scholarly journals Characterization and Inkjet Printing of an RNA Aptamer for Paper-Based Biosensing of Ciprofloxacin

Biosensors ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 7 ◽  
Author(s):  
Jeannine Jaeger ◽  
Florian Groher ◽  
Jacqueline Stamm ◽  
Dieter Spiehl ◽  
Johannes Braun ◽  
...  
Keyword(s):  
Low Cost ◽  
Rna Aptamers ◽  
Potential Range ◽  
Rna Aptamer ◽  
Proof Of Concept ◽  
Multiple Antibiotic Resistance ◽  
High Affinity ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Relevant Range

The excessive use of antibiotics in food-producing animals causes a steady rise of multiple antibiotic resistance in foodborne bacteria. Next to sulfonamides, the most common antibiotics groups are fluoroquinolones, aminoglycosides, and ß-lactams. Therefore, there is a need for a quick, efficient, and low-cost detection procedure for antibiotics. In this study, we propose an inkjet-printed aptamer-based biosensor developed for the detection of the fluoroquinolone ciprofloxacin. Due to their extraordinary high affinity and specificity, aptamers are already widely used in various applications. Here we present a ciprofloxacin-binding RNA aptamer developed by systematic evolution of ligands by exponential enrichment (SELEX). We characterized the secondary structure of the aptamer and determined the KD to 36 nM that allow detection of antibiotic contamination in a relevant range. We demonstrate that RNA aptamers can be inkjet-printed, dried, and resolved while keeping their functionality consistently intact. With this proof of concept, we are paving the way for a potential range of additional aptamer-based, printable biosensors.

scholarly journals Specific inhibition of FGF5-induced cell proliferation by RNA aptamers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryo Amano ◽  
Masato Namekata ◽  
Masataka Horiuchi ◽  
Minami Saso ◽  
Takuya Yanagisawa ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Surface Plasmon Resonance ◽  
Growth Factor ◽  
Hair Growth ◽  
Rna Aptamers ◽  
Specific Inhibition ◽  
Fibroblast Growth ◽  
High Affinity ◽  
Systematic Evolution ◽  
Exponential Enrichment

AbstractFibroblast growth factor 5 (FGF5) is a crucial regulator of hair growth and an oncogenic factor in several human cancers. To generate FGF5 inhibitors, we performed Systematic Evolution of Ligands by EXponential enrichment and obtained novel RNA aptamers that have high affinity to human FGF5. These aptamers inhibited FGF5-induced cell proliferation, but did not inhibit FGF2-induced cell proliferation. Surface plasmon resonance demonstrated that one of the aptamers, F5f1, binds to FGF5 tightly (Kd = 0.7 ± 0.2 nM), but did not fully to FGF1, FGF2, FGF4, FGF6, or FGFR1. Based on sequence and secondary structure similarities of the aptamers, we generated the truncated aptamer, F5f1_56, which has higher affinity (Kd = 0.118 ± 0.003 nM) than the original F5f1. Since the aptamers have high affinity and specificity to FGF5 and inhibit FGF5-induced cell proliferation, they may be candidates for therapeutic use with FGF5-related diseases or hair disorders.

