scholarly journals DNA-aptamer gating membranes

2015 ◽  
Vol 51 (25) ◽  
pp. 5471-5474 ◽  
Author(s):  
Thomas Schäfer ◽  
Veli Cengiz Özalp
Keyword(s):  
Adenosine Triphosphate ◽  
Small Molecule ◽  
Dna Aptamer ◽  
Membrane Barrier

This report describes a membrane barrier whose permeability is modulated through the recognition of a small-molecule target, adenosine triphosphate (ATP), by a DNA-aptamer.

DNA Aptamer‐Cyanine Complexes as Generic Colorimetric Small‐Molecule Sensors

2021 ◽  
Author(s):  
Obtin Alkhamis ◽  
Juan Canoura ◽  
Konstantin V. Bukhryakov ◽  
Anamary Tarifa ◽  
Anthony P. DeCaprio ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dna Aptamer

scholarly journals Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease

2020 ◽  
Vol 48 (20) ◽  
pp. e120-e120 ◽  
Author(s):  
Obtin Alkhamis ◽  
Weijuan Yang ◽  
Rifat Farhana ◽  
Haixiang Yu ◽  
Yi Xiao
Keyword(s):  
Ligand Binding ◽  
Small Molecule ◽  
High Throughput ◽  
Dna Aptamer ◽  
Label Free ◽  
General Applicability ◽  
Gold Standard Method ◽  
Characterization Methods ◽  
Increased Risk

Abstract In vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.

scholarly journals First report of the use of a saxitoxin–protein conjugate to develop a DNA aptamer to a small molecule toxin

Toxicon ◽  
2013 ◽  
Vol 61 ◽  
pp. 30-37 ◽  
Author(s):  
Sara M. Handy ◽  
Betsy Jean Yakes ◽  
Jeffrey A. DeGrasse ◽  
Katrina Campbell ◽  
Christopher T. Elliott ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dna Aptamer ◽  
First Report ◽  
Protein Conjugate

Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development

2021 ◽  
Author(s):  
Haixiang Yu ◽  
Obtin Alkhamis ◽  
Juan Canoura ◽  
Yingzhu Liu ◽  
Yi Xiao
Keyword(s):  
Small Molecule ◽  
Dna Aptamer ◽  
Sensor Development

scholarly journals In vitro isolation of class-specific oligonucleotide-based small-molecule receptors

2019 ◽  
Vol 47 (12) ◽  
pp. e71-e71 ◽  
Author(s):  
Weijuan Yang ◽  
Haixiang Yu ◽  
Obtin Alkhamis ◽  
Yingzhu Liu ◽  
Juan Canoura ◽  
...  
Keyword(s):  
Small Molecule ◽  
Colorimetric Detection ◽  
Cross Reactivity ◽  
Synthetic Cathinones ◽  
Designer Drugs ◽  
Dna Aptamer ◽  
Single Atom ◽  
Selection Strategy ◽  
Small Molecule Receptors

Abstract Class-specific bioreceptors are highly desirable for recognizing structurally similar small molecules, but the generation of such affinity elements has proven challenging. We here develop a novel ‘parallel-and-serial’ selection strategy for isolating class-specific oligonucleotide-based receptors (aptamers) in vitro. This strategy first entails parallel selection to selectively enrich cross-reactive binding sequences, followed by serial selection that enriches aptamers binding to a designated target family. As a demonstration, we isolate a class-specific DNA aptamer against a family of designer drugs known as synthetic cathinones. The aptamer binds to 12 diverse synthetic cathinones with nanomolar affinity and does not respond to 11 structurally similar non-target compounds, some of which differ from the cathinone targets by a single atom. This is the first account of an aptamer exhibiting a combination of broad target cross-reactivity, high affinity and remarkable specificity. Leveraging the qualities of this aptamer, instantaneous colorimetric detection of synthetic cathinones at nanomolar concentrations in biological samples is achieved. Our findings significantly expand the binding capabilities of aptamers as class-specific bioreceptors and further demonstrate the power of rationally designed selection strategies for isolating customized aptamers with desired binding profiles. We believe that our aptamer isolation approach can be broadly applied to isolate class-specific aptamers for various small molecule families.

Highly sensitive surface-enhanced Raman scattering detection of adenosine triphosphate based on core–satellite assemblies

2017 ◽  
Vol 9 (42) ◽  
pp. 6038-6043 ◽  
Author(s):  
Ya-Fei Tian ◽  
Wen Zhou ◽  
Bin-Cheng Yin ◽  
Bang-Ce Ye
Keyword(s):  
Raman Scattering ◽  
Adenosine Triphosphate ◽  
Small Molecule ◽  
Cell Metabolism ◽  
Surface Enhanced Raman Scattering ◽  
Biochemical Reactions ◽  
Highly Sensitive ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering

As an important small molecule, adenosine triphosphate (ATP) plays an important role in the regulation of cell metabolism and supplies energy for various biochemical reactions in organisms.

Synthesis of Bempedoic Acid through Electrochemical Decarboxylation of Dialkylated Malonic Acid

Synthesis ◽  
2021 ◽  
Author(s):  
Zhimin Xu ◽  
Yue Zheng ◽  
Lifang Tian ◽  
Yahui Wang
Keyword(s):  
Adenosine Triphosphate ◽  
Small Molecule ◽  
Malonic Acid ◽  
Industrial Production ◽  
High Efficiency ◽  
Small Molecule Inhibitors ◽  
New Method ◽  
Mild Conditions ◽  
Citrate Lyase ◽  
Ketone Formation

Bempedoic acid is a kind of small-molecule inhibitors of adenosine triphosphate-citrate lyase (ACL) which is effective in the treatment of hypercholesterolemia and hypertension. In this paper, a new method of six-step synthesis of bempedoic acid with 42% overall yield is reported and the ketone formation by electrochemical decarboxylation of dialkylated malonic acid is introduced as the key step of this process. This method with mild conditions and high efficiency is potentially suitable for industrial production.

DNA Aptamer‐Cyanine Complexes as Generic Colorimetric Small‐Molecule Sensors

2021 ◽  
Author(s):  
Obtin Alkhamis ◽  
Juan Canoura ◽  
Konstantin V. Bukhryakov ◽  
Anamary Tarifa ◽  
Anthony P. DeCaprio ◽  
...  
Keyword(s):  
Small Molecule ◽  
Dna Aptamer
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