scholarly journals A systematic evolution of ligands by exponential enrichment workflow with consolidated counterselection to efficiently isolate high‐affinity aptamers

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Jonah C. Rosch ◽  
Daniel A. Balikov ◽  
Franklin Gong ◽  
Ethan S. Lippmann
Keyword(s):  
High Affinity ◽  
Systematic Evolution ◽  
Exponential Enrichment

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 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.

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.

scholarly journals Using Aptamers for Cancer Biomarker Discovery

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Yun Min Chang ◽  
Michael J. Donovan ◽  
Weihong Tan
Keyword(s):  
Iterative Method ◽  
Cancer Diagnosis ◽  
Biomarker Discovery ◽  
Clinical Medicine ◽  
High Specificity ◽  
Specific Target ◽  
Synthetic Dna ◽  
High Affinity ◽  
Systematic Evolution ◽  
Exponential Enrichment

Aptamers are single-stranded synthetic DNA- or RNA-based oligonucleotides that fold into various shapes to bind to a specific target, which includes proteins, metals, and molecules. Aptamers have high affinity and high specificity that are comparable to that of antibodies. They are obtained using iterative method, called (Systematic Evolution of Ligands by Exponential Enrichment) SELEX and cell-based SELEX (cell-SELEX). Aptamers can be paired with recent advances in nanotechnology, microarray, microfluidics, and other technologies for applications in clinical medicine. One particular area that aptamers can shed a light on is biomarker discovery. Biomarkers are important in diagnosis and treatment of cancer. In this paper, we will describe ways in which aptamers can be used to discover biomarkers for cancer diagnosis and therapeutics.

scholarly journals Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sepehr Manochehry ◽  
Erin M. McConnell ◽  
Yingfu Li
Keyword(s):  
Binding Site ◽  
De Novo ◽  
Mobility Shift ◽  
High Affinity ◽  
Two Component ◽  
Systematic Evolution ◽  
Dimeric Protein ◽  
Enrichment Experiments ◽  
Exponential Enrichment ◽  
Electrophoretic Mobility Shift Assays

AbstractHigh-affinity aptamers can be derived de novo by using stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments or can be engineered post SELEX via dimerization of selected aptamers. Using electrophoretic mobility shift assays, we studied a series of heterodimeric and homodimeric aptamers, constructed from two DNA aptamers with distinct primary sequences and secondary structures, previously isolated for VEGF-165, a homodimeric protein. We investigated four factors envisaged to impact the affinity of a dimeric aptamer to a dimeric protein: (1) length of the linker between two aptamer domains, (2) linking orientation, (3) binding-site compatibility of two component aptamers in a heterodimeric aptamer, and (4) steric acceptability of the two identical aptamers in a homodimeric aptamer. All heterodimeric aptamers for VEGF-165 were found to exhibit monomeric aptamer-like affinity and the lack of affinity enhancement was attributed to binding-site overlap by the constituent aptamers. The best homodimeric aptamer showed 2.8-fold better affinity than its monomeric unit (Kd = 13.6 ± 2.7 nM compared to 37.9 ± 14 nM), however the barrier to further affinity enhancement was ascribed to steric interference of the constituent aptamers. Our findings point to the need to consider the issues of binding-site compatibility and spatial requirement of aptamers for the development of dimeric aptamers capable of bivalent recognition. Thus, determinants highlighted herein should be assessed in future multimerization efforts.

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.

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