FEATURES OF ORGANOPHOSPHATES IMMOBILIZATION VIA STREPTAVIDIN-BIOTIN SYSTEM FOR EXPERIMENTS ON SELECTION OF APTAMERS

2020 ◽  
pp. 12-20
Author(s):  
D. A. Belinskaya ◽  
Yu. V. Chelusnova ◽  
V. V. Abzianidze ◽  
N. V. Goncharov
Keyword(s):  
Polyethylene Glycol ◽  
Organophosphorus Compounds ◽  
Binding Energies ◽  
Rna Aptamers ◽  
Main Method ◽  
Modeling Methods ◽  
Molecular Dynamics Methods ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Poisoning with organophosphorus compounds occupy one of the leading places in exotoxicosis. At the first stage, the detoxification of organophosphates can be provided with the help of DNA or RNA aptamers that bind the poison in the bloodstream. Currently, the main method of searching for aptamers is the experimental method of systematic evolution of ligands by exponential enrichment (SELEX). In the process of aptamer selection, the target molecule must be immobilized via the streptavidin-biotin complex. Since the poison molecule is small in size, to increase its availability for binding to aptamer, it is necessary to use a spacer between organophosphorus compounds and biotin. The aim of this work was to optimize the selection of aptamers for organophosphorus compounds by increasing the availability of a poison molecule immobilized via the streptavidin-biotin complex on the example of paraoxon. For this purpose, three spacers between organophosphorus compounds and biotin were tested using molecular modeling methods: three links of polyethylene glycol (3-PEG), four links of polyethylene glycol (4-PEG) and aminohexyl. The conformation of the biotinylated paraoxon complex with streptavidin and the interaction of paraoxon with the binding fragment of the aptamer were modeled using molecular docking and molecular dynamics methods. The ability of biotinylated paraoxon to bind to the aptamer has been evaluated by analyzing the surface area of the paraoxon available to the solvent, as well as by calculating the free binding energies. It has been shown that only in the case of aminohexyl immobilized paraoxon can contact the aptamer. At the final stage, the synthesis of paraoxon bound to biotin via aminohexyl was carried out.

scholarly journals Aptamer-iRNAs as Therapeutics for Cancer Treatment

2018 ◽  
Vol 11 (4) ◽  
pp. 108 ◽  
Author(s):  
Mario Soldevilla ◽  
Daniel Meraviglia-Crivelli de Caso ◽  
Ashwathi Menon ◽  
Fernando Pastor
Keyword(s):  
Cancer Therapy ◽  
Cancer Treatment ◽  
Antisense Oligonucleotides ◽  
Tertiary Structure ◽  
Potential Treatment ◽  
High Affinity ◽  
Different Types ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Aptamers are single-stranded oligonucleotides (ssDNA or ssRNA) that bind and recognize their targets with high affinity and specificity due to their complex tertiary structure. Aptamers are selected by a method called SELEX (Systematic Evolution of Ligands by EXponential enrichment). This method has allowed the selection of aptamers to different types of molecules. Since then, many aptamers have been described for the potential treatment of several diseases including cancer. It has been described over the last few years that aptamers represent a very useful tool as therapeutics, especially for cancer therapy. Aptamers, thanks to their intrinsic oligonucleotide nature, present inherent advantages over other molecules, such as cell-based products. Owing to their higher tissue penetrability, safer profile, and targeting capacity, aptamers are likely to become a novel platform for the delivery of many different types of therapeutic cargos. Here we focus the review on interfering RNAs (iRNAs) as aptamer-based targeting delivered agents. We have gathered the most reliable information on aptamers as targeting and carrier agents for the specific delivery of siRNAs, shRNA, microRNAs, and antisense oligonucleotides (ASOs) published in the last few years in the context of cancer therapy.

scholarly journals Bioapplications of Cell-SELEX-Generated Aptamers in Cancer Diagnostics, Therapeutics, Theranostics and Biomarker Discovery: A Comprehensive Review

Cancers ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 47 ◽  
Author(s):  
Xuehui Pang ◽  
Cheng Cui ◽  
Shuo Wan ◽  
Ying Jiang ◽  
Liangliang Zhang ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Drug Carriers ◽  
Cancer Diagnostics ◽  
High Affinity ◽  
Protein Receptors ◽  
Target Molecules ◽  
Systematic Evolution ◽  
Multifunctional Molecules ◽  
Exponential Enrichment ◽  
Single Stranded Oligonucleotide

