Crisscross cooperative self-assembly
Provided herein, in some embodiments, are methods, compositions and kits for controlling nucleation and assembly of molecular nanostructures, microstructures and macrostructures.
1. A crisscross nucleic acid slat, comprising:
(a) a first plurality of at least four single-stranded nucleic acid strands aligned parallel to each other; each strand of the first plurality having a length of at least 21 nucleotides; and
(b) a second plurality of at least four single-stranded nucleic acid strands aligned parallel to each, each strand of the second plurality having a length of at least 21 nucleotides, wherein the at least four nucleic acid strands of the first plurality are bound to and rotated at an angle relative to the at least four nucleic acid strands of the second plurality,
wherein a single nucleic acid strand of (b) binds to multiple nucleic acid strands of (a), each through a single cooperative binding site, and a single nucleic acid strand of (a) binds to multiple nucleic acid strands of (b), each through a single cooperative binding site.
2. A nucleic acid nanostructure, comprising a nucleic acid scaffold strand folded into multiple stacked parallel loops that are bound to at least one crisscross nucleic acid slat of claim 1 .
3. The nucleic acid nanostructure of claim 2 , wherein the length of the nucleic acid scaffold strand is longer than 1 kilobase.
4. The nucleic acid nanostructure of claim 2 , wherein the nanostructure is a DNA nanostructure.
5. A nucleic acid nanostructure comprising a stack of parallel nucleic acid loops bound to a plurality of nucleic acid slats of claim 1 .
6. A method of detecting a biomolecule, comprising
(a) combining in a reaction mixture
(i) a sample comprising a biomolecule;
(ii) a nucleic acid strand capable of self-assembling into a nanostructure that comprises stacked parallel strands;
(iii) at least two crisscross nucleic acid slats of claim 1 , wherein the at least two slats bind to the stacked parallel strands of (ii), and wherein at least one nucleic acid strand of the at least two slats is linked to a biomolecule binding partner that specifically binds to the biomolecule in the sample;
(b) incubating the reaction mixture under conditions that permit binding of the biomolecule binding partners to the biomolecule, assembly of the nanostructure into stacked parallel strands, and binding of the crisscross nucleic acid slats to the stacked parallel strands to form a three-dimensional nanostructure; and
(c) visualizing the three-dimensional nanostructure, thereby detecting the biomolecule.
7. The method of claim 6 , wherein the sample is a biological sample.
8. The method of claim 6 , wherein the biomolecule is a macromolecule.
9. The method of claim 8 , wherein the macromolecule is a protein.
10. The method of claim 9 , wherein the biomolecule binding partner is selected from antibodies, antibody fragments, and aptamers.
11. The method of claim 10 , wherein the biomolecule binding partner is an antibody.
12. The method of claim 10 , wherein the biomolecule binding partner is an antibody fragment selected from Fab, F(ab′)2, Fe, scFv, and vhh antibody fragments.
13. A method of detecting a biomolecule, comprising:
(a) combining in a reaction mixture
(i) a sample comprising a biomolecule, and
(ii) nucleic acid nanostructure comprising (i) a nucleic acid scaffold strand and nucleic acid staple strands capable of assembling into multiple stacked parallel loops and (ii) at least two crisscross nucleic acid slats of claim 1 that bind to the loops of (i), wherein a biomolecule binding partner that specifically binds to the biomolecule is linked to at least one nucleic acid strand of the at least two slats such that in the presence of the biomolecule the biomolecule binding partners bind to the biomolecule and the nucleic acid nanostructure folds into multiple stacked parallel loops; and incubating the reaction mixture to assemble multiple stacked parallel loops; and
(b) visualizing the three-dimensional nanostructure, thereby detecting the biomolecule.
14. The method of claim 13 , wherein the sample is a biological sample.
15. The method of claim 13 , wherein the biomolecule is a macromolecule.
16. The method of claim 15 , wherein the macromolecule is a protein.
17. The crisscross nucleic acid slat of claim 1 , wherein the first plurality and/or the second plurality comprises 4-100 nucleic acid strands.
18. The crisscross nucleic acid slat of claim 1 , wherein the nucleic acid strands of (a) and/or (b) are DNA strands.
19. The crisscross nucleic acid slat of claim 1 , wherein nucleic acid strands of the first plurality and/or nucleic acid strands of the second plurality have a length of 21-30 nucleotides.
20. The crisscross nucleic acid slat of claim 1 , wherein the angle is between 10 and 170 degrees.
21. The crisscross nucleic acid slat of claim 1 , wherein the angle is between 60 and 120 degrees.
22. The crisscross nucleic acid slat of claim 1 , wherein nucleic acid strands of the first plurality and/or nucleic acid strands of the second plurality have a length of 21, 42, 63, 84, 105 or 126 nucleotides.
23. A method comprising
(a) combining in a reaction mixture
(i) a sample comprising a biomolecule;
(ii) a nucleic acid strand capable of self-assembling; into a nanostructure that comprises stacked parallel strands;
(iii) at least two crisscross nucleic acid slats of claim 1 , wherein the at least two slats bind to the stacked parallel strands of GO, and wherein at least one nucleic acid strand of the at least two slats is linked to a biomolecule binding partner that specifically binds to the biomolecule in the sample; and
(b) incubating the reaction mixture under conditions that permit binding of the biomolecule binding partners to the biomolecule, assembly of the nanostructure into stacked parallel strands, and binding of the crisscross nucleic acid slats to the stacked parallel strands to form a three-dimensional nanostructure.