Origami DNA

Edson P. Bellido Sosa

What DNA is?

•DNA stands for Deoxyribonucleic acid

•Contains the genetic instructions of living organisms

•Polymer of nucleotides, with backbones of sugars and phosphate groups joined by ester bonds.

•A base is attached to each sugar.

•The sequence of bases encodes information.

http://upload.wikimedia.org/wikipedia/commons/4/43/Deoxyribose.pnghttp://www.thestandard.org.nz/wp-content/uploads/2009/01/phosphate.gifhttp://med.mui.ac.ir/slide/genetic/dna_molecule.gifhttp://upload.wikimedia.org/wikipedia/commons/c/cf/Adenine_chemical_structure.png

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Phosphate 2-deoxyribose Base (adenine)

Watson–Crick base pairing

•The DNA double helix is stabilized by hydrogen bonds between the bases.•The four bases are adenine (A), cytosine (C), guanine (G) and thymine (T).

•Each type of base on one strand forms a bond with just one type of base on the other strand. This is called complementary base pairing.

•A bonds only with T, and C bonds only with G.

•Hydrogen bonds are weak, they can be broken and rejoined relatively easily.

•The two strands of DNA in a double helix can pulled apart by a mechanical force or high temperature.

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

Branched DNA

•DNA is normally a linear molecule, in that its axis is unbranched.

•DNA molecules containing junctions can also be made using individual DNA strands which are complementary to each other in the correct pattern.

•Due to Watson-Crick base pairing, only complementary portions of the strands will attach to each other.

• One example is the "double-crossover“.

•Two DNA duplexes lie next to each other, and share two junction points where strands cross from one duplex into the other.

•The junction points are now constrained to a single orientation.

•Suitable as a structural building block for larger DNA complexes

http://upload.wikimedia.org/wikipedia/commons/9/92/Holliday_junction_coloured.pnghttp://upload.wikimedia.org/wikipedia/commons/f/f4/Holliday_Junction.pnghttp://www.dna.caltech.edu/Images/DAO-WCr.gifhttp://upload.wikimedia.org/wikipedia/commons/3/3d/Mao-DX-schematic-2.jpg

Design of complex DNA structures

•The first step is to build a geometric model of a DNA structure that will approximate the desired shape.

•The shape is filled from top to bottom by an even number of parallel double helices, idealized as cylinders.

•The helices are cut to fit the shape in sequential pairs and are constrained to be an integer number of turns in length.

•To hold the helices together, a periodic array of crossovers is incorporated.

•The resulting model approximates the shape within one turn (3.6 nm) in the x-direction and roughly two helical widths (4 nm) in the y-direction

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

Design of complex DNA structures

•The second step is to fold a single long scaffold strand back and forth in a raster fill pattern so that it comprises one of the two strands in every helix.

•progression of the scaffold from one helix to another creates an additional set of crossovers.

• The fundamental constraint on a folding path is that the scaffold can form a crossover only at those locations where the DNA twist places it at a tangent point between helices.

•Thus for the scaffold to raster progressively from one helix to another and onto a third, the distance between successive scaffold crossovers must be an odd number of half turns.

•Conversely, where the raster reverses direction vertically and returns to a previously visited helix, the distance between scaffold crossovers must be an even number of half-turns.

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

Design of complex DNA structures

•The geometric model and a folding path are represented as lists of DNA lengths and offsets in units of half turns.

•These lists, along with the DNA sequence of the actual scaffold to be used, are input to a computer program that designs a set of ‘staple strands’ that provide Watson–Crick complements for the scaffold and create the periodic crossovers.

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

Design of complex DNA structures

•In the final step, pairs of adjacent staples are merged across nicks to yield fewer and longer staples.

•To strengthen a seam, an additional pattern of breaks and merges may be imposed to yield staples that cross the seam.

• All merge patterns create the same shape but the merge pattern dictates the type of grid underlying any pixel pattern later applied to the shape.

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

Synthesis of DNA origami

•Rothemund combined the DNA of a common virus M13mp18 , 250 helper strands and magnesium buffer.

•The mixture of strands is then heated to near boiling (90 °C) and cooled back to room temperature (20 °C) over the course of about 2 hours. Fig.

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

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

Synthesis of DNA origami

Patterning and combining DNA origami

•Staple strands can serve as decorating shapes with arbitrary patterns of binary pixels.

•The original set of staples represent binary “0”s and a new set of labelled staples represent binary “1”s.

•A variety of DNA modifications could be used as labels for example, biotinor fluorophores.

•Rothemund used “dumbbell hairpins” in the middle of 32-mer staples at the position of merges made during design.

•Depending on the merge pattern, the resulting pixel pattern was either rectilinear,with adjacent columns of hairpins on alternate faces of the shape, or not uniform and nearly hexagonally packed, with all hairpins on the same face.

•In AFM images labelled staples give greater height contrast (3nm above the mica) than unlabelled staples (,1.5 nm), which results in a pattern of light “1” and dark “0” pixels.

Patterning and combining DNA origami

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

Positioning of DNA origami

•DNA origami can serve as a template to organize nanostructures •One can use lithography to make templates onto which discrete components can self-assemble.

•This components will also organize structures with even smaller features.

Kershner, R. J. et al. Nature Nanotech. 4, 557–561 (2009).

TMS=trimethylsilylDCL=diamond-like carbon films

Positioning of DNA origami

The DNA triangles are positioned on the E-beam patterned triangles on and in the 300nm optically patterned lines on TMS/SiO2.

Also the triangles are positioned on 110 nm E-beam patterned triangles and 200nm patterned lines on a DLC/DLC on silicon surface.

500nm 500nm

500nm 500nm

Kershner, R. J. et al. Nature Nanotech. 4, 557–561 (2009).

Positioning of DNA origami

Kershner, R. J. et al. Nature Nanotech. 4, 557–561 (2009).

•Also geometric structures were fabricated on DCL/DCL.

•The DNA triangles are expected to bind and resemble the structures

1µm

DNA origami base Nano-devices (future research)

•Combination of top-down and bottom-up approach (lithography).

•DNA origami and combinations of DNA origami and other biomolecules as a building blocks (biotin).

•Use of the structural proteins that naturally bind DNA to fabricate bio sensors(histones, antibodies).

•Use of DNA origami as gene sequencer

•Use of DNA origami as breadboard for molecular electronics

Au

Au

Si

SiO2

Antibody

Antigen

DNA origami

DNA origami

CNT