(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).

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 Self-Assembly 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).

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

(2.3) Self-assembly of 2D LATTICES of DNA Tiles

We experimentally constructed for the first time large 2D arrays of DNA tiles via self-assembly. 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:

Also see:

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:

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 2-state 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.

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.