[tt] eurekalert, newscientist: arranging nanoparticles by DNA linkers, now in 3D

[Alejandro Dubrovsky]

(
http://technology.newscientist.com/channel/tech/dn13254-dna-construction-kit-selfassembles-3d-crystals.html?feedId=online-news_rss20
and
http://www.eurekalert.org/pub_releases/2008-01/nu-dib012508.php
)

DNA construction kit self-assembles 3D crystals

 * 18:00 30 January 2008
 * NewScientist.com news service
 * Mason Inman

Strands of DNA can be programmed to assemble nanoparticles into 3D
structures, pointing towards a new way to engineer materials from the
bottom up.

Two research groups have demonstrated the technique, using squid-like
gold nanoparticles with "arms" made of DNA. After that the nanoparticles
just need to be mixed together. The DNA strands start linking to one
another, corralling the particles into sponge-like crystals.

"These are fundamentally new structures of matter," says Chad Mirkin of
Northwestern University in Evanston, US, who led one of the groups.

Mirkin and colleagues hope this new approach to building materials could
find a host of uses, from assembling crystals for optical communications
to building structures inside the body to attack disease.
New dimension

Previously, only flat shapes have been assembled in this way. Attempts
to make 3D structures only produced amorphous clumps of particles.

Now Mirkin's team and another led by Oleg Gang of Brookhaven National
Laboratory in New York, US, have shown how to reach up into the third
dimension. A key step was to make the DNA strands more flexible, giving
them more freedom to connect with their neighbours.

"This is the first step in demonstrating that it is possible to obtain
ordered 3D structures," Gang says. "It opens so many avenues for
researchers, and this is why it is so exciting."

"We are now closer to the dream of learning how to break everything down
into fundamental building blocks, which for us are nanoparticles, and
reassembling them into whatever structure we want," Mirkin says.
Sticky DNA

Both teams started with tiny spheres of gold around 10 nanometres
across, and attached short strands of DNA. Choosing the sequence of
bases, or "letters" in that DNA can program them to reliably bind
together in particular ways.

Using slightly different techniques, the two groups both designed DNA
strands with "sticky ends" that would bind only to particular strands on
other particles.

The teams programmed their DNA to coax around a million of the
nanoparticles into a crystal shape called "body centered cubic", the
same structure as iron. Nanoparticles are arranged to form the corners
of a cube with another particle at its centre. Mirkin's group also
programmed a different crystal structure known as 'face centred cubic'.

By varying the length of the DNA strands and design of the sticky ends,
it should be possible to build in different styles. "You could sprinkle
in one kind of DNA for this structure, and sprinkle in another DNA for a
different structure," Mirkin says.
Sticky when wet

There is one catch, however – the structures made so far must stay wet,
otherwise the strands' sticky ends lose their grip. It may become
possible to 'fix' the spongy structures rigid, but they could have their
uses even now.

Since they are mostly water, "a lot of molecules can flow through and
interact with the nanoparticles," Gang says. He imagines using such a
structure built from a mix of catalytic particles, to control chemical
reactions in a flow of liquid.

"Their technique should work for other varities of technologically
exciting nanoparticles," says John Crocker of the University of
Pennsylvania in Phildelphia, US.

Using the method on nanoparticles with different shapes would allow the
creation of much more complex structures, he adds. The group at
Northwestern University is already working on that.

Journal references: Nature (DOI: 10.1038/nature06508 and
DOI:10.1038/nature06560

---


Contact: Megan Fellman
fellman at northwestern.edu
847-491-3115
Northwestern University
DNA is blueprint, contractor and construction worker for new structures

DNA is the blueprint of all life, giving instruction and function to
organisms ranging from simple one-celled bacteria to complex human
beings. Now Northwestern University researchers report they have used
DNA as the blueprint, contractor and construction worker to build a
three-dimensional structure out of gold, a lifeless material.

Using just one kind of nanoparticle (gold) the researchers built two
common but very different crystalline structures by merely changing one
thing -- the strands of synthesized DNA attached to the tiny gold
spheres. A different DNA sequence in the strand resulted in the
formation of a different crystal.

The technique, to be published Jan. 31 as the cover story in the journal
Nature and reflecting more than a decade of work, is a major and
fundamental step toward building functional “designer” materials using
programmable self-assembly. This “bottom-up” approach will allow
scientists to take inorganic materials and build structures with
specific properties for a given application, such as therapeutics,
biodiagnostics, optics, electronics or catalysis.

Most gems, such as diamonds, rubies and sapphires, are crystalline
inorganic materials. Within each crystal structure, the atoms have
precise locations, which give each material its unique properties.
Diamond’s renowned hardness and refractive properties are due to its
structure -- the precise location of its carbon atoms.

In the Northwestern study, gold nanoparticles take the place of atoms.
The novel part of the work is that the researchers use DNA to drive the
assembly of the crystal. Changing the DNA strand’s sequence of As, Ts,
Gs and Cs changes the blueprint, and thus the shape, of the crystalline
structure. The two crystals reported in Nature, both made of gold, have
different properties because the particles are arranged differently.

“We are now closer to the dream of learning, as nanoscientists, how to
break everything down into fundamental building blocks, which for us are
nanoparticles, and reassembling them into whatever structure we want
that gives us the properties needed for certain applications,” said Chad
A. Mirkin, one of the paper’s senior authors and George B. Rathmann
Professor of Chemistry in the Weinberg College of Arts and Sciences,
professor of medicine and professor of materials science and
engineering. In addition to Mirkin, George C. Schatz, Morrison Professor
of Chemistry, directed the work.

By changing the type of DNA on the surface of the particles, the
Northwestern team can get the particles to arrange differently in space.
The structures that finally form are the ones that maximize DNA
hybridization. DNA is the stabilizing force, the glue that holds the
structure together. “These structures are a new form of matter,” said
Mirkin, “that would be difficult, if not impossible, to make any other
way.”

He likens the process to building a house. Starting with basic materials
such as bricks, wood, siding, stone and shingles, a construction team
can build many different types of houses out of the same building
blocks. In the Northwestern work, the DNA controls where the building
blocks (the gold nanoparticles) are positioned in the final crystal
structure, arranging the particles in a functional way. The DNA does all
the heavy lifting so the researchers don’t have to.

Mirkin, Schatz and their team just used one building block, gold
spheres, but as the method is further developed, a multitude of building
blocks of different sizes can be used -- with different composition
(gold, silver and fluorescent particles, for example) and different
shapes (spheres, rods, cubes and triangles). Controlling the distance
between the nanoparticles is also key to the structure’s function.

“Once you get good at this you can build anything you want,” said
Mirkin, director of Northwestern’s International Institute for
Nanotechnology.

“The rules that govern self-assembly are not known, however,” said
Schatz, “and determining how to combine nanoparticles into interesting
structures is one of the big challenges of the field.”

The Northwestern researchers started with gold nanoparticles (15
nanometers in diameter) and attached double-stranded DNA to each
particle with one of the strands significantly longer than the other.
The single-stranded portion of this DNA serves as the “linker DNA,”
which seeks out a complementary single strand of DNA attached to another
gold nanoparticle. The binding of the two single strands of linker DNA
to each other completes the double helix, tightly binding the particles
to each other.

Each gold nanoparticle has multiple strands of DNA attached to its
surface so the nanoparticle is binding in many directions, resulting in
a three-dimensional structure -- a crystal. One sequence of linker DNA,
programmed by the researchers, results in one type of crystal structure
while a different sequence of linker DNA results in a different
structure.

“We even found a case where the same linker could give different
structures, depending on the temperatures at which the particles were
mixed,” said Schatz.

Using the extremely brilliant X-rays produced by the Advanced Photon
Source synchrotron at Argonne National Laboratory in combination with
computational simulations, the research team imaged the crystals to
determine the exact location of the particles throughout the structure.
The final crystals have approximately 1 million nanoparticles.

“It took scientists decades of work to learn how to synthesize DNA,”
said Mirkin. “Now we’ve learned how to use the synthesized form outside
the body to arrange lifeless matter into things that are useful, which
is really quite spectacular.”

###

The Nature paper is titled “DNA-programmable nanoparticle
crystallization.” In addition to Mirkin and Schatz, other authors are
Sung Yong Park, a former postdoctoral fellow in Schatz’s lab and now at
the University of Rochester (lead author); graduate student Abigail K.
R. Lytton-Jean, Northwestern University; Byeongdu Lee, Advanced Photon
Source, Argonne National Laboratory; and Steven Weigand, Northwestern’s
DND-CAT Synchrotron Research Center at Argonne’s Advanced Photon Source.