Use of modular nucleic acid scaffolds to create nanoscale energy harvesting and focusing arrays

Patent metadata

Field	Value
Publication number	US-9970049-B2
Application number	US-201514685836-A
Country	US
Kind code	B2
Filing date	Apr 14, 2015
Priority date	Apr 15, 2014
Publication date	May 15, 2018
Grant date	May 15, 2018

Abstract

The invention relates to a nanoscale antenna including a nucleic acid scaffold having a structure selected from the group consisting of a Holliday junction, a star, and a dendrimer; and a plurality of fluorophores attached to the scaffold and configured as a FRET cascade comprising at least three different types of fluorophores, arranged with (a) a plurality of initial donor fluorophores fixed in exterior positions on the structure, (b) a terminal acceptor fluorophore fixed in a central position on the structure, and (c) a plurality of intermediate fluorophores fixed in positions on the scaffold between the initial acceptor fluorophores and the terminal acceptor fluorophores.

First claim

What is claimed is:

1. A nanoscale antenna comprising:
a nucleic acid scaffold having a structure selected from the group consisting of a Holliday junction, a star, and a dendrimer; and
a plurality of fluorophores attached to the scaffold and configured as a FRET cascade comprising at least three different types of fluorophores, arranged with (a) a plurality of initial donor fluorophores fixed in exterior positions on the structure, (b) one or more terminal acceptor fluorophores fixed in a central position on the structure, and (c) a plurality of intermediate fluorophores fixed in positions on the scaffold between the initial acceptor fluorophores and the terminal acceptor fluorophores,
wherein one or more portions of said scaffold incorporating intermediate fluorophores further comprise a toehold sequence, and are detachable from said scaffold upon contact with a sequence complementary to the toehold sequence.

2. The nanoscale antenna of claim 1 , wherein each type of flurophore is a fluorescent dye.

3. The nanoscale antenna of claim 2 , wherein said nucleic acid is DNA and wherein each said fluorescent dye is integrated into the DNA via phosphoramidite chemistry; succinimidyl ester chemistry; maleimide thiol chemistry; a carboxyl-amine amide bond; azide-alkyne cycloaddition; or a combination thereof.

4. The nanoscale antenna of claim 1 , wherein said FRET cascade includes a total of 3, 4, 5, or 6 different types of fluorophores.

5. The nanoscale antenna of claim 1 , wherein said terminal acceptor comprises one or more fluorophores configured donors in FRET for a post-terminal flurophore acceptor located away from said central position.

6. A nanoscale antenna comprising:
a nucleic acid scaffold having a dendrimer structure, and
a plurality of fluorophores attached to the scaffold and configured as a FRET cascade comprising at least three different types of fluorophores, arranged with (a) a plurality of initial donor fluorophores fixed in exterior positions on the structure, (b) one or more terminal acceptor fluorophores fixed in a central position on the structure, and (c) a plurality of intermediate fluorophores fixed in positions on the scaffold between the initial acceptor fluorophores and the terminal acceptor fluorophores,
wherein one or more portions of said scaffold incorporating intermediate fluorophores further comprise a toehold sequence, and are detachable from said scaffold upon contact with a sequence complementary to the toehold sequence.

7. The nanoscale antenna of claim 6 , wherein each type of flurophore is a fluorescent dye.

8. The nanoscale antenna of claim 7 , wherein said nucleic acid is DNA and wherein each said fluorescent dye is integrated into the DNA via phosphoramidite chemistry; succinimidyl ester chemistry; maleimide thiol chemistry; a carboxyl-amine amide bond; azide-alkyne cycloaddition; or a combination thereof.

9. The nanoscale antenna of claim 6 , wherein said FRET cascade includes a total of 3, 4, 5, or 6 different types of fluorophores.

10. The nanoscale antenna of claim 6 , wherein said terminal acceptor comprises one or more fluorophores configured donors in FRET for a post-terminal flurophore acceptor located away from said central position.

11. A method of using a nanoscale antenna, the method comprising:
providing a nanoscale antenna comprising: a nucleic acid scaffold having a structure selected from the group consisting of a Holliday junction, a star, and a dendrimer; and a plurality of fluorophores attached to the scaffold and configured as a FRET cascade comprising at least three different types of fluorophores, arranged with (a) a plurality of initial donor fluorophores fixed in exterior positions on the structure, (b) one or more terminal acceptor fluorophores fixed in a central position on the structure, and (c) a plurality of intermediate fluorophores fixed in positions on the scaffold between the initial acceptor fluorophores and the terminal acceptor fluorophores, wherein one or more portions of said scaffold incorporating intermediate fluorophores further comprise a toehold sequence, and are detachable from said scaffold upon contact with a sequence complementary to the toehold sequence;
contacting said nanoscale antenna with an analyte;
exciting the antenna with a light source to excite the FRET cascade; and
measuring a response of said nanoscale antenna following the excitation, wherein the response indicates a degree of presence in the analyte of the sequence complementary to the toehold sequence.

12. The method of claim 11 , wherein each type of flurophore is a fluorescent dye.

13. The method of claim 12 , wherein said nucleic acid is DNA and wherein each said fluorescent dye is integrated into the DNA via phosphoramidite chemistry; succinimidyl ester chemistry; maleimide thiol chemistry; a carboxyl-amine amide bond; azide-alkyne cycloaddition; or a combination thereof.

14. The method of claim 11 , wherein said FRET cascade includes a total of 3, 4, 5, or 6 different types of fluorophores.

Assignees

• Buckhout White Susan
• Ancona Mario
• Goldman Ellen R
• Medintz Igor L
• Melinger Joseph S
• Us Navy

Inventors

• Buckhout-White Susan
• Ancona Mario
• Goldman Ellen R
• Medintz Igor L
• Melinger Joseph S

Classifications

• C12Q1/6818 Primary

  involving interaction of two or more labels, e.g. resonant energy transfer · CPC title

• G01N21/6428

  Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" (in vivo A61B5/00; immunoassay G01N33/53) · CPC title

• C12Q2563/155

  Particles of a defined size, e.g. nanoparticles · CPC title