DNA Polymerase Variants with High Processivity and Accuracy for Encoding and Decoding Locked Nucleic Acid Sequences

2020 ◽  
Vol 142 (51) ◽  
pp. 21530-21537
Author(s):  
Hidekazu Hoshino ◽  
Yuuya Kasahara ◽  
Masayasu Kuwahara ◽  
Satoshi Obika
Keyword(s):  
Nucleic Acid ◽  
Dna Polymerase ◽  
Locked Nucleic Acid ◽  
Nucleic Acid Sequences

scholarly journals REQUIREMENTS FOR EFFICIENT PCR CLAMPING BY LOCKED NUCLEIC ACID OLIGONUCLEOTIES FOR SIMPLE AND SENSITIVE DETECTION OF SOMATIC MUTATIONS

2018 ◽  
Vol 17 (4) ◽  
pp. 30-35
Author(s):  
V. A. Shamanin ◽  
I. V. Karpov ◽  
E. E. Pisareva ◽  
N. I. Gutkina ◽  
S. P. Kovalenko
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Dna Polymerase ◽  
Real Time Pcr ◽  
Sanger Sequencing ◽  
Somatic Mutations ◽  
Locked Nucleic Acid ◽  
Sensitive Detection ◽  
Taq Dna Polymerase ◽  
Detection Of Mutations

PCR clamping/wild-type blocking PCR with non-extendable locked nucleic acid (LNA) oligonucleotides is used for sensitive detection of somatic mutations in tumors. Various  versions of the technique use different DNA polymerases and LNA oligonucleotides with and  without additional phosphorothioate modifications. Here we studied requirements for successful  PCR clamping with LNA oligonucleotides and Taq DNA polymerase for analysis of mutations in  KRAS and BRAF genes by means of real-time PCR and Sanger sequencing. We found that  addition of phosphorothioate linkages at the 5’-end of LNA oligonucleotide to protect from 5’- exonuclease activity of Taq DNA polymerase did not improve clamping. For most target  sequences, efficient clamping was observed at melting temperature of LNA oligonucleotide  20‑25°C above annealing/extension temperature of the PCR with a 2-step protocol. Under such  conditions, simple and sensitive detection of mutations in KRAS and BRAF genes was feasible using real-time PCR with TaqMan probes or Sanger sequencing.

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 Structural motifs and intramolecular interactions in non-canonical G-quadruplexes

2021 ◽  
Author(s):  
Jagannath Jana ◽  
Swantje Mohr ◽  
Yoanes Maria Vianney ◽  
Klaus Weisz
Keyword(s):  
Nucleic Acid ◽  
Structural Features ◽  
Intramolecular Interactions ◽  
Structural Motifs ◽  
Nucleic Acid Sequences

G-rich nucleic acid sequences encompassing G-tracts of varying lengths can fold into different non-canonical G-quadruplexes with distinct structural features.

scholarly journals Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021 ◽  
Author(s):  
Noemi Bellassai ◽  
Roberta D’Agata ◽  
Giuseppe Spoto
Keyword(s):  
Nucleic Acid ◽  
Structural Properties ◽  
Molecular Beacon ◽  
Dna Origami ◽  
Molecular Beacons ◽  
Conformational Polymorphism ◽  
Functional Systems ◽  
Similarities And Differences ◽  
Nucleic Acid Structures ◽  
Nucleic Acid Sequences

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

Trinucleotide Cap Analogue Bearing a Locked Nucleic Acid Moiety: Synthesis, mRNA Modification, and Translation for Therapeutic Applications

2021 ◽  
Author(s):  
Annamalai Senthilvelan ◽  
Tyson Vonderfecht ◽  
Muthian Shanmugasundaram ◽  
Indra Pal ◽  
Jason Potter ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Acid Moiety ◽  
Therapeutic Applications
Sign in / Sign up

Export Citation Format

Share Document