scholarly journals Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion

2021 ◽  
Vol 22 (19) ◽  
pp. 10846
Author(s):  
Kien Hong Trinh ◽  
Ulhas Sopanrao Kadam ◽  
Jinnan Song ◽  
Yuhan Cho ◽  
Chang Ho Kang ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
High Specificity ◽  
Cross Reactivity ◽  
Dna Aptamers ◽  
Label Free ◽  
Wide Range ◽  
Label Free Detection ◽  
Detection Mode ◽  
Aptamer Sensor

Fenitrothion is an insecticide belonging to the organophosphate family of pesticides that is widely used around the world in agriculture and living environments. Today, it is one of the most hazardous chemicals that causes severe environmental pollution. However, detection of fenitrothion residues in the environment is considered a significant challenge due to the small molecule nature of the insecticide and lack of molecular recognition elements that can detect it with high specificity. We performed in vitro selection experiments using the SELEX process to isolate the DNA aptamers that can bind to fenitrothion. We found that newly discovered DNA aptamers have a strong ability to distinguish fenitrothion from other organophosphate insecticides (non-specific targets). Furthermore, we identified a fenitrothion-specific aptamer; FenA2, that can interact with Thioflavin T (ThT) to produce a label-free detection mode with a Kd of 33.57 nM (9.30 ppb) and LOD of 14 nM (3.88 ppb). Additionally, the FenA2 aptamer exhibited very low cross-reactivity with non-specific targets. This is the first report showing an aptamer sensor with a G4-quadruplex-like structure to detect fenitrothion. Moreover, these aptamers have the potential to be further developed into analytical tools for real-time detection of fenitrothion from a wide range of samples.

scholarly journals Predicting Future Prospects of Aptamers in Field-Effect Transistor Biosensors

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 680 ◽  
Author(s):  
Cao-An Vu ◽  
Wen-Yih Chen
Keyword(s):  
Small Molecules ◽  
Field Effect ◽  
Field Effect Transistor ◽  
Field Effect Transistors ◽  
High Specificity ◽  
Label Free ◽  
Sensing Technology ◽  
Wide Range ◽  
Label Free Detection ◽  
Effect Transistor

Aptamers, in sensing technology, are famous for their role as receptors in versatile applications due to their high specificity and selectivity to a wide range of targets including proteins, small molecules, oligonucleotides, metal ions, viruses, and cells. The outburst of field-effect transistors provides a label-free detection and ultra-sensitive technique with significantly improved results in terms of detection of substances. However, their combination in this field is challenged by several factors. Recent advances in the discovery of aptamers and studies of Field-Effect Transistor (FET) aptasensors overcome these limitations and potentially expand the dominance of aptamers in the biosensor market.

scholarly journals PCR-free, label-free detection of sequence-specific DNA with single-molecule sensitivity using in vitro N-hybrid system in microfluidic drops

2022 ◽  
Author(s):  
Yizhe Zhang ◽  
David A Weitz
Keyword(s):  
Single Molecule ◽  
High Specificity ◽  
Label Free ◽  
Hybrid Strategy ◽  
Single Molecule Level ◽  
Target Dna ◽  
Label Free Detection ◽  
Novel Method ◽  
Picoliter Droplet

We propose a novel method that can detect DNA with high specificity at the single-molecule level by employing the in vitro N-hybrid strategy realized in sub-picoliter microfluidic drops. It detects target DNA based on the specific interactions of the target-encoded proteins with their partner molecules, and achieves single-molecule sensitivity via signal-transduction and signal-amplification during gene-expression processes in a sub-picoliter droplet, therefore effectively avoiding complicated procedures in labeling-based methods or biases and artifacts in PCR-based methods.

Y-shaped probe for convenient and label-free detection of microRNA-21 in vitro

2016 ◽  
Vol 499 ◽  
pp. 8-14 ◽  
Author(s):  
Kui He ◽  
Rong Liao ◽  
Changqun Cai ◽  
Caishuang Liang ◽  
Chan Liu ◽  
...  
Keyword(s):  
Label Free ◽  
Label Free Detection

scholarly journals Secondary Structure Libraries for Artificial Evolution Experiments

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1671
Author(s):  
Ráchel Sgallová ◽  
Edward A. Curtis
Keyword(s):  
Secondary Structure ◽  
Sequence Space ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Random Mutagenesis ◽  
Nucleotide Composition ◽  
Artificial Evolution ◽  
Wide Range ◽  
Range Of Functions

Methods of artificial evolution such as SELEX and in vitro selection have made it possible to isolate RNA and DNA motifs with a wide range of functions from large random sequence libraries. Once the primary sequence of a functional motif is known, the sequence space around it can be comprehensively explored using a combination of random mutagenesis and selection. However, methods to explore the sequence space of a secondary structure are not as well characterized. Here we address this question by describing a method to construct libraries in a single synthesis which are enriched for sequences with the potential to form a specific secondary structure, such as that of an aptamer, ribozyme, or deoxyribozyme. Although interactions such as base pairs cannot be encoded in a library using conventional DNA synthesizers, it is possible to modulate the probability that two positions will have the potential to pair by biasing the nucleotide composition at these positions. Here we show how to maximize this probability for each of the possible ways to encode a pair (in this study defined as A-U or U-A or C-G or G-C or G.U or U.G). We then use these optimized coding schemes to calculate the number of different variants of model stems and secondary structures expected to occur in a library for a series of structures in which the number of pairs and the extent of conservation of unpaired positions is systematically varied. Our calculations reveal a tradeoff between maximizing the probability of forming a pair and maximizing the number of possible variants of a desired secondary structure that can occur in the library. They also indicate that the optimal coding strategy for a library depends on the complexity of the motif being characterized. Because this approach provides a simple way to generate libraries enriched for sequences with the potential to form a specific secondary structure, we anticipate that it should be useful for the optimization and structural characterization of functional nucleic acid motifs.

Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties

2004 ◽  
Vol 76 (7-8) ◽  
pp. 1547-1561 ◽  
Author(s):  
R. Nutiu ◽  
Shirley Mei ◽  
Zhongjie Liu ◽  
Y. Li
Keyword(s):  
Dna Sequences ◽  
Rational Design ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Pair Potential ◽  
Dna Aptamers ◽  
Dna Molecules ◽  
Dna Enzymes ◽  
Fluorescence Signaling

Single-stranded DNA molecules with ligand-binding ability and catalytic function, referred to as DNA aptamers and DNA enzymes, respectively, are special DNA sequences isolated from random-sequence DNA libraries by “in vitro selection”. These two new classes of artificial DNA molecules have the potential of being used as molecular tools in a variety of innovative applications ranging from biosensing to gene regulation. Our laboratory is interested in engineering fluorescence-signaling DNA aptamers and DNA enzymes that can be widely exploited for detection-directed applications. In this article, we will first discuss our recent efforts on the rational design of a new class of signaling aptamers denoted “structure- switching signaling aptamers”, which report target binding by switching structures from DNA/DNA duplex to DNA/target complex. We will then describe the in vitro selection of fluorescence-signaling DNA enzymes that exhibit a synchronized catalysis-signaling capability by cleaving a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by closely spaced fluorophore-quencher pair. Potential utilities of these signaling DNA molecules will also be discussed.

In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target

2017 ◽  
Vol 9 (4) ◽  
pp. 233-268 ◽  
Author(s):  
Annamaria Ruscito ◽  
Erin M. McConnell ◽  
Anna Koudrina ◽  
Ranganathan Velu ◽  
Christopher Mattice ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Vitro Selection ◽  
Dna Aptamers

In vitro selection of DNA aptamers against human osteosarcoma

2021 ◽  
Author(s):  
Khaliunsarnai Tsogtbaatar ◽  
Diana A. Sousa ◽  
Debora Ferreira ◽  
Atakan Tevlek ◽  
Halil Murat Aydın ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Dna Aptamers ◽  
Human Osteosarcoma ◽  
Selection Of

In Vitro Selection of New DNA Aptamers for Human Vascular Endothelial Growth Factor 165

ChemBioChem ◽  
2020 ◽  
Vol 21 (14) ◽  
pp. 2029-2036 ◽  
Author(s):  
Sepehr Manochehry ◽  
Jimmy Gu ◽  
Erin M. McConnell ◽  
Bruno J. Salena ◽  
Yingfu Li
Keyword(s):  
Vascular Endothelial Growth Factor ◽  
Growth Factor ◽  
In Vitro Selection ◽  
Dna Aptamers ◽  
Vascular Endothelial ◽  
Endothelial Growth Factor ◽  
Selection Of

scholarly journals 2′-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP)

2018 ◽  
Vol 19 (12) ◽  
pp. 3883 ◽  
Author(s):  
Jasmin Aldag ◽  
Tina Persson ◽  
Roland Hartmann
Keyword(s):  
In Vitro Selection ◽  
Binding Protein ◽  
High Specificity ◽  
Rna Aptamers ◽  
Pyrimidine Nucleotides ◽  
Consensus Sequences ◽  
Structure Probing ◽  
Potential Applications ◽  
Nuclease Degradation

Lipopolysaccaride binding protein (LBP), a glycosylated acute phase protein, plays an important role in the pathophysiology of sepsis. LBP binds with high affinity to the lipid part of bacterial lipopolysaccaride (LPS). Inhibition of the LPS-LBP interaction or blockage of LBP-mediated transfer of LPS monomers to CD14 may be therapeutical strategies to prevent septic shock. LBP is also of interest as a biomarker to identify septic patients at high risk for death, as LBP levels are elevated during early stages of severe sepsis. As a first step toward such potential applications, we isolated aptamers specific for murine LBP (mLBP) by in vitro selection from a library containing a 60-nucleotide randomized region. Modified RNA pools were transcribed in the presence of 2′-fluoro-modified pyrimidine nucleotides to stabilize transcripts against nuclease degradation. As verified for one aptamer experimentally, the selected aptamers adopt a “three-helix junction” architecture, presenting single-stranded 7-nt (5′-YGCTTCY) or 6-nt (5′-RTTTCY) consensus sequences in their core. The best binder (aptamer A011; Kd of 270 nM for binding to mLBP), characterized in more detail by structure probing and boundary analysis, was demonstrated to bind with high specificity to murine LBP.

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