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Introduction to DNA Origami

Synthesis of DNA origami

Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
What DNA is?

Phosphate 2-deoxyribose Base (adenine)

+ +

http://upload.wikimedia.org/wikipedia/commons/4/43/Deoxyribose.png
http://www.thestandard.org.nz/wp-content/uploads/2009/01/phosphate.gif
http://med.mui.ac.ir/slide/genetic/dna_molecule.gif
http://upload.wikimedia.org/wikipedia/commons/c/cf/Adenine_chemical_structure.png
DNA Structure
Watson–Crick base pairing

http://www.bio.miami.edu/~cmallery/150/gene/c16x6base-pairs.jpg
Branched DNA

http://upload.wikimedia.org/wikipedia/commons/9/92/Holliday_junction_coloured.png
http://upload.wikimedia.org/wikipedia/commons/f/f4/Holliday_Junction.png
http://www.dna.caltech.edu/Images/DAO-WCr.gif
http://upload.wikimedia.org/wikipedia/commons/3/3d/Mao-DX-schematic-2.jpg
Design of complex DNA structures

Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
The dirty details
Step 1 (in design process) – DNA double strand folded back on itself:

Natural point to make a new link

Place where red (secondary / non-master) strand comes into close alignment

A Hands-on Introduction to Nanoscience:


www.virlab.virginia.edu/Nanoscience_class/Nanoscience_class.htm
The dirty details (cont'd)
Step 2 – Cut secondary strand at this point:

How to reconnect between double strands?

MUST take into account direction (5' => 3') of DNA backbone
Making sure that connection maintains this progression (see arrows)

A Hands-on Introduction to Nanoscience:


www.virlab.virginia.edu/Nanoscience_class/Nanoscience_class.htm
Oh, but I forgot something major:

Can't engineer segments as continuous strings!

A Hands-on Introduction to Nanoscience: www.virlab.virginia.edu/Nanoscience_class/Nanoscience_class.htm


Design of complex DNA structures

Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
The dirty details (cont'd)
Step 3 – Connect up what will become "staple" segment:

New red = Staple segment

Blue & Yellow = non-staple segments

OR if merge blue/yellow at appropriate point, they could become second


staple

A Hands-on Introduction to Nanoscience:


www.virlab.virginia.edu/Nanoscience_class/Nanoscience_class.htm
Design of complex DNA structures

Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
Design of complex DNA structures

Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
Synthesis of DNA origami

Rothemund P W K 2005 Design of DNA origami ICCAD’05: Int. Conf. on Computer Aided Design pp 471–8
Visualization of DNA Origami

Atomic Force Microscope


But the design programming sounds REALLY complex

But there is now a free, downloadable, do-it-


yourself DNA Origami design program!
Developed by the Dana Farber Cancer Lab & Harvard's Wyss Institute

www.cadnano.org
Small Smiley Faces Are Sort of Interesting but What Else Can I Make That
Is Useful

You can build a nanorobot!!!!

http://www.virlab.virginia.edu/Nanoscience_class/lecture_notes/Seeing%20at%20the%20Nanoscale.pptx
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. SM Douglas, I Bachelet, GM Church (2012) Science. 335:831–4
Short DNA extensions serve as LOCKS to fold structure together

http://www.virlab.virginia.edu/Nanoscience_class/lecture_notes/Seeing%20at%20the%20Nanoscale.pptx
These antigen-binding single DNA strands are known as aptamers

When the lock springs open it exposes the antigen-releasing cell to the nanobot's deadly cargo

Amir Y, Ben-Ishay E, Levner D, Ittah S, Abu-Horowitz A, Bachelet I. Universal computing by DNA origami robots in a living animal. Nature nanotechnology.
2014;9(5):353-357. doi:10.1038/nnano.2014.58.
We Could Also Start Designing
Dynamic DNA Nanomachines

Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components Thomas Gerling,
Klaus F. Wagenbauer, Andrea M. Neuner, and Hendrik Dietz
Science 27 March 2015: 347 (6229), 1446-1452. [DOI:10.1126/science.aaa5372]
Resources
• CadNano: http://cadnano.org/
• DIY AFM:
http://lego2nano.openwisdomlab.net/index.ht
ml
• Solve for X - Ido Bachelet - Surgical
Nanorobotics:
https://www.youtube.com/watch?v=aA-
H0L3eEo0
• BioMOD Previous Years Projects:
http://openwetware.org/wiki/Biomod
• biomod.net