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Communicated by Jane S. Richardson, Duke University Medical Center, Durham, NC, May 15, 2003 (received for review February 10, 2003)
The programmed self-assembly of patterned aperiodic molecu- chemistries (20–26). The diversity of materials with known DNA
lar structures is a major challenge in nanotechnology and has attachment chemistries considerably enhances the attractiveness
numerous potential applications for nanofabrication of complex of DNA nanostructures, which can be used to form superstruc-
structures and useful devices. Here we report the construction of tures on which other materials may be assembled.
an aperiodic patterned DNA lattice (barcode lattice) by a self- Self-assembling DNA tiling lattices represent a versatile sys-
assembly process of directed nucleation of DNA tiles around a tem for nanoscale construction (27, 28). The methodology of
scaffold DNA strand. The input DNA scaffold strand, constructed DNA lattice self-assembly begins with the chemical synthesis of
by ligation of shorter synthetic oligonucleotides, provides layers single-stranded DNA molecules, which self-assemble into DNA
of the DNA lattice with barcode patterning information repre- branched motif building blocks known as tiles. DNA tiles can
sented by the presence or absence of DNA hairpin loops pro- carry sticky ends that preferentially match the sticky ends of
truding out of the lattice plane. Self-assembly of multiple DNA other particular DNA tiles, thereby facilitating the further
tiles around the scaffold strand was shown to result in a assembly into tiling lattices. Self-assembled 2D DNA tiling
patterned lattice containing barcode information of 01101. We lattices composed of tens of thousands of tiles have been
have also demonstrated the reprogramming of the system to demonstrated by the Seeman, Winfree, and Reif groups and
CHEMISTRY
another patterning. An inverted barcode pattern of 10010 was visualized by molecular imaging techniques such as atomic force
achieved by modifying the scaffold strands and one of the microscopy (AFM) (6–9). Recent experiments by the Seeman
strands composing each tile. A ribbon lattice, consisting of and Reif groups have demonstrated computation (logical exclu-
repetitions of the barcode pattern with expected periodicity, sive or) via molecular assembly of DNA tiles (15, 17).
was also constructed by the addition of sticky ends. The pat- Previous DNA self-assembly systems provided either small
terning of both classes of lattices was clearly observable via computational assemblies or large lattices with simple periodic
atomic force microscopy. These results represent a step toward patterning. There remains the further challenge of programming
implementation of a visual readout system capable of convert- the self-assembly of patterned aperiodic DNA lattices with
ing information encoded on a 1D DNA strand into a 2D form increasing size and increasing pattern complexity. This holds the
readable by advanced microscopic techniques. A functioning potential of allowing us to build templates, on which molecular
visual output method would not only increase the readout speed electronics and robotics components can be positioned with
of DNA-based computers, but may also find use in other se- precision and specificity. A fully programmable aperiodic DNA
quence identification techniques such as mutation or allele tiling system will also find use as a visual readout method that
mapping. will increase the ease and speed of output from DNA-based
computers.
There are at least three major strategies for the formation of
T he field of nanotechnology holds tremendous promise. If
the molecular and supramolecular world can be controlled
at will, then it may be possible to achieve vastly better
patterned DNA tiling lattice self-assemblies:
(i) Unmediated algorithmic self-assembly is the most gen-
eral method for 2D pattern formation. It entails the use of a
performance for computers and memories, and it might open
small set of DNA tiles that self-assemble in a predictable
up a host of other applications in materials science, medicine,
manner. Unmediated algorithmic self-assembly is Turing-
and biology. Because of this promise, numerous research
universal (29) and is thus theoretically capable of creating
teams have embarked on the development of various detailed
complex structures from simple rules. This method has the
aspects of nanotechnology, such as the use of physically strong
advantage of being very general and not requiring an input
and electrically active fullerene materials (1), and organic
DNA strand encoding a pattern; instead, the 2D pattern is
molecules that have electrical switching properties (2). The
generated de novo based on the neighbor relations encoded
construction of molecular-scale structures is one of the key
within the DNA tile set. Unmediated algorithmic self-assembly
challenges facing science and technology in the 21st century. of complex patterns requires delicate control of physical
There are two distinct approaches to the fabrication of nano- phenomena, which include nucleation rates, crystal growth
materials: top-down methods and bottom-up approaches. Top- rates, spontaneous nucleation, and error rates in solutions
down methods, exemplified by e-beam lithography, may be containing many distinct DNA tile types.
