balakrishna Marrapu, Chandrashekhar Voshavar, Rasagna Nadella, Vignesh Kumar Rangasami, R V Shaji, Salar Abbas, R B N Prasad, Shiva Shanker Kaki, Srujan Marepally
Development of safe non-viral carrier systems for efficient intra-cellular delivery of drugs and genes hold promise in the area of translational research. Liposome based delivery systems have emerged as one of the attractive strategies for efficient delivery of drugs and nucleic acids. To this end, number of investigations was carried on liposomal formulations using lipids for achieving higher efficiency in transfection with lower cytotoxicities. In our efforts to develop safer and efficient liposomal delivery systems, we synthesized a novel anti-oxidant lipid, α-lipoyl, oleyl-sn-phosphatidylcholine (LOPC) and used as a helper lipid in combination with a cationic amphiphile, Di-Stearyl Dihydroxy Ethyl Ammonium Chloride (DSDEAC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) at varying concentrations of LOPC...
January 10, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28103440/carbon-nanotubes-mediate-fusion-of-lipid-vesicles
#10
Ramachandra Moorthy Bhaskara, Stephanie M Linker, Martin Vögele, Juergen Koefinger, Gerhard Hummer
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets...
January 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28102964/plasmonic-chirality-imprinting-on-nucleobase-displaying-supramolecular-nanohelices-by-metal-nucleobase-recognition
#11
Yiyang Lin, E Thomas Pashuck, Michael R Thomas, Nadav Amdursky, Shih-Ting Wang, Lesley W Chow, Molly M Stevens
Supramolecular self-assembly is an important process that enables the conception of complex structures mimicking biological motifs. Herein, we constructed helical fibrils through chiral self-assembly of nucleobase-peptide conjugates (NPCs), where achiral nucleobases are helically displayed on the surface of fibrils, comparable to polymerized nucleic acids. Selective binding between DNA and the NPC fibrils was observed with fluorescence polarization. Taking advantage of metal-nucleobase recognition, we highlight the possibility of deposition/assembly of plasmonic nanoparticles onto the fibrillar constructs...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28102461/rnahelix-computational-modeling-of-nucleic-acid-structures-with-watson-crick-and-non-canonical-base-pairs
#12
Dhananjay Bhattacharyya, Sukanya Halder, Sankar Basu, Debasish Mukherjee, Prasun Kumar, Manju Bansal
Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs...
January 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28102441/the-effect-of-land-use-on-bacterial-communities-in-saline-alkali-soil
#13
Mu Peng, Hongbai Jia, Qiuyu Wang
Saline-alkali soil can inhibit the growth of crops as a consequence of cellular damage through oxidation of lipids and proteins and degradation of nucleic acids, ultimately leading to cell death. The bacterial community composition and diversity in saline-alkali soil across different land uses, such as agricultural land, forest land, and grassland, were evaluated using high-throughput sequencing of the bacterial 16S rRNA gene. Significant differences in the soil physicochemical characteristics and bacterial community among different land uses were observed in this study...
January 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28101966/the-free-energy-of-locking-a-ring-changing-a-deoxyribonucleoside-to-a-locked-nucleic-acid
#14
You Xu, Alessandra Villa, Lennart Nilsson
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28101245/apobec3b-expression-in-human-leptomeninges-and-meningiomas
#15
Mahlon D Johnson, Jay E Reeder, Mary O'Connell
Nucleic acid-editing enzymes of the apolipoprotein B mRNA-editing enzyme (APOBEC) family have been associated with somatic mutation in cancer. However, the role of APOBEC catalytic subunit 3B (APOBEC3B) editing in the pathogenesis of base substitutions in meningiomas is unknown. In the present study, the expression of APOBEC3B was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analyses in five fetal and one adult human leptomeninges and 38 meningiomas. Genomic DNA was sequenced using the Illumina Tru-Seq Cancer Panel...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100696/the-24th-annual-nucleic-acids-research-database-issue-a-look-back-and-upcoming-changes
#16
Michael Y Galperin, Xosé M Fernández-Suárez, Daniel J Rigden
No abstract text is available yet for this article.
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100695/mapping-the-affinity-landscape-of-thrombin-binding-aptamers-on-2-f-ana-dna-chimeric-g-quadruplex-microarrays
#17
Jory Lietard, Hala Abou Assi, Irene Gómez-Pinto, Carlos González, Mark M Somoza, Masad J Damha
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2'-Fluoroarabinonucleic acid (2'F-ANA) is a prime candidate for such use in microarrays. Indeed, 2'F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100494/quantification-of-bk-virus-standards-by-quantitative-real-time-pcr-and-droplet-digital-pcr-is-confounded-by-multiple-virus-populations-in-the-who-bkv-international-standard
#18
Allen C Bateman, Alexander L Greninger, Ederlyn E Atienza, Ajit P Limaye, Keith R Jerome, Linda Cook
BACKGROUND: The WHO recently released a BK virus (BKV) international standard. This study evaluated the WHO international standard and commercially available BKV standards by quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). METHODS: WHO, Exact Diagnostics, Acrometrix, and Zeptometrix BKV standards were tested by qPCR and ddPCR. Two preparations of NIST BKV clones were also tested. Nucleic acid was extracted with the Roche MP96 and MPLC, followed by quantification in duplicate...
January 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28100311/the-evaluation-of-three-different-bottles-in-bactec-9240-automated-blood-culture-system-and-direct-identification-of-candida-species-to-shorten-the-turnaround-time-of-blood-culture
#19
Egemen Gokbolat, Yasemin Oz, Selma Metintas
Candida spp. are the most common causes of fungemia. Rapid and accurate diagnostic methods are very important for appropriate management of candidemia. At present, blood culture is the essential diagnostic test despite it has a long detection time and low sensitivity rate. We aimed to investigate the ways to shorten the turnaround time from blood culture collection to final identification in candidemia. Sixty clinical bloodstream isolates of Candida were included and the Plus Aerobic/F, Peds Plus/F and Mycosis IC/F (MICF) bottles were used with BACTEC 9240 blood culture instrument...
January 16, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28099008/critical-analysis-of-rate-constants-and-turnover-frequency-in-nucleic-acid-templated-reactions-reaching-terminal-velocity
#20
Dalu Chang, Eric Lindberg, Nicolas Winssinger
Nucleic acid-templated reactions have attracted significant attention for nucleic acid sensing and imaging. The level of signal amplification obtained from templated reactions is a function of the template turnover, wherein the template acts as the catalyst. Herein, we report the application of a pyridinium linker that immolates upon photocatalytic reduction with a ru-thenium complex to yield the fastest nucleic acid tem-plated reaction reported to date. We show that the tem-plated reaction turnover is limited by the duplex dissoci-ation kinetics beyond probes longer than a 6-mer and proceeded fastest for a 5-mer PNA probe...
January 18, 2017: Journal of the American Chemical Society
keyword
keyword
22731
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"