Development of a DNA aptamer selection method based on the heterogeneous sandwich form and its application in a colorimetric assay for influenza A virus detection

In this paper, we introduce an effective method for selecting aptamer that increases the signal-to-noise ratio in a heterogenous sandwich-type immunosensor and confirm the efficiency of selected aptamer candidates in the colorimetric assay. Using the proposed method, four aptamer candidates withKdvalues ranging from 77.6 nM to 125.7 nM were obtained.

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The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

International Journal of Molecular Sciences ◽

10.3390/ijms22052409 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2409

Author(s):

Anastasia A. Bizyaeva ◽

Dmitry A. Bunin ◽

Valeria L. Moiseenko ◽

Alexandra S. Gambaryan ◽

Sonja Balk ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Core Structure ◽

Dna Aptamer ◽

Tertiary Structures ◽

Quadruplex Dna ◽

G Quadruplex ◽

Flanking Sequences ◽

Related Proteins

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.

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Next-Generation Sequencing Confirmation of Real-Time RT-PCR False Positive Influenza-A Virus Detection in Waterfowl and Swine Swab Samples

Journal of Next Generation Sequencing & Applications ◽

10.4172/2469-9853.1000134 ◽

2016 ◽

Vol 3 (2) ◽

Cited By ~ 3

Author(s):

Lu H ◽

Yi Tang ◽

Lin Lin

Keyword(s):

Next Generation Sequencing ◽

Real Time ◽

Influenza A Virus ◽

False Positive ◽

Influenza A ◽

Virus Detection ◽

Next Generation ◽

Rt Pcr ◽

Generation Sequencing

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Computational Method for Classification of Avian Influenza A Virus Using DNA Sequence Information and Physicochemical Properties

Frontiers in Genetics ◽

10.3389/fgene.2021.599321 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fahad Humayun ◽

Fatima Khan ◽

Nasim Fawad ◽

Shazia Shamas ◽

Sahar Fazal ◽

...

Keyword(s):

Feature Selection ◽

Decision Tree ◽

Avian Influenza ◽

Physicochemical Properties ◽

Influenza A Virus ◽

Dna Sequence ◽

Influenza A ◽

Feature Selection Method ◽

Selection Method ◽

Avian Influenza A Virus

Accurate and fast characterization of the subtype sequences of Avian influenza A virus (AIAV) hemagglutinin (HA) and neuraminidase (NA) depends on expanding diagnostic services and is embedded in molecular epidemiological studies. A new approach for classifying the AIAV sequences of the HA and NA genes into subtypes using DNA sequence data and physicochemical properties is proposed. This method simply requires unaligned, full-length, or partial sequences of HA or NA DNA as input. It allows for quick and highly accurate assignments of HA sequences to subtypes H1–H16 and NA sequences to subtypes N1–N9. For feature extraction, k-gram, discrete wavelet transformation, and multivariate mutual information were used, and different classifiers were trained for prediction. Four different classifiers, Naïve Bayes, Support Vector Machine (SVM), K nearest neighbor (KNN), and Decision Tree, were compared using our feature selection method. This comparison is based on the 30% dataset separated from the original dataset for testing purposes. Among the four classifiers, Decision Tree was the best, and Precision, Recall, F1 score, and Accuracy were 0.9514, 0.9535, 0.9524, and 0.9571, respectively. Decision Tree had considerable improvements over the other three classifiers using our method. Results show that the proposed feature selection method, when trained with a Decision Tree classifier, gives the best results for accurate prediction of the AIAV subtype.

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Nasal Wipes for Influenza A Virus Detection and Isolation from Swine

Journal of Visualized Experiments ◽

10.3791/53313 ◽

2015 ◽

Cited By ~ 3

Author(s):

Jacqueline M. Nolting ◽

Christine M. Szablewski ◽

Jody L. Edwards ◽

Sarah W. Nelson ◽

Andrew S. Bowman

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Virus Detection

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Integration of reverse transcriptase loop-mediated isothermal amplification with an immunochromatographic strip on a centrifugal microdevice for influenza A virus identification

Lab on a Chip ◽

10.1039/c4lc01033g ◽

2015 ◽

Vol 15 (3) ◽

pp. 718-725 ◽

Cited By ~ 36

Author(s):

J. H. Jung ◽

B. H. Park ◽

S. J. Oh ◽

G. Choi ◽

T. S. Seo

Keyword(s):

Reverse Transcriptase ◽

Influenza A Virus ◽

Influenza A ◽

Virus Detection ◽

Isothermal Amplification ◽

Immunochromatographic Strip ◽

Virus Identification ◽

Loop Mediated Isothermal Amplification

In this paper, we demonstrated an integrated centrifugal microdevice which could perform reverse transcriptase loop-mediated isothermal amplification and immunochromatographic strip based amplicon analysis for rapid, sensitive, and multiplex influenza A virus detection.

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Cross-Protection of Influenza A Virus Infection by a DNA Aptamer Targeting the PA Endonuclease Domain

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00306-15 ◽

2015 ◽

Vol 59 (7) ◽

pp. 4082-4093 ◽

Cited By ~ 23

Author(s):

Shuofeng Yuan ◽

Naru Zhang ◽

Kailash Singh ◽

Huiping Shuai ◽

Hin Chu ◽

...

Keyword(s):

Virus Infection ◽

Influenza A Virus ◽

Influenza A ◽

H5n1 Virus ◽

Influenza Viruses ◽

Cross Protection ◽

Dna Aptamer ◽

Endonuclease Activity ◽

Endonuclease Domain

ABSTRACTAmino acid residues in the N-terminal of the PA subunit (PAN) of the influenza A virus polymerase play critical roles in endonuclease activity, protein stability, and viral RNA (vRNA) promoter binding. In addition, PANis highly conserved among different subtypes of influenza virus, which suggests PANto be a desired target in the development of anti-influenza agents. We selected DNA aptamers targeting the intact PA protein or the PANdomain of an H5N1 virus strain using systematic evolution of ligands by exponential enrichment (SELEX). The binding affinities of selected aptamers were measured, followed by an evaluation ofin vitroendonuclease inhibitory activity. Next, the antiviral effects of enriched aptamers against influenza A virus infections were examined. A total of three aptamers targeting PA and six aptamers targeting PANwere selected. Our data demonstrated that all three PA-selected aptamers neither inhibited endonuclease activity nor exhibited antiviral efficacy, whereas four of the six PAN-selected aptamers inhibited both endonuclease activity and H5N1 virus infection. Among the four effective aptamers, one exhibited cross-protection against infections of H1N1, H5N1, H7N7, and H7N9 influenza viruses, with a 50% inhibitory concentration (IC50) of around 10 nM. Notably, this aptamer was identified at the 5th round but disappeared after the 10th round of selection, suggesting that the identification and evaluation of aptamers at early rounds of selection may be highly helpful for screening effective aptamers. Overall, our study provides novel insights for screening and developing effective aptamers for use as anti-influenza drugs.

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