Compositions and methods for fractal assembly of micron-scale nucleic acid structures

Patent metadata

Field	Value
Publication number	US-11001606-B2
Application number	US-201816118425-A
Country	US
Kind code	B2
Filing date	Aug 30, 2018
Priority date	Aug 30, 2017
Publication date	May 11, 2021
Grant date	May 11, 2021

Abstract

Compositions and methods of the present disclosure provide for staged assembly of nucleic acid microstructures made of an array of x number of polynucleotide tiles, where each of the polynucleotide tiles is a polygon configuration and is made from a single-stranded helical polynucleotide scaffold and a plurality of single-stranded polynucleotide staple strands of y number of unique staple sequences corresponding to the selected tile configuration, the y number of unique staple sequences capable of being constant for any value of x.

First claim

What is claimed is:

1. A nucleic acid microstructure comprising:
an n×n array of n 2 polynucleotide square tiles, each of the n 2 polynucleotide square tiles comprising:
a single-stranded helical polynucleotide scaffold of a known sequence; and
a plurality of selected single-stranded polynucleotide staple strands being at least partially complementary to the polynucleotide scaffold and annealed to the polynucleotide scaffold to form a square tile shape;

the n×n array of n 2 polynucleotide square tiles further comprising a plurality of 2×2 sub-arrays, each of the plurality of 2×2 sub-arrays comprising a set of four polynucleotide square tiles, each of the four polynucleotide square tiles having p number of inside single-tile extended polynucleotide staple strands or p number of inside single-tile truncated polynucleotide staple strands, the inside single tile extended polynucleotide staple strands being annealed with the inside single-tile truncated polynucleotide staple strands to form the plurality of 2×2 sub-arrays, wherein each of the plurality of 2×2 subarrays comprise four two-tile edges and any inside two-tile edges in any of the plurality of 2×2 sub-arrays have less than p number of inside two-tile extended polynucleotide staple strands or less than p number of inside two-tile truncated polynucleotide staple strands, where the inside two-tile extended polynucleotide staple strands are annealed with the inside two-tile truncated polynucleotide staple strands to form at least one 4×4 subarray.

2. The nucleic acid microstructure of claim 1 , wherein n is 2, 4, or 8.

3. The nucleic acid microstructure of claim 1 , wherein the single-stranded helical polynucleotide scaffold is derived from M13mp18 DNA.

4. A method of assembling the nucleic acid microstructure of claim 1 , the method comprising:
selecting a value for n in the n by n array of n 2 polynucleotide square tiles;
determining a number of subarray annealing stages as log 2 n; and
preparing n 2 mixtures for each of the n 2 polynucleotide square tiles, each mixture comprising the single-stranded helical polynucleotide scaffold and corresponding single-stranded polynucleotide staple strands specific to each of the n 2 polynucleotide square tiles out of the plurality of selected single-stranded polynucleotide staple strands.

Assignees

• California Inst Of Techn

Inventors

• Tikhomirov Grigory
• Petersen Philip F
• Qian Lulu

Classifications

• B82B3/0047

  Bonding two or more elements · CPC title

• B81C1/00007

  Assembling automatically hinged components, i.e. self-assembly processes (self-assembly mechanisms B81B7/0003) · CPC title

• C07H21/04 Primary

  with deoxyribosyl as saccharide radical · CPC title

• B81B1/006

  Microdevices formed as a single homogeneous piece, i.e. wherein the mechanical function is obtained by the use of the device, e.g. cutters · CPC title