Rothemund lab at Caltech:

Publications

(...under (re)construction, paper commentaries are from the the old joint publications page ...)

Ashwin's new placement paper

Sungwooks 2D surface crystallization paper.

Cody and Ebbe's RNA origami science paper

Commentary with Ebbe.

Sturdier tubes with Deborah

Put very old grubbs paper at end.


Sungwook's PhD Thesis: Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions. *
144 pages. California Institute of Technology. Submitted May 2013.
Sungwook Woo. Thesis advisor: Paul W.K. Rothemund.
Central to DNA nanotechnology is the Watson-Crick base pair. The exquisite specificity, predictable strength, and combinatorial diversity of hybridization reactions based on complementary DNA sequences is what enables us to create sophisticated molecular programs. But what other bases for complementary binding interactions might there be? Might we be able to construct a new type of bonding with the specificity and combinatorial diversity of DNA hybridization, but which has new and different properties, perhaps allowing for easier reconfiguration of self-assembled nanomachine parts? In his PhD thesis, Sungwook starts from the simple observation that DNA origami stick together at their edges via blunt-end stacking, and constructs and studies a new system for combining origami based on binary- and shape-coded stacking interactions. Sungwook applies stacking interactions towards two different goals: the creation of large two-dimensional origami crystals on surfaces, and the origanization of expanding protein filaments to create large-scale self-assembled geometries. Just as strand displacement enabled a whole host of molecular programs which were unavailable to simple equilibrium DNA hybridization, perhaps programmable stacking bonds will enable a class of new molecular programs which undergo large scale geometric rearrangement.
[ PhD thesis, 46 MB (better @ 82 MB); Caltech ETD.]


  • Programmable molecular recognition based on the geometry of DNA nanostructures. *
    Sungwook Woo and Paul W. K. Rothemund.
    Benoit Mandelbrot famously noted that the geometry of natural objects is often fractal -- that self-similar structures appear at many scales, resulting in a fractional dimensional exponent. Self-similarity can appear not only in static objects, but in dynamic behavior patterns, or even in concepts. Here, Sungwook and Paul show that the principles of sequence-specific binding, which we enjoy at the nanometer scale in DNA and RNA, reappear at a ten times larger scale when engineering nanostructures (and eventually nanomachines) using DNA origami.
    [ Nature Chemistry: online 10 July 2011 (8 pages): article, 3.5MB and SI, 7.2MB See also Nature Chemistry News and View ; reporting in Nature Methods ]
  • Programmable Control of Nucleation for Algorithmic Self-Assembly. (Journal version, December 4, 2009) see below
  • Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. *
    Hareem T. Maune, Si-Ping Han, Robert D. Barish, Marc Bockrath, William A. Goddard III, Paul W. K. Rothemund, Erik Winfree.
    Carbon nanotubes are amazing molecules -- rolled up sheets of hexagonal carbon mesh with astounding thermal and electrical properties, they're the nanocircuit engineer's dream. But they're oh so hard to handle! Too small and too slippery to pick up and put them where you want, most researchers either study individual nanotubes, make do with regular arrays of nanotubes, look for chance circuits in randomly scattered piles of nanotubes, or rely on bulk properties of tangled tubes. Here we suggest a way to self-assemble complex nanotube circuits in parallel -- by sticking them in precise locations on DNA origami nanobreadboards. In the future, we envision this technique being expanded from the two-nanotube devices demonstrated in this paper, to multiple nanotube circuits on individual origami, to large-scale nanotube circuits on origami placed on lithographically-patterned surfaces. Dream on!
    [ Nature Nanotechnology, 5: 61-66, 2010 (online 8 November, 2009; 5 pages): paper, 1.3 MB, supplementary information, 2.1 MB.]
    (Caltech press release, Eric Drexler's blog )