Introduction to DNA Origami Synthesis of DNA origami

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Introduction to DNA Origami

Introduction to DNA Origami

Synthesis of DNA origami Rothemund P W K 2006 Folding DNA to create nanoscale

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 + http: //upload. wikimedia. org/wikipedia/commons/4/43/Deoxyribose. png http: //www.

What DNA is? Phosphate 2 -deoxyribose + 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 Base (adenine) +

DNA Structure

DNA Structure

Watson–Crick base pairing http: //www. bio. miami. edu/~cmallery/150/gene/c 16 x 6 base-pairs. jpg

Watson–Crick base pairing http: //www. bio. miami. edu/~cmallery/150/gene/c 16 x 6 base-pairs. jpg

Branched DNA http: //upload. wikimedia. org/wikipedia/commons/9/92/Holliday_junction_coloured. png http: //upload. wikimedia. org/wikipedia/commons/f/f 4/Holliday_Junction. png http:

Branched DNA http: //upload. wikimedia. org/wikipedia/commons/9/92/Holliday_junction_coloured. png http: //upload. wikimedia. org/wikipedia/commons/f/f 4/Holliday_Junction. png http: //www. dna. caltech. edu/Images/DAO-WCr. gif http: //upload. wikimedia. org/wikipedia/commons/3/3 d/Mao-DX-schematic-2. jpg

Design of complex DNA structures Rothemund P W K 2006 Folding DNA to create

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

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. htm

The dirty details (cont'd) Step 2 – Cut secondary strand at this point: How

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. htm

Oh, but I forgot something major: Can't engineer segments as continuous strings! A Hands-on

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. htm

Design of complex DNA structures Rothemund P W K 2006 Folding DNA to create

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:

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. htm

Design of complex DNA structures Rothemund P W K 2006 Folding DNA to create

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

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’

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

Visualization of DNA Origami Atomic Force Microscope

But the design programming sounds REALLY complex But there is now a free, downloadable,

But the design programming sounds REALLY complex But there is now a free, downloadable, do-ityourself 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

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%20 at%20 the%20 Nanoscale. 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.

Short DNA extensions serve as LOCKS to fold structure together http: //www. virlab. virginia. edu/Nanoscience_class/lecture_notes/Seeing%20 at%20 the%20 Nanoscale. pptx

These antigen-binding single DNA strands are known as aptamers When the lock springs open

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

We Could Also Start Designing Dynamic DNA Nanomachines Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3 D components Thomas Gerling, Klaus F. Wagenbauer, Andrea M. Neuner, and Hendrik Dietz Science 27 March 2015: 347 (6229), 1446 -1452. [DOI: 10. 1126/science. aaa 5372]

Resources • Cad. Nano: http: //cadnano. org/ • DIY AFM: http: //lego 2 nano.

Resources • Cad. Nano: http: //cadnano. org/ • DIY AFM: http: //lego 2 nano. openwisdomlab. net/index. ht ml • Solve for X - Ido Bachelet - Surgical Nanorobotics: https: //www. youtube. com/watch? v=a. AH 0 L 3 e. Eo 0 • Bio. MOD Previous Years Projects: http: //openwetware. org/wiki/Biomod • biomod. net