Evolution of a highly functional circular DNA aptamer in serum

Abstract Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery of a circular aptamer, named CTBA4T-B1, that exhibits very high binding affinity (with a dissociation constant of 19 pM), excellent anticoagulation activity (with the half maximal inhibitory concentration of 90 pM) and high stability (with a half-life of 8 h) in human serum, highlighting the advantage of performing aptamer selection directly in the environment where the application is intended. CTBA4T-B1 is predicted to adopt a unique structural fold with a central two-tiered guanine quadruplex capped by two long stem–loops. This structural arrangement differs from all known thrombin binding linear DNA aptamers, demonstrating the added advantage of evolving aptamers from circular DNA libraries. The method described here permits the derivation of circular DNA aptamers directly in biological fluids and could potentially be adapted to generate other types of aptamers for therapeutic applications.

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Module-Activity Relationship of G-quadruplex Based DNA Aptamers for Human Thrombin

Current Medicinal Chemistry ◽

10.2174/09298673113206660283 ◽

2013 ◽

Vol 20 (38) ◽

pp. 4836-4843 ◽

Cited By ~ 15

Author(s):

E. Zavyalova ◽

A. Golovin ◽

G. Pavlova ◽

A. Kopylov

Keyword(s):

Activity Relationship ◽

Dna Aptamers ◽

G Quadruplex ◽

Human Thrombin ◽

Relationship Of

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Nuclease Hydrolysis Does Not Drive the Rapid Signaling Decay of DNA Aptamer-Based Electrochemical Sensors in Biological Fluids

Langmuir ◽

10.1021/acs.langmuir.1c00166 ◽

2021 ◽

Vol 37 (17) ◽

pp. 5213-5221

Author(s):

Alexander Shaver ◽

Nandini Kundu ◽

Brian E. Young ◽

Philip A. Vieira ◽

Jonathan T. Sczepanski ◽

...

Keyword(s):

Electrochemical Sensors ◽

Biological Fluids ◽

Dna Aptamer ◽

Rapid Signaling

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A single-round selection of selective DNA aptamers for mammalian cells by polymer-enhanced capillary transient isotachophoresis

The Analyst ◽

10.1039/c7an00909g ◽

2017 ◽

Vol 142 (21) ◽

pp. 4030-4038 ◽

Cited By ~ 12

Author(s):

Kazuki Hirose ◽

Maho Tsuchida ◽

Hinako Asakura ◽

Koji Wakui ◽

Keitaro Yoshimoto ◽

...

Keyword(s):

Capillary Electrophoresis ◽

Mammalian Cells ◽

Dna Aptamer ◽

Dna Aptamers ◽

Aptamer Selection ◽

Selection For ◽

First Time ◽

Selection Of

A single-round DNA aptamer selection for mammalian cells was successfully achieved for the first time using a capillary electrophoresis (CE)-based methodology.

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Detection of Nonylphenol with a Gold-Nanoparticle-Based Small-Molecule Sensing System Using an ssDNA Aptamer

International Journal of Molecular Sciences ◽

10.3390/ijms21010208 ◽

2019 ◽

Vol 21 (1) ◽

pp. 208 ◽

Cited By ~ 1

Author(s):

A-Ru Kim ◽

Sang-Heon Kim ◽

Dabin Kim ◽

Seo Won Cho ◽

Ahjeong Son ◽

...

Keyword(s):

Gold Nanoparticles ◽

Detection System ◽

Endocrine Disrupting Chemicals ◽

Dna Aptamer ◽

Sensor System ◽

Sexual Hormones ◽

Dna Library ◽

Reduced Graphene ◽

Endocrine Disrupting ◽

High Binding Affinity

Endocrine-disrupting chemicals (EDCs) threaten many kinds of life throughout the world. These compounds function the same as sexual hormones, inducing precocious puberty, gynecomastia, etc., in the human body. To prevent excess exposure to nonylphenol (NP), a simple and rapid detection system is needed. In this study, we develop a nonylphenol-specific aptamer from a random single-stranded DNA library and test a rapid sensor system based on the aptamer and gold nanoparticles (AuNPs). The aptamer was screened by a methodology involving reduced graphene oxide (rGO). As a result of screening and sequencing, a DNA aptamer was developed that recognizes the target with high binding affinity (Kd = 194.2 ± 65.9 nM) and specificity. The sensor system developed using the aptamer and gold nanoparticles is sensitive (LOD = 2.239 nM). Circular dichroism (CD) spectrometry results show that the free aptamer binds to the target molecule. The aptamer was characterized using gold nanoparticles to measure UV absorbance. Our results suggest that the sensor system developed using this aptamer is useful for field diagnosis of small molecules.