limited by their serial nature, whereas bottom-up methods (ii) Another approach is sequential stepwise assembly, similar
using self-assembly are by nature highly parallel. Although to strategies used frequently in synthetic chemistry. It begins
self-assembly methods are well known and have been long used with separate assembly of a small number of distinct molecular
by chemists, they conventionally result in structures with building blocks (MBBs). These MBBs are then combined to
limited complexity (e.g., regular, periodic patterning with a construct larger assemblies in a stepwise fashion, possibly with
small number of programmed association rules), and most an initial building block attached to a solid support, to enable
current methods do not allow the self-assembly to be readily removal of excess reactants after each step. In the context of
reprogrammable. DNA lattices, these MBBs may be DNA tiles, as described above.
In recent years, DNA has been advanced as a useful material
for constructing periodically patterned structures (3–9), nano-
mechanical devices (10–13), and molecular computing systems Abbreviations: AFM, atomic force microscopy; MBB, molecular building block; DX, double
(14–19). DNA also has been designed to direct the assembly of crossover.
other functional molecules by the use of appropriate attachment *To whom correspondence should be addressed. E-mail: reif@cs.duke.edu.
CHEMISTRY
components beyond that possible in a large 2D periodic DNA tile feasible for assembling moderately sized 2D patterned DNA
lattice (6–9). Protein–protein or protein–DNA interaction can lattices.
be studied by controlling the distance between binding sites. DNA self-assembly is expected to be useful in various
The helix-stacking effect between blunt-end DNA double- applications in nanofabrication and for arrangement of mo-
helices described above suggests that its importance in self- lecular components. An illustrative example of a more com-
assembly of DNA tiles, lattice, and higher-order superstruc- plex target pattern is to create the layout for a demultiplexed
tures should not be neglected. Sticky ends provide specificity random access memory (RAM) circuit, which could poten-
to helix– helix associations, but the importance of base- tially serve as a template for molecular electronics (36). A
stacking energetics in these interactions (even devoid of RAM circuit essentially consists of a periodic lattice of
single-stranded DNA base-pairing) is revealed by the preva- memory elements coupled to a means to specifically address
lence of stacking between lattice pieces. A special DNA unit any given element for writing or reading a logical bit. Directed
lattice with defined dimensions could be designed to study nucleation self-assembly may also permit the fabrication of
helix stacking between DNA double-helices with different other patterns useful for nanoelectronic and nanoscale objects
base pair contents. To avoid helix stacking in the self-assembly for other fields of technology.
of DNA tile lattices, capping loops [unpaired poly(T) sequenc-
es] could be placed on the ends of some or all portions of the We thank Prof. Erik Winfree (California Institute of Technology,
barcode lattice helices. Pasadena) for providing access to a Multimode Nanoscope IIIa AFM,
Drs. Paul Rothemund and Nick Papadakis for useful advice on the
The scaffold strands described here encode 1D information. operation of the AFM, and Arnold E. Reif for helpful editorial sugges-
However, 2D patterns might also be constructed by the self- tions. This work was supported by National Science Foundation Grants
assembly of tiles around a DNA scaffold strand, as illustrated in EIA-00-86015 (to J.H.R.), EIA-0218376 (to T.H.L.), and EIA-0218359
Fig. 5, where the DNA sequence information to generate a letter (to H.Y.) and Defense Advanced Research Projects AgencyyAir Force
D is encoded in the scaffold strand. Once the rest of the tiles Office of Scientific Research Grant F30602-01-2-0561 (to J.H.R.).
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