Compositions and methods for detecting viral nucleic acids

Abstract

Described herein are compositions that may be used to detect viral nucleic acid. For example, these compositions may comprise a DNA-nanostructure, a capture oligonucleotide and a protector oligonucleotide, wherein the components are designed based on a duo-toehold-mediated displacement reaction (duo-TMDR) strategy. In this strategy, a first TMDR can switch off a Foster resonance energy transfer (FRET) process and a second TMDR can release the target viral nucleic acid and amplify the signal. Methods of using such compositions are also provided herein.

What is claimed is: 
     
         1 . A composition for detecting a viral nucleic acid in a sample, the composition comprising:
 a DNA-nanostructure, a capture oligonucleotide and a protector oligonucleotide;   wherein the DNA-nanostructure is operably linked to a fluorophore and the protector oligonucleotide is operably linked to a quencher or the DNA-nanostructure is operably linked to a quencher and the protector oligonucleotide is operably linked to a fluorophore; and wherein the quencher is capable of quenching the fluorescent light emitted from the fluorophore;   wherein the protector oligonucleotide is capable of hybridizing to the DNA-nanostructure;   wherein the viral nucleic acid is capable of displacing the protector oligonucleotide and hybridizing to the DNA-nanostructure; and   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.   
     
     
         2 . The composition of  claim 1 , wherein the DNA-nanostructure comprises at least one single stranded region. 
     
     
         3 . The composition of  claim 2 , wherein the single stranded region comprises a nucleic acid sequence that comprises a first toehold domain, a hybridization region and a second toehold domain. 
     
     
         4 . The composition of  claim 3 , wherein the first toehold domain comprises a nucleic acid sequence that is complementary to a portion of the viral nucleic acid. 
     
     
         5 . The composition of  claim 3 , wherein the protector oligonucleotide is not capable of hybridizing to the first toehold domain. 
     
     
         6 . The composition of  claim 3 , wherein the second toehold domain comprises a nucleic acid sequence that is complementary to a portion of the protector oligonucleotide and a portion of the capture oligonucleotide. 
     
     
         7 . The composition of  claim 3 , wherein the viral nucleic acid is not capable of hybridizing to the second toehold domain. 
     
     
         8 . The composition of  claim 3 , wherein the hybridization region comprises a nucleic acid sequence that is complementary to a portion of the viral nucleic acid, a portion of the protector oligonucleotide and a portion of the capture oligonucleotide. 
     
     
         9 . The composition of  claim 1 , wherein the DNA-nanostructure is a DNA-tetrahedron. 
     
     
         10 . The composition of  claim 9 , wherein the DNA-tetrahedron comprises five double-stranded edges and one single stranded edge. 
     
     
         11 . The composition of  claim 10 , wherein the fluorophore or quencher is operably linked at the tetrahedron vertex, proximal to the single stranded edge. 
     
     
         12 . The composition of  claim 9 , wherein the DNA-tetrahedron comprises four oligonucleotides having at least about 90% sequence identity to SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:4. 
     
     
         13 . The composition of  claim 1 , wherein the protector oligonucleotide is between about 15 to about 25 nucleotides in length. 
     
     
         14 . The composition of  claim 1 , wherein the fluorophore or quencher is operably linked to the 5′ or 3′ end of the protector oligonucleotide. 
     
     
         15 . The composition of  claim 1 , wherein the protector oligonucleotide comprises a nucleic acid sequence having at least about 90% sequence identity to SEQ ID NO:5, SEQ ID NO:6 or SEQ ID NO:7. 
     
     
         16 . The composition of  claim 1 , wherein the capture oligonucleotide is between about 15 to about 30 nucleotides in length. 
     
     
         17 . The composition of  claim 1 , wherein the capture oligonucleotide comprises a nucleic acid sequence that is complementary to a toehold domain in the DNA-nanostructure, and wherein the toehold domain is linked to a nucleic acid sequence in the DNA-nanostructure that is capable of hybridizing to the viral nucleic acid. 
     
     
         18 . The composition of  claim 1 , wherein the capture oligonucleotide comprises a nucleic acid sequence having at least about 90% sequence identity to SEQ ID NO:8, SEQ ID NO:9 or SEQ ID NO:10. 
     
     
         19 . The composition of  claim 1 , wherein the viral nucleic acid is from  dengue virus, Ebola virus, human immunodeficiency virus  (HIV), hepatitis B, hepatitis C, Influenza, SARS, measles, Zika, yellow fever, West Nile fever, smallpox,  Marburg viruses,  human papillomavirus, Kaposi's sarcoma-associated herpesvirus or human T-lymphotropic virus. 
     
     
         20 . The composition of  claim 1 , wherein the viral nucleic acid is from  Dengue virus.