scholarly journals Visual detection and differentiation of Classic Swine Fever Virus strains using nucleic acid sequence-based amplification (NASBA) and G-quadruplex DNAzyme assay

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Xiaolu Lu ◽  
Xueyao Shi ◽  
Gege Wu ◽  
Tiantian Wu ◽  
Rui Qin ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Visual Detection ◽  
Fever Virus ◽  
Nucleic Acid Sequence ◽  
G Quadruplex ◽  
Classic Swine Fever Virus ◽  
Virus Strains

Gold-Aptamer-Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences

2019 ◽  
Author(s):  
Veeren Chauhan ◽  
Mohamed M Elsutohy ◽  
C Patrick McClure ◽  
Will Irving ◽  
Neil Roddis ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
In Silico ◽  
Point Of Care ◽  
Lateral Flow ◽  
Nucleic Acid Sequence ◽  
In Silico Screening ◽  
Lateral Flow Assays ◽  
Life Threatening ◽  
Software And Hardware ◽  
Nucleic Acid Sequences

<p>Enteroviruses are a ubiquitous mammalian pathogen that can produce mild to life-threatening disease. Bearing this in mind, we have developed a rapid, accurate and economical point-of-care biosensor that can detect a nucleic acid sequences conserved amongst 96% of all known enteroviruses. The biosensor harnesses the physicochemical properties of gold nanoparticles and aptamers to provide colourimetric, spectroscopic and lateral flow-based identification of an exclusive enteroviral RNA sequence (23 bases), which was identified through in silico screening. Aptamers were designed to demonstrate specific complementarity towards the target enteroviral RNA to produce aggregated gold-aptamer nanoconstructs. Conserved target enteroviral nucleic acid sequence (≥ 1x10<sup>-7</sup> M, ≥1.4×10<sup>-14</sup> g/mL), initiates gold-aptamer-nanoconstructs disaggregation and a signal transduction mechanism, producing a colourimetric and spectroscopic blueshift (544 nm (purple) > 524 nm (red)). Furthermore, lateral-flow-assays that utilise gold-aptamer-nanoconstructs were unaffected by contaminating human genomic DNA, demonstrated rapid detection of conserved target enteroviral nucleic acid sequence (< 60 s) and could be interpreted with a bespoke software and hardware electronic interface. We anticipate our methodology will translate in-silico screening of nucleic acid databases to a tangible enteroviral desktop detector, which could be readily translated to related organisms. This will pave-the-way forward in the clinical evaluation of disease and complement existing strategies at overcoming antimicrobial resistance.</p>

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

Rapid and simultaneous detection of three major diarrhea-causing viruses by multiplex real-time nucleic acid sequence-based amplification

2015 ◽  
Vol 160 (3) ◽  
pp. 719-725 ◽  
Author(s):  
Qiu-Hua Mo ◽  
Hai-Bo Wang ◽  
Hui-Rong Dai ◽  
Ji-Can Lin ◽  
Hua Tan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Simultaneous Detection ◽  
Nucleic Acid Sequence

Complete nisin A gene cluster from Lactococcus lactis M78 (HM219853) — obtaining the nucleic acid sequence and comparing it to other published nisin sequences

2011 ◽  
Vol 33 (3) ◽  
pp. 217-221 ◽  
Author(s):  
Aljoša Trmčić ◽  
John Samelis ◽  
Christophe Monnet ◽  
Irena Rogelj ◽  
Bojana Bogovič Matijašić
Keyword(s):  
Nucleic Acid ◽  
Gene Cluster ◽  
Lactococcus Lactis ◽  
Nucleic Acid Sequence

scholarly journals The Untranslated Regions of Classic Swine Fever Virus RNA Trigger Apoptosis

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88863 ◽  
Author(s):  
Wei-Li Hsu ◽  
Chung-Lun Chen ◽  
Shi-Wei Huang ◽  
Chia-Chen Wu ◽  
I-Hsuan Chen ◽  
...  
Keyword(s):  
Fever Virus ◽  
Untranslated Regions ◽  
Virus Rna ◽  
Classic Swine Fever Virus

Viral nucleic acid sequence transfer between fungi and plants

1997 ◽  
Vol 13 (7) ◽  
pp. 260-261 ◽  
Author(s):  
Joachim R. Marienfeld ◽  
Michael Unseld ◽  
Petra Brandt ◽  
Axel Brennicke
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Viral Nucleic Acid

Nucleic Acid Sequence Database IV

DNA ◽  
1982 ◽  
Vol 1 (4) ◽  
pp. 365-374 ◽  
Author(s):  
H.R. CHEN ◽  
M.O. DAYHOFF ◽  
W.C. BARKER ◽  
L.T. HUNT ◽  
L.-S. YEH ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Sequence Database

Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species

1999 ◽  
Vol 38 (1-2) ◽  
pp. 81-90 ◽  
Author(s):  
Myra N. Widjojoatmodjo ◽  
Annemarie Borst ◽  
Rianne A.F. Schukkink ◽  
Adrienne T.A. Box ◽  
Nicole M.M. Tacken ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Candida Species ◽  
Nucleic Acid Sequence
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