Download 5 Conclusion - Duke Computer Science

(TASK 2) NANO-CONSTRUCTION:
DETAILS OF RECENT PROGRESS:
(2.1): DNA NANOSTRUCTURES. Designed and experimentally tested in the lab a new
DNA tile (TAO35) which is a rectangular shaped triple crossover molecule with sticky
ends on each side that can match with other such tiles and with a "reporter" ssDNA
sequence that runs through the tile from lower left to upper right, facilitating output of the
tiling computation. This tile and its unique properties will be key to our subsequent
experiments in massively parallel arithmetic using self-assembly of DNA tiles.
LaBean, T. H., H. Yan, J. H. Reif and N. Seeman, Construction and Analysis of a DNA
Triple Crossover Molecule, submitted for publication, (1999).
(2.2) DNA COMPUTATIONS using Self Assembly of Tilings
We have made significant progress with experimental implementation of DNA-based
computers which perform calculations during self-assembly of specific nanoscale tilings.
We have successfully prototyped a novel read-in method for tiling-based computers: we
have demonstrated for the first time that long single-strand DNA molecules, which we
refer to as scaffold strands, effectively serve as nucleation regions for the formation of
specific, multi-component tile assemblies. These scaffold strands have been used to
generate a variety of tile assemblies and are useful directly as a means of reading specific
inputs into current DNA tiling assembly computers. In addition, we have produced
detailed designs for an improved DNA-based ("string tile") computer which makes
optimal use of local parallelism by producing linear assemblies, thereby avoiding several
potential experimental limitations inherent in previous 2-dimensional tile-assembly
schemes.
LaBean, T. H., E. Winfree, J. H. Reif, Experimental Progress in Computation by SelfAssembly of DNA Tilings, 5th International Meeting on DNA Based Computers(DNA5),
MIT, Cambridge, MA, (June, 1999). To appear in DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, ed. E. Winfree, (1999).
http://www.cs.duke.edu/~thl/tilings/labean.ps
Graphics and Slides:
http://www.cs.duke.edu/~reif/paper/DNAtiling/tiling.slides/index.htm
http://www.cs.duke.edu/~thl/tilings/TileTalkSlides.hqx
Lagoudakis, M. G., T. H. LaBean, 2D DNA Self-Assembly for Satisfiability, 5th
International Meeting on DNA Based Computers(DNA5), MIT, Cambridge, MA, (June,
1999). To appear in DIMACS Series in Discrete Mathematics and Theoretical Computer
Science, ed. E. Winfree, (1999).
Reif, J.H., Local Parallel Biomolecular Computation, DIMACS Workshop on DNA Based
Computers, Series in Discrete Mathematics and Theoretical Computer Science, vol. 44 ,
American Mathematical Society, ed. H. Rubin, published Sept. 1998. Postscript versions
of this paper and its figures are at
http://www.cs.duke.edu/~reif/paper/Assembly.ps
http://www.cs.duke.edu/~reif/paper/Assembly.fig.ps
(2.3) Self-assembly of 2D LATTICES of DNA Tiles
We experimentally constructed for the first time large 2D arrays of DNA tiles via selfassembly. The arrays ranged in size up to thousands of tiles. These DNA tilings used
identical or nearly identical DNA tiles. The tilings were verified by a variety of
techniques, including spectacular images using an atomic force microscope(AFM) and
also "reporter" ssDNA sequences. This provides the first experimental evidence of the
feasibility of the nano-construction of large arrays via self-assembly of DNA tiles. In
particular, a system of two double-crossover (DX) units was designed to self-assemble
into a periodic 2D lattice. A hairpin sequence was inserted into one of the units to provide
a topographic contrast agent, resulting in 25 nm stripes in the lattice. Winfree have
confirmed both lattices by atomic force microscopy (AFM), with supporting evidence
from ligation studies. In Seeman's lab, a similar system of two larger DX units has
produced lattices with 32 nm stripes; the design was elaborated to a four-unit system
producing 64 nm stripes, clearly demonstrating the programmable nature of the DX
system. These results were reported in fall, 1998 in (Winfree, Liu, Wenzler, Seeman,
1998).
*Spectacular AFM Images of the first Large Scale DNA Tilings are at:
http://seemanlab4.chem.nyu.edu/two.d.html
Also see:
http://seemanlab4.chem.nyu.edu/abstar.gif
http://seemanlab4.chem.nyu.edu/fl32nm.gif
http://seemanlab4.chem.nyu.edu/abcdstar.gif
http://seemanlab4.chem.nyu.edu/fl64nm.gif
http://seemanlab4.chem.nyu.edu/12.gif
Further Recent 1999 Progress:
-We have built planar arrays from triple crossover molecules. This demonstrates that
previous results can be extended to triple crossover molecules.
-We have built arrays from triple crossover molecules containing roughly orthogonal
components as precursor to constructing 3D arrays. This demonstrates that the gaps in
triple crossover arrays can be filled with other multi-crossover molecules, and the
feasibility of using this approach to get to 3D.
- We have built arrays from parallelograms of single-crossover components. This
demonstrates that a new, and possibly simpler, motif is available for use as DNA cellular
automata.
- We have constructed single-crossover molecules from complexes containing 5',5' and
3',3' linkages. This demonstrates that head-to-head and tail-to-tail stands can be
incorporated in arrays. These are likely to be components of molecules that exhibit
sequence-dependent transitions.
Recent Paper abstracts by Seeman:
http://seemanlab4.chem.nyu.edu/darpa.0499.2.html
E. Winfree, F. Liu, Lisa A. Wenzler, N. C. Seeman, Design and Self-Assembly of Two
Dimensional DNA Crystals, Nature 394: 539--544, 1998. (1998).
N.C. Seeman, Nucleic Acid Nanostructures and Topology. Angewandte Chemie. 110,
3408-3428 (1998); Angewandte Chemie International Edition 37, 3220-3238, (1998).
F. Liu, R. Sha and N.C. Seeman, Modifying the Surface Features of Two-Dimensional
DNA Crystals, Journal of the American Chemical Society 121, 917-922 (1999).
(Demonstrates that patterns generated by self-assembly can be modified using standard
DNA biotechnology. Will permit attachment of new chemistries at particular places to
mark particular features in an assembly.)
R. Sha, F. Liu, M.F. Bruist and N.C. Seeman, Parallel Helical Domains in DNA
Branched Junctions Containing 5', 5' and 3', 3' Linkages, Biochemistry 38, 2832-2841
(1999). (Demonstrates that it is possible to include 5', 5' and 3', 3' linkages in branched
DNA motifs. This is important, because it appears that these elements are key to the
successful construction of molecules that can undergo sequence dependent mechanical
transitions.)
(2.2) DNA NANOMOTORS. We also developed DNA molecules that reconfigure for
possible use as nano-scale motors. We designed and experimentally tested in the lab a 2state DNA nano-device that changes shape in response to a chemical stimulus. In
particular, we constructed a molecular device that consists of two rigid DNA double
crossover (DX) molecules connected by 4.5 double helical turns; one domain of each DX
molecule is attached to the connecting helix. We have used the B-Z transition as the basis
for the structural alteration we wish to induce. It changes shape predicated on this B-Z
transition. We detected relative strand position changes by fluorescence resonance energy
transfer(FRET), because the separation of two dyes attached to the device changes as a
consequence of the transition. We obtained FRET evidence that we can cycle this device.
Control measurements were performed to confirm this finding. This provides the first
experimental methodology for nano-construction of a DNA motor. We are beginning
electrophoretic mobility characterization of sequence-independent identity testing (SIIT),
complete SIIT characterization by electrophoretic mobility, and characterize SIIT by
FRET.
See Figure of DNA Motor at: http://seemanlab4.chem.nyu.edu/device.jpeg
For more details and graphics see: http://seemanlab4.chem.nyu.edu/device.html
C. Mao, W. Sun, Z. Shen and N.C. Seeman, A DNA Nanomechanical Device Based on
the B-Z Transition, Nature 397, 144-146 (1999).
(Demonstrates that we can control DNA molecular transitions, and that we can detect
those same motions. We can now apply the same methodology to sequence-dependent
transitions, once we get the chemistry to work. The importance of sequence-dependent
transitions (the molecular equivalent of a Dirac delta function for a given sequence) for
DNA computing and nano-manufacturing is evident.)
(2.3) Assembly Simulations Using Plastic Tiles. A new system for performing
computation via self-assembly was explored. Plastic tiles 1 cm on a side self-assemble to
form segments of the famous Penrose tiling. This tiling has been used to model the
structure of quasicrystals. These tiles form aperiodic patterns that correspond to
Fibonacci sequences--the self-assembly of the tiles 'computes' the sequences.
Graphics URL:
Self-assembling Penrose tiles (http://www-scf.usc.edu/~pwkr/BMC/penrose.gif, 75 KB)
Paul W.K. Rothemund and Leonard M. Adleman, Programmed self-assembly using
lateral capillary forces, submitted to Nature, 1999.