DNA Nanostructures and Self-Assembly

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Questions and Answers

What is the primary function of the lock-key system in the DNA cubic box lid?

To enhance the structural integrity of the box

To control the opening of the lid (correct)

To prevent the box from being closed

To connect the sheets of the box

Tetrahedra are constructed using five strands of DNA.

False

What structural feature connects the neighboring faces in the DNA cubic box?

hinge strands

The DNA cubic box was designed by _______ et al.

Andersen Signup and view all the answers

Match the following concepts with their descriptions:

Tetrahedron = Formed from four DNA strands DNA cubic box = Has a controllable lid FRET switches = Used to read out the lid's opening Shih's group = Innovators in custom 3D shapes design Signup and view all the answers

What is a Holliday junction (HJ) in DNA nanotechnology?

A 4-arm junction formed from a single crossover between two double helices Signup and view all the answers

A double crossover (DX) requires two exchanges between two double helices.

True Signup and view all the answers

What are the three types of key motifs that involve exchanges between helices?

Holliday junction, double crossover, triple crossover Signup and view all the answers

In DNA structure, the ___ refers to strands that can interact cohesively due to sticky ends.

sticky-ended cohesion Signup and view all the answers

What type of structure can be assembled using branched DNA molecules with sticky ends?

1D, 2D and 3D structures Signup and view all the answers

Paranemic crossover (PX) involves exchanges between strands of opposite polarity.

False Signup and view all the answers

Match the following DNA structures with their descriptions:

Holliday junction (HJ) = 4-arm junction from a single exchange Double crossover (DX) = Molecule resulting from two exchanges Triple crossover (TX) = Involves two successive double exchanges Paranemic crossover (PX) = Exchanges strands at proximity points Signup and view all the answers

A two-dimensional DNA array can be formed from the self-assembly of ___ triangle tiles.

DNA Signup and view all the answers

What is the role of 'staple' DNA strands in DNA origami structures?

To attach multiple parts of the long scaffold strand Signup and view all the answers

DNA nanotubes serve as structural components within cells.

False Signup and view all the answers

What is the scaffold material used in the DNA origami structures described?

7 kilobase circular genomic DNA from the virus M13mp18 Signup and view all the answers

A family of rigid three-dimensional DNA _________ was constructed with edge lengths of 10 nm.

tetrahedra Signup and view all the answers

Match the following DNA structures with their descriptions:

DNA lattice = Self-assembled hexagonal structures DNA origami = Complex shapes fabricated from a long single-stranded DNA DNA nanotubes = Templates for biomimicry of microtubules DNA tetrahedra = Rigid, three-dimensional constructs with 10 nm edges Signup and view all the answers

What kind of symmetry does the cross-shaped tile structure in the DNA lattice possess?

C4 symmetry Signup and view all the answers

The staple DNA strands used in DNA origami have identical sequences.

False Signup and view all the answers

What technique was used to fabricate arbitrary two-dimensional shapes in DNA origami?

Self-assembly of long, single-stranded DNA Signup and view all the answers

Study Notes

Self-Assembly of DNA Nanostructures

DNA nanostructures are structures built from DNA molecules.
These structures can be one-dimensional (1D), two-dimensional (2D), or three-dimensional (3D).

Key Motifs in Structural DNA Nanotechnology

Holliday Junction (HJ): A four-arm junction formed by a single reciprocal exchange between two double helices.
Double Crossover (DX): A molecule resulting from a double exchange between two double helices.
Triple Crossover (TX): A molecule resulting from two successive double reciprocal exchanges between three double helices.
Paranemic Crossover (PX): A molecule where two double helices exchange strands at every possible point of proximity.
JX2 Molecule: A molecule that lacks two of the crossovers of the PX molecule.

Two-Dimensional DNA Array Structures

DNA Lattice Structures: Composed of repeating tiles that self-assemble into arrays.
- Triangles: Self-assemble into 2D arrays.
- Hexagons: Formed from six equilateral triangle complexes.
- Cross-shaped tiles: Self-assemble into fixed-size arrays.
- Three-pointed Star Motifs: Self-assemble into hexagonal lattices.
DNA Origami Structures:
- Constructed using a long, single-stranded DNA scaffold.
- Short "staple" strands bind to the scaffold, folding it into a desired shape.
- Allows for the creation of complex 2D shapes, including words and images.
DNA Nanotube Structures:
- Promise to be useful for biomimicry, particularly in the reproduction of microtubules.
- DAE-E tiles, containing five DNA strands, self-assemble into rigid rectangular cores.

Three-Dimensional DNA Nanostructures

Tetrahedra:
- Rigid 3D structures with edge lengths of 10 nm.
- Self-assemble quickly and can be connected by programmable DNA linkers.
DNA Cubic Box with a Controllable Lid:
- Constructed using an M13 strand divided into six sections, with each section forming a sheet (face).
- Faces are connected by "hinge" strands.
- The lid is functionalized with a lock-key system.
- Its opening can be controlled and read out by FRET switches.
Shih's Group Strategy:
- 3D shapes are composed of multiple "stacked" DNA origami sheets.
- This approach enables the building of custom 3D shapes.

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Description

Explore the fascinating world of DNA nanostructures, including their self-assembly into one-dimensional, two-dimensional, and three-dimensional forms. This quiz covers key motifs in structural DNA nanotechnology, such as Holliday Junctions and Double Crossovers. Test your knowledge on the innovative applications of DNA lattice structures.