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DNA Aptamers for Human Thrombin with High Anticoagulant Activity Demonstrate Target- and Species-Specificity

Current Medicinal Chemistry ◽

10.2174/092986712803530575 ◽

2012 ◽

Vol 19 (30) ◽

pp. 5232-5237 ◽

Cited By ~ 12

Author(s):

E. Zavyalova ◽

A. Golovin ◽

T. Timoshenko ◽

A. Babiy ◽

G. Pavlova ◽

...

Keyword(s):

Anticoagulant Activity ◽

Species Specificity ◽

Dna Aptamers ◽

Human Thrombin

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Cellular uptake of aptamer by Quantum Dots (QDs)

Biomarkers and Drug Discovery ◽

10.31579/2642-9799/004 ◽

2018 ◽

Vol 1 (1) ◽

pp. 01-01

Author(s):

Haleena Kaur

Keyword(s):

Binding Affinity ◽

Biological Fluids ◽

High Specificity ◽

Binding Domain ◽

Dna Aptamer ◽

Heparin Binding ◽

Stem Loop ◽

Diagnostic Potential ◽

Phosphate Backbone ◽

Aptamer Sequence

Aptamers are short single stranded oligonucleotide sequences that exhibit high binding affinity and high specificity against their target molecule. Binding affinity and specificity are crucial features for aptamers in order to exploit their therapeutic and diagnostic potential and to make them an appealing candidate for the commercial market1,2. Aptamers contain functional moieties that can fold into different conformation such as hairpin stem and loops, G-quadruplexes, and pseudoknots. A study led by Dr Harleen Kaur involving unique stem-loop truncation strategy was employed to find the binding domain in a 66-mer long DNA aptamer sequence against the heparin binding domain of vascular endothelial growth factor (VEGF165) protein1. The results from the work demonstrated identification of a 26-mer long aptamer sequence referred as SL2-B in the paper with improvement in the binding affinity by more than 200-folds (Kd = 0.5nM) against VEGF protein. To improve the biostability of the aptamer in the biological fluids, the phosphorothioate linkages (PS-linkages) in the phosphate backbone of the DNA were introduced at the 5’-and 3’-termini of the obtained SL2-B aptamer sequence. The PS-modified SL2-B aptamer sequence demonstrated significant improvement in the stability without comprising

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In Vitro Selection of Circular DNA Aptamers for Biosensing Applications

Angewandte Chemie International Edition ◽

10.1002/anie.201901192 ◽

2019 ◽

Vol 58 (24) ◽

pp. 8013-8017 ◽

Cited By ~ 17

Author(s):

Meng Liu ◽

Qingxin Yin ◽

Yangyang Chang ◽

Qiang Zhang ◽

John D. Brennan ◽

...

Keyword(s):

In Vitro Selection ◽

Dna Aptamers ◽

Circular Dna ◽

Selection Of

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Rapid acquisition of high-affinity DNA aptamer motifs recognizing microbial cell surfaces using polymer-enhanced capillary transient isotachophoresis

Chemical Communications ◽

10.1039/c5cc07268a ◽

2016 ◽

Vol 52 (3) ◽

pp. 461-464 ◽

Cited By ~ 20

Author(s):

Shingo Saito ◽

Kazuki Hirose ◽

Maho Tsuchida ◽

Koji Wakui ◽

Keitaro Yoshimoto ◽

...

Keyword(s):

Microbial Cell ◽

Dna Aptamer ◽

Dna Aptamers ◽

Cell Surfaces ◽

Rapid Acquisition ◽

High Affinity ◽

Selection Methodology

A polymer-enhanced capillary transient isotachophoresis selection methodology was developed for rapid acquisition of high affinity DNA aptamers recognizing microbial cell surfaces.

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