Reliable Fluorometric Detection of SARS-CoV-2 by Targeting the G-Quadruplex through pH-Triggered Conformational Polymorphism

Pratihar, S and Agrawal, R and Pal, VK and Singh, A and Govindaraju, T (2022) Reliable Fluorometric Detection of SARS-CoV-2 by Targeting the G-Quadruplex through pH-Triggered Conformational Polymorphism. In: ACS Sensors, 7 (2). 453 -459.

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Abstract

Unravelling unique molecular targets specific to viruses is challenging yet critical for diagnosing emerging viral diseases. Nucleic acids and proteins are the major targets in diagnostic assays of viral pathogens. Identification of novel sequences and conformations of nucleic acids as targets is desirable for developing diagnostic assays specific to a virus of interest. Here, we disclose the identification and characterization of a highly conserved antiparallel G-quadruplex (GQ)-forming DNA sequence present within the SARS-CoV-2 genome. The two-quartet GQ with unique loop compositions formed a distinct recognition motif. Design, synthesis, and fine tuning of structure-activity of a set of small molecules led to the identification of a benzobisthiazole-based fluorogenic probe which unambiguously recognizes the target SARS-CoV-2 GQ DNA. A robust cost-effective assay was developed through thermal cycler PCR-based amplification of the antiparallel GQ-forming ORF1ab region of the SARS-CoV-2 genome and endpoint fluorescence detection with the probe. An exclusive pH window (3.5-4) helped trigger reliable conformational polymorphism (RCP) involving DNA duplex to GQ transformation, which aided the development of a GQ-RCP platform for the diagnosis of SARS-CoV-2 clinical samples. This general strategy can be adapted for the development of specific diagnostic assays targeting different noncanonical nucleic acid sequences.

Item Type:	Journal Article
Publication:	ACS Sensors
Publisher:	American Chemical Society
Additional Information:	The copyright for this article belongs to the American Chemical Society.
Keywords:	Conformations; Cost effectiveness; Diagnosis; Diseases; DNA; Fluorescence; Polymerase chain reaction; Polymorphism; Probes; Synthesis (chemical), Conformational polymorphisms; Design synthesis; Design tuning; Diagnostic assays; Fine tuning; Fluorometric detection; G-quadruplexes; Molecular targets; SARS-CoV-2; Viral disease, SARS
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology Division of Biological Sciences > Centre for Infectious Disease Research
Date Deposited:	16 Mar 2022 06:04
Last Modified:	29 Jun 2022 05:09
URI:	https://eprints.iisc.ac.in/id/eprint/71414

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