DNA-Directed Assembly of Nanophase Materials: An Updated Review - DNA Nanotechnology: From Structure to Function - page 154

macroscopic as well as discrete nanostructures [ 13 , 14 ]. It is also noteworthy
that Xiao and Seeman et al. made the first attempt of using designer DNA
nanostructures to guide the organization of gold nanocrystals and achieved some
initial success [ 15 ].
In order to maximize the fidelity of DNA-directed nanoassembly and suppress
the formation of wrongly assembled structures, it is critical to control the valence
of DNA bonding on a nanoparticle motif. For example, a DNA monofunctionalized
gold nanoparticle can be treated as being “monovalent,” which efficiently solves
the cross-linking problem between or within the assembled structures. Actually, a
gold nanoparticle-tagged DNA oligonucleotide has no intrinsic difference from a
small molecule (e.g., a fluorescent dye) modified DNA strand, except that the bulkier
size and the more complicated surface chemistry of a nanoparticle do need special
cares. Therefore, by simply mixing all DNA stands (including the gold nanoparticle
tagged one) at appropriate stoichiometric ratios, it will be possible to generate free-
standing nanoparticle assemblies by virtue of the highly specific DNA base-pairing
interactions. This idea was first tried with great success by Alivisatos et al. for the
construction of small and finite size nanoassemblies containing a discrete number
of gold nanoparticles [ 14 , 16 ]. It was soon found by the Alivisatos group that gold
nanoparticles bearing different numbers (valences) of DNA ligands could run into
discrete bands during agarose gel electrophoresis [ 17 , 18 ]. This important finding
allowed them to isolate DNA monofunctionalized gold nanoparticles as an ideal
building block for DNA-directed nanoparticle assembly.
The first example of using DNA monofunctionalized gold nanoparticle as a
monovalence building block and a micrometer-long DNA single strand as a template
to assemble an extended one-dimensional (1D) nanoparticle array was demonstrated
by Deng and Mao et al. in 2005 [ 19 ]. With the help of a rolling circle polymerization
technique [ 20 , 21 ], Deng et al. synthesized a DNA single strand containing hundreds
of tandemly linked repeats of a 53-base DNA sequence, which then served well as
a linear template to guide the assembly of DNA monofunctionalized AuNPs into
an extended 1D nanoarray. The assembly took place in a homogeneous solution
and was accelerated by a thermal annealing of the sample. Inter- or intra-cross-
linkings of the as-formed linear nanoparticle arrays were not observed, benefiting
from the use of monovalent DNA-nanoparticle conjugates. The assembled structure
combined the nanoscopic properties of gold nanoparticles and the microscopic
manipulability of a micrometer-long DNA molecule. As a result, the linear nanopar-
ticle arrays could be stretched and aligned in parallel on a carbon-coated TEM
grid or a silicon wafer through a fluidic force-assisted molecular combing process
previously elaborated by Deng et al. [ 22 ], providing a chance to interface self-
assembled nanostructures with microelectronic device developments.
Yan et al. utilized 4 4 DNA tiles (each tile contained four four-way junctions)
to direct the assembly of gold nanoparticles into two-dimensional (2D) periodical
arrays [ 23 ]. In this work, the authors employed a forest-like protective coating of
T5 oligomers on DNA (much longer than the T5 oligomer) monofunctionalized
gold nanoparticles to achieve enhanced salt resistance, as the two-dimensional DNA