Angewandte Chemie International Edition ,
Nano-Softball Made of DNA
“Programmed” oligonucleotides with three branches organize themselves into dodecahedra
Contact: Günter von Kiedrowski, Ruhr-Universität Bochum (Germany)
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Self-Assembly of a DNA Dodecahedron from 20 Trisoligonucleotides with C3h Linkers
For quite some time, DNA, the stuff our genes are made of, has also been
considered the building material of choice for nanoscale objects. A team
led by Günter von Kiedrowski at the Ruhr University in Bochum has now
made a dodecahedron (a geometric shape with twelve surfaces) from DNA
building blocks. As reported in the journal Angewandte Chemie,
these objects are formed in a self-assembly process from 20 individual
trisoligonucleotides, building blocks consisting of a “branching
junction” and three short DNA strands.
A regular dodecahedron is a geometric shape made of 12 pentagons of
equal size, three of which are connected at every vertex. This results
in a structure with 30 edges and 20 vertices. In order to produce a
hollow dodecahedral object from DNA, the researchers used 20
“three-legged” building blocks (three DNA strands connected together at
one point). The centers of these building blocks represent the vertices
of the dodecahedron. The three edges projecting from each vertex are
formed when a single strand of DNA converts two neighboring bridging
components into a double strand.
In order for this process to result in a dodecahedron and not some other
random geometric object, all of the DNA strands must have a different
sequence. Among these, there must, however, be pairs of complementary
strands that can bind to each other.
By using a computer program, the researchers identified a set of 30
independent, 15-base-pair-long, double-stranded DNA sequences with
similar physical properties. The double-stranded sequences were assigned
to the individual edges of the dodecahedron and to specific vertices for
termination. It was then determined which three single-stranded
sequences needed to be attached to each three-legged junction for the
predetermined structure to form.
The team synthesized the 20 computed trisoligonucleotides by means of a
solid-phase synthesis. The three DNA strands were always attached by way
of an aromatic six-membered carbon ring. When mixed in equal parts in a
buffer solution, these building blocks do aggregate to form the expected
product: regular dodecahedra. Atomic force microscopy images reveal them
to be uniform particles with a diameter of about 20 nm. Under pressure,
the dodecahedra are quite flexible, the can be deformed like “soft
balls” without incurring any damage.
If the trisoligonucleotides are equipped with pendant “arms”, the
dodecahedra can be outfitted with additional functional molecules. In
this way, highly complex nanoconstructs, resembling little viruses in
shape and size, should be accessible in the future. Potential
applications range from medical diagnostics to nanoelectronics.