Design Strategies for DNA Nanostructures

+Design Strategies for DNA Nanostructures

Presented By: Jacob Girard & Keith Randall

With collaboration from: Andrew Gilbert, Daniel Lewis, & Brian Goodhue

+ OutlineIntroduction & Problem Statement

Differentiating the Molecular Building BlocksCategorization GraphingOctet Truss OrientationCohesive Ends Approach

ConstructionsTetrahedron Truncated OctahedronTruncated Tetrahedron CuboctahedronOctahedron

Conclusions

Extensions

Future Problem Statement

Questions or Answers

Acknowledgements

References

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Source: MS Office Clip Art

+Introduction

DNA and Math?

Chemical composition determines structure

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Source: MS Office Clip Art

+What is a tile?

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A tile Branched-Junction Molecule

+What are self-assembled DNA nanostructues?

A self-assembled DNA cube and Octahedron

http://seemanlab4.chem.nyu.edu/nanotech.html

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+The molecular building blocks

D. Luo, “The road from biology to materials,” Materials Today, 6 (2003), 38-43

ATTCGTAAGCCCATTG

GGTAACATTCG TAAGC

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+Cohesive Ends

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Depicted by hatted (prime) and un-hatted letter labels

Each edge needs a complimenting edge. Chemically this is this different bases pairing.

c ĉ.

ATTCGTAAGCCCATTG

GGTAACATTCG TAAGC

c ĉ.

+ Terminology and Definitions

A tile is a branched junction molecule with specific half edge orientation and type.

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+Problem Statement

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The goal is to build self assembling DNA Nanostructures within the octet truss using minimal tile types.

+ The Octet Truss10

Why is the Octet Truss a good construct?

What else is it used for?

Why do we use it?

Source: Wikimedia CommonsDistributed under GNU Free Documentation license.

+ Differentiating the Molecular Building Blocks

π/3 radians

π/2 radians

(2π)/3 radians

π radians

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Categorizations

Only four possible angles

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Graphing

Naming Tiles Schlegel diagrams

It is very helpful to be able to picture these molecules as one dimensional and 3D dimensional.

+Orientation

The problem of orientation

What are equivalent tiles?

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Tile A

Tile DTile C

Tile B

c ĉ.

c ĉ.

+Constraints

1. Arms are straight and rigid

2. The positions of the arms are fixed

3. The arms do not bend or twist in order to bond.

4. No molecule has more than 12 arms or less than 2 arms.

5. Final DNA structures must be complete.

6. No design may allow structures smaller than the target structure to form.

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+Approach

What exists within the octet truss for possible arm configurations?

What can we build by just looking at the octet truss?

What do we think we can build?

What about the Platonic & Archimedean Solids?

How can we do this in as few different tile types as possible?

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+Constructions

Platonic Solids Tetrahedron Octahedron

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Archimedean Solids Cuboctahedron Truncated Tetrahedron Truncated Octahedron

+Tetrahedron

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Truncated Tetrahedron


+Octahedron

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+Octahedron Construction

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Truncated Octahedron


+Cuboctahedron

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+Conclusions

Development of the Tile Model

Constructs Categorization Cohesive Ends Orientation

Determined Platonic and Archimedean Solids do fit in Octet Truss. Proof by Tile Model

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+Extensions

Looking for a better way to talk about orientations of tiles and arms.

Model is limited in some respects.

Arms are not entirely rigid in reality and this does affect the problem statement.

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+Future Problem Statement

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What we know: We have all the 2 and 3 arm configurations We possibly have all the 4 configurations

Need to find all the structures that can be made from one tile type with an even number of arms, and two tile types with an odd number of arms.

Hopefully we will be able to find some pattern and be able to create a generalization of rule, but we will need data and examples first.

+Questions or Answers?

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Acknowledgements

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References

Documents

Design Strategies for DNA Nanostructures