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.
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)
+
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.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
•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
Synthesis of DNA origami
Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297–302
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, biotin
or 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
TMS=trimethylsilyl
DCL=diamond-like carbon films
•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).
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.
500nm
500nm
Also the triangles are positioned on 110 nm E-beam patterned triangles and 200nm
patterned lines on a DLC/DLC on silicon surface.
500nm
Kershner, R. J. et al. Nature Nanotech. 4, 557–561 (2009).
500nm
Positioning of DNA origami
•Also geometric structures were fabricated on
DCL/DCL.
•The DNA triangles are expected to bind and
resemble the structures
1µm
Kershner, R. J. et al. Nature Nanotech. 4, 557–561 (2009).
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).
CNT
DNA origami
•Use of DNA origami as gene sequencer
•Use of DNA origami as breadboard for molecular electronics
Antigen
Antibody
Au
DNA origami
Au
SiO2
Si