Currently, functional single-stranded oligonucleotide probes, termed aptamers, generated by an iterative technology, Systematic Evolution of Ligands by Exponential Enrichment (SELEX), are utilized to selectively target molecules or cells with high affinity. Aptamers hold considerable promise as multifunctional molecules or conjugates for challenging nanotechnologies or bioapplications now and in the future. In this review, we first describe recent endeavors to select aptamers towards live cancer cells via cell-SELEX. We then introduce several characteristic applications of selected aptamers, especially in imaging, drug delivery and therapy. In part, these advances have been made possible via synthesis of aptamer-based nanomaterials, which, by their sizes, shapes, and physicochemical properties, allow such aptamer-nanomaterial complexes to function as signal reporters or drug carriers. We also describe how these aptamer-based molecular tools contribute to cancer biomarker discovery through high-affinity recognition of membrane protein receptors.

scholarly journals Preparation of a Specific ssDNA Aptamer for Brevetoxin-2 Using SELEX

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Rui-Yun Tian ◽  
Chao Lin ◽  
Shi-Yu Yu ◽  
Sheng Gong ◽  
Pan Hu ◽  
...  
Keyword(s):  
Research Direction ◽  
High Affinity ◽  
Complex Processes ◽  
Ssdna Aptamer ◽  
Coefficient Corrélation ◽  
Recognition Probe ◽  
Detection Probe ◽  
Systematic Evolution ◽  
Alternative Detection ◽  
Exponential Enrichment

The existing assays for detecting brevetoxin (BTX) depend on expensive equipment with a professional operator or on an antibody with limited stability, which requires complex processes, a high cost, and a considerable amount of time. The development of an alternative detection probe is another promising research direction. This paper reports the use of aptamers binding to BTX-2 in an analytical assay using the systematic evolution of ligands by exponential enrichment (SELEX). After 12 rounds of selection, the secondary structures of 25 sequences were predicted. Compared to other aptamers, Bap5 has relatively high affinity with the lowest dissociation constant of 4.83 μM, and IC50is 73.81 ng mL−1. A good linear regression formula ofy=30.688x-7.329with a coefficient correlation ofR2= 0.9798 was obtained using a biotin-avidin ELISA. Moreover, there is no cross-reaction with the detected marine toxins, except for BTX-2. Thus, Bap5 has potential to detect BTX-2 in shellfish in the future as a substitute for the recognition probe.

scholarly journals In vitro selection of an RNA aptamer yields an interleukin-6/interleukin-6 receptor interaction inhibitor

2021 ◽  
Author(s):  
Takehiro Ando ◽  
Mizuki Yamamoto ◽  
Yukio Takamori ◽  
Keita Tsukamoto ◽  
Daisuke Fuji ◽  
...  
Keyword(s):  
Interleukin 6 ◽  
In Vitro Selection ◽  
Receptor Interaction ◽  
Rna Aptamer ◽  
Cytokine Storm ◽  
Interleukin 6 Receptor ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

ABSTRACT Interleukin-6 (IL-6) binds to IL-6 receptor (IL-6R) subunit, related to autoimmune diseases and cytokine storm in COVID-19. In this study we performed Systematic Evolution of Ligands by Exponential enrichment (SELEX) and identified a novel RNA aptamer. This RNA aptamer not only bound to IL-6R with a dissociation constant of 200 nM, but also inhibited the interaction of IL-6R with IL-6.

scholarly journals An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment

2018 ◽  
Vol 200 (7) ◽  
Author(s):  
Katherine J. Fenstermacher ◽  
Vasudevan Achuthan ◽  
Thomas D. Schneider ◽  
Jeffrey J. DeStefano
Keyword(s):  
Core Promoter ◽  
Dna Polymerases ◽  
Promoter Sequence ◽  
Rna Polymerases ◽  
Sequence Specificity ◽  
High Affinity ◽  
Phage T7 ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Dna Primers

ABSTRACTDNA polymerases (DNAPs) recognize 3′ recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity toTaqand Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. TwoTaq-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls toTaqwere identified. TaqI contained 8 nucleotides (5′-CACTAAAG-3′) that matched the phage T3 RNAP “core” promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease−Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5′-ACTATAG-3′). For bothTaqand Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.IMPORTANCEThis work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity forTaqand Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.

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