Nucleic acid nanostructure barcode probes

• US 10,024,796 B2
• Filed: 10/28/2011
• Issued: 07/17/2018
• Est. Priority Date: 10/29/2010
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: Dana-Farber Cancer Institute, President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Lin, Chenxiang, Li, Chao, Shih, William M., Yin, Peng, Jungmann, Ralf
• Primary Examiner(s): Priest, Aaron A
• Application Number:
  US13/882,223
• Publication Number:
  US 20130261019A1
• Time in Patent Office: 2,454 Days
• Field of Search: None
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/157 Nanotubes or nanorods
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]
• CPC Class Codes: G01N 21/6486 Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence

Abstract

Provided herein are, inter alia, barcode probes comprised of transiently or stably fluorescently labeled nucleic acid nanostructures that are fully addressable and able to be read using standard fluorescent microscope and methods of use thereof including methods of use as detectable labels for probes.

Claims

1. A composition comprising at least two distinct nucleic acid barcode probes that each comprise a nucleic acid nanorod bound to an antibody,

wherein at least two of the nanorods comprise a distinct barcode pattern formed by the position and color of at least two fluorescently-labeled regions that are separated from each other by a fixed distance of less than 200 nm, and

wherein each fluorescently-labeled region comprises a docking strand capable of binding to a fluorescently-labeled imager strand.

2. The composition of claim 1, wherein the docking strand is transiently bound to the fluorescently-labeled imager strand.

3. The composition of claim 1 comprising at least 10 distinct nucleic acid barcode probes.

4. The composition of claim 3 comprising at least 50 distinct nucleic acid barcode probes.

5. The composition of claim 1, wherein each nanorod comprises at least three fluorescently-labeled regions separated from each other by a fixed distance of less than 200 nm.

6. The composition of claim 1, wherein each fluorescently-labeled region comprises at least two docking strands, and wherein each docking strand is transiently bound to a fluorescently-labeled imager strand.

7. The composition of claim 1, wherein the nanorod of at least one of the barcode probes comprises a first fluorescently-labeled region separated from a second fluorescently-labeled region by a fixed distance of less than 200 nm,

wherein the first fluorescently-labeled region comprises a docking strand transiently bound to a fluorescently-labeled imager strand containing a first fluorophore, and the second fluorescently-labeled region comprises a docking strand transiently bound to a fluorescently-labeled imager strand containing a second fluorophore, and

wherein the color of the first fluorophore is different from the color of the second fluorophore.

8. The composition of claim 1, wherein the nanorod of at least one of the barcode probes comprises a first fluorescently-labeled region separated from a second fluorescently-labeled region by a fixed distance of less than 200 nm,

wherein the first fluorescently-labeled region comprises a docking strand transiently bound to a fluorescently-labeled imager strand containing a first fluorophore, and the second fluorescently-labeled region comprises at least two docking strands, each docking strand transiently bound to a fluorescently-labeled imager strand containing a second fluorophore.

9. The composition of claim 8, wherein the color of the first fluorophore is different from the color of the second fluorophore.

10. The composition of claim 1, wherein the nanorod of at least one of the barcode probes comprises a first fluorescently-labeled region, a second fluorescently-labeled region, and a third fluorescently-labeled region, and the distance between the first fluorescently-labeled region and second fluorescently-labeled region is shorter than the distance between the second fluorescently-labeled region and third fluorescently-labeled region.

11. The composition of claim 1, wherein the nanorod of at least one of the barcode probes has a length of at least 200 nm.

12. The composition of claim 1 further comprising a sample.

13. The composition of claim 1, wherein the nucleic acid barcode probes are immobilized.