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Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
What DNA is?
+ +
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:
Place where red (secondary / non-master) strand comes into close alignment
MUST take into account direction (5' => 3') of DNA backbone
Making sure that connection maintains this progression (see arrows)
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:
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
www.cadnano.org
Small Smiley Faces Are Sort of Interesting but What Else Can I Make That
Is Useful
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