In Vitro Selection of a DNA Aptamer Targeting Degraded Protein Fragments for Biosensing

Protein biomarkers often exist as degradation fragments in biological samples, and affinity agents derived using a purified protein may not recognize them, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by selecting aptamers against a degraded form o...

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Bibliographic Details
Published in:Angewandte Chemie International Edition 2020-05, Vol.59 (20), p.7706-7710
Main Authors: Liu, Meng, Wang, Jiayi, Chang, Yangyang, Zhang, Qiang, Chang, Dingran, Hui, Christy Y., Brennan, John D., Li, Yingfu
Format: Article
Language:English
Subjects:
Aptamers
Aptamers, Nucleotide - metabolism
Biological properties
Biological samples
Biomarkers
Biosensing Techniques - methods
Biosensors
Clostridium difficile
Colorimetry
Degradation
Deoxyribonucleic acid
Diagnosis
DNA
Feces - chemistry
Fragments
Humans
in vitro selection
paper-based analytical devices
Peptide Fragments - metabolism
protein degradation
Proteins
Proteolysis
Toxin B
Toxins
Toxins, Biological - analysis
Toxins, Biological - chemistry
Toxins, Biological - metabolism
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Summary:Protein biomarkers often exist as degradation fragments in biological samples, and affinity agents derived using a purified protein may not recognize them, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by selecting aptamers against a degraded form of the toxin B protein, which is a marker for diagnosing toxigenic Clostridium difficile infections. This approach has led to isolation of a DNA aptamer that recognizes degraded toxin B, fresh toxin B, and toxin B spiked into human stool samples. DNA aptamers selected using intact recombinant toxin B failed to recognize degraded toxin B, which is the form present in stored stool samples. Using this new aptamer, we produced a simple paper‐based analytical device for colorimetric detection of toxin B in stool samples, or in the NAP1 strain of Clostridium difficile. The combined aptamer‐selection and paper‐sensing strategy can expand the practical utility of DNA aptamers in clinical diagnosis. Degraded but useful: The use of degradation fragments of protein biomarkers as targets for aptamer selection can produce a DNA aptamer that is compatible with disease diagnosis using clinical samples, as illustrated by an aptamer selected using naturally degraded fragments of Clostridium difficile toxin B.
ISSN:1433-7851
1521-3773
DOI:10.1002/anie.202000025