scholarly journals RE-SELEX: Restriction Enzyme-Based Evolution of Structure-Switching Aptamer Biosensors 

2021 ◽  
Author(s):  
Aimee Alice Sanford ◽  
Alexandra E Rangel ◽  
Trevor A Feagin ◽  
Robert G Lowery ◽  
Hector S Argueta-Gonzalez ◽  
...  
Keyword(s):  
Small Molecule ◽  
Restriction Enzyme ◽  
High Affinity ◽  
Recognition Elements ◽  
Evolution Of Structure ◽  
Structure Switching

Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising...

scholarly journals RE-SELEX: Restriction Enzyme-Based Evolution of Structure-Switching Aptamer Biosensors

2021 ◽  
Author(s):  
Aimee A. Sanford ◽  
Alexandra E. Rangel ◽  
Trevor A. Feagin ◽  
Robert G. Lowery ◽  
Hector Argueta-Gonzalez ◽  
...  
Keyword(s):  
Conformational Change ◽  
Small Molecule ◽  
High Selectivity ◽  
Restriction Enzymes ◽  
Selection Methods ◽  
Recognition Elements ◽  
Evolution Of Structure ◽  
Significant Conformational Change ◽  
Structure Switching ◽  
General Method

<p><b>ABSTRACT </b></p> <p>Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to an output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 µM – 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small molecule targets.</p>

scholarly journals RE-SELEX: Restriction Enzyme-Based Evolution of Structure-Switching Aptamer Biosensors

2021 ◽  
Author(s):  
Aimee A. Sanford ◽  
Alexandra E. Rangel ◽  
Trevor A. Feagin ◽  
Robert G. Lowery ◽  
Hector Argueta-Gonzalez ◽  
...  
Keyword(s):  
Conformational Change ◽  
Small Molecule ◽  
High Selectivity ◽  
Restriction Enzymes ◽  
Selection Methods ◽  
Recognition Elements ◽  
Evolution Of Structure ◽  
Significant Conformational Change ◽  
Structure Switching ◽  
General Method

<p><b>ABSTRACT </b></p> <p>Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to an output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 µM – 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small molecule targets.</p>

scholarly journals RE-SELEX: Restriction Enzyme-Based Evolution of Structure-Switching Aptamer Biosensors

2021 ◽  
Author(s):  
Aimee A. Sanford ◽  
Alexandra E. Rangel ◽  
Trevor A. Feagin ◽  
Robert G. Lowery ◽  
Hector Argueta-Gonzalez ◽  
...  
Keyword(s):  
Conformational Change ◽  
Small Molecule ◽  
High Selectivity ◽  
Restriction Enzymes ◽  
Selection Methods ◽  
Recognition Elements ◽  
Evolution Of Structure ◽  
Significant Conformational Change ◽  
Structure Switching ◽  
General Method

<p><b>ABSTRACT </b></p> <p>Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to an output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 µM – 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small molecule targets.</p>

scholarly journals Challenges and Opportunities for Small Molecule Aptamer Development

2012 ◽  
Vol 2012 ◽  
pp. 1-20 ◽  
Author(s):  
Maureen McKeague ◽  
Maria C. DeRosa
Keyword(s):  
Molecular Recognition ◽  
Small Molecules ◽  
Small Molecule ◽  
Chemical Biology ◽  
Biological Functions ◽  
High Affinity ◽  
Challenges And Opportunities ◽  
Recognition Elements ◽  
Technical Challenges ◽  
Viable Approach

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

scholarly journals Recent Advances in Conventional Methods and Electrochemical Aptasensors for Mycotoxin Detection

Foods ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1437
Author(s):  
Jing Yi Ong ◽  
Andrew Pike ◽  
Ling Ling Tan
Keyword(s):  
Quantitative Analysis ◽  
Animal Feed ◽  
Cost Effective ◽  
Preventive Action ◽  
High Affinity ◽  
Recent Advances ◽  
Recognition Elements ◽  
Key Features ◽  
Pre Treatment ◽  
And Performance

The presence of mycotoxins in foodstuffs and feedstuffs is a serious concern for human health. The detection of mycotoxins is therefore necessary as a preventive action to avoid the harmful contamination of foodstuffs and animal feed. In comparison with the considerable expense of treating contaminated foodstuffs, early detection is a cost-effective way to ensure food safety. The high affinity of bio-recognition molecules to mycotoxins has led to the development of affinity columns for sample pre-treatment and the development of biosensors for the quantitative analysis of mycotoxins. Aptamers are a very attractive class of biological receptors that are currently in great demand for the development of new biosensors. In this review, the improvement in the materials and methodology, and the working principles and performance of both conventional and recently developed methods are discussed. The key features and applications of the fundamental recognition elements, such as antibodies and aptamers are addressed. Recent advances in aptasensors that are based on different electrochemical (EC) transducers are reviewed in detail, especially from the perspective of the diagnostic mechanism; in addition, a brief introduction of some commercially available mycotoxin detection kits is provided.

scholarly journals Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation

2018 ◽  
Vol 46 (13) ◽  
pp. e81-e81 ◽  
Author(s):  
Zongwen Wang ◽  
Haixiang Yu ◽  
Juan Canoura ◽  
Yingzhu Liu ◽  
Obtin Alkhamis ◽  
...  
Keyword(s):  
Small Molecule ◽  
Structure Switching

scholarly journals Lab-on-a-Chip Systems for Aptamer-Based Biosensing

Micromachines ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 220 ◽  
Author(s):  
Niazul I. Khan ◽  
Edward Song
Keyword(s):  
Point Of Care ◽  
Lab On A Chip ◽  
Review Article ◽  
Microfluidic Chips ◽  
High Affinity ◽  
Sensing Platforms ◽  
Personal Medicine ◽  
Paper Based Microfluidics ◽  
Recognition Elements ◽  
Analyte Detection

Aptamers are oligonucleotides or peptides that are selected from a pool of random sequences that exhibit high affinity toward a specific biomolecular species of interest. Therefore, they are ideal for use as recognition elements and ligands for binding to the target. In recent years, aptamers have gained a great deal of attention in the field of biosensing as the next-generation target receptors that could potentially replace the functions of antibodies. Consequently, it is increasingly becoming popular to integrate aptamers into a variety of sensing platforms to enhance specificity and selectivity in analyte detection. Simultaneously, as the fields of lab-on-a-chip (LOC) technology, point-of-care (POC) diagnostics, and personal medicine become topics of great interest, integration of such aptamer-based sensors with LOC devices are showing promising results as evidenced by the recent growth of literature in this area. The focus of this review article is to highlight the recent progress in aptamer-based biosensor development with emphasis on the integration between aptamers and the various forms of LOC devices including microfluidic chips and paper-based microfluidics. As aptamers are extremely versatile in terms of their utilization in different detection principles, a broad range of techniques are covered including electrochemical, optical, colorimetric, and gravimetric sensing as well as surface acoustics waves and transistor-based detection.

Discovery and characterization of potent small molecule inhibitors of the high affinity proline transporter

2009 ◽  
Vol 451 (3) ◽  
pp. 212-216 ◽  
Author(s):  
Xuan-Chuan Yu ◽  
Wandong Zhang ◽  
Arian Oldham ◽  
Eric Buxton ◽  
Shiv Patel ◽  
...  
Keyword(s):  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
High Affinity

scholarly journals Development of Aptamer-Based TID Assays Using Thermophoresis and Microarrays

Biosensors ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 124 ◽  
Author(s):  
Kurth ◽  
Witt ◽  
Bolten ◽  
Waniek ◽  
Kortmann ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Detection ◽  
Model System ◽  
Vascular Endothelial ◽  
Protein Biomarkers ◽  
High Affinity ◽  
Model Protein ◽  
Recognition Elements ◽  
Systematic Development ◽  
Endothelial Growth Factor

Aptamers are single-stranded oligonucleotides which can be used as alternative recognition elements for protein detection, because aptamers bind their targets with a high affinity similar to antibodies. Due to the targetinduced conformational changes of aptamers, these oligonucleotides can be applied in various biosensing platforms. In this work, aptamers directed against the vascular endothelial growth factor (VEGF) were used as a model system. VEGF plays a key role in physiological angiogenesis and vasculogenesis. Furthermore, VEGF is involved in the development and growth of cancer and other diseases like agerelated macular degeneration, rheumatoid arthritis, diabetes mellitus, and neurodegenerative disorders. Detecting the protein biomarker VEGF is therefore of great importance for medical research and diagnostics. In this research, VEGFbinding aptamers were investigated for the systematic development of a targetinduced dissociation (TID) assay utilizing thermophoresis and microarrays. The established aptamer-microarray allowed for the detection of 0.1 nM of VEGF. Furthermore, the systematic development of the TID method using the VEGF model protein could help to develop further TID assays for the detection of various protein biomarkers.

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