Selective detection of different dengue virus RNA serotypes using tandem toehold-mediated displacement reactions
Inventors
Hecht, Sidney • Waggoner, Jesse • Gao, Mingxuan • Chen, Shengxi
Assignees
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Publication Number
US-12577627-B2
Publication Date
2026-03-17
Expiration Date
Abstract
Described herein are systems and methods that may be used to differentially detect viral serotype specific nucleic acid. For example, these systems may comprise multiple DNA-nanostructures, capture oligonucleotides and protector oligonucleotides, wherein each DNA-nanostructure and its associated capture oligonucleotide and protector oligonucleotide are specific for a unique viral type or serotype.
Core Innovation
The invention provides a system and kit for detecting a nucleic acid from a virus or viral subtype in a sample using at least four DNA-nanostructures. Each DNA-nanostructure includes a hybridization region specific for a nucleic acid molecule from a unique viral type or viral serotype selected from DENV1, DENV2, DENV3, and DENV4, and is operably linked to a fluorophore or a quencher selected from a fluorophore quencher pair.
For each DNA-nanostructure, at least four protector oligonucleotides are provided, where each protector oligonucleotide is specific for hybridization to a unique DNA-nanostructure. At least four capture oligonucleotides are provided, where each capture oligonucleotide is specific for hybridization to a unique DNA-nanostructure, and the protector oligonucleotide is operably linked to the other of the fluorophore and quencher.
The viral nucleic acid is capable of displacing the protector oligonucleotide and hybridizing to the DNA-nanostructure. The capture oligonucleotide is capable of displacing the viral nucleic acid and hybridizing to the DNA-nanostructure but is not capable of displacing the protector oligonucleotide, enabling fluorescence measurement from the displaced protector oligonucleotide and differential diagnosis of a subject as having a specific viral or viral serotype infection based on detection of fluorescence.
Claims Coverage
The partial content includes three independent claims directed to a detection system, a detection kit, and a diagnostic method. Across these independent claims, there are four inventive features centered on at least four serotype-specific DNA-nanostructures, protector/capture oligonucleotides, fluorophore/quencher behavior, and fluorescence-based diagnosis.
At least four serotype-specific DNA-nanostructures
At least four DNA-nanostructures, each comprising a hybridization region specific for a nucleic acid molecule from a unique viral type or viral serotype selected from DENV1, DENV2, DENV3, and DENV4.
Protector-linked fluorophore/quencher controlled by displacement
Each DNA-nanostructure is operably linked to one of a fluorophore or a quencher selected from a fluorophore quencher pair, and the protector oligonucleotide is operably linked to the other of the fluorophore and quencher; the viral nucleic acid displaces the protector oligonucleotide and hybridizes to the DNA-nanostructure.
Capture oligonucleotide displaces viral nucleic acid but not protector
At least four capture oligonucleotides, each specific for hybridization to a unique DNA-nanostructure, wherein the capture oligonucleotide is capable of displacing the viral nucleic acid and hybridizing to the DNA-nanostructure but is not capable of displacing the protector oligonucleotide.
Differential diagnosis based on fluorescence from displaced protector
Contacting a sample with at least four DNA-nanostructures and a set of at least four capture oligonucleotides, measuring fluorescence from the displaced protector oligonucleotide, and differentially diagnosing the subject as having a specific viral or viral serotype infection based on detection of fluorescence.
The independent-claim coverage centers on serotype-specific detection using at least four DNA-nanostructures for DENV1–DENV4, fluorescence behavior driven by protector displacement in a fluorophore/quencher pair, and a capture step that displaces viral nucleic acid without displacing the protector, enabling differential serotype diagnosis from measured fluorescence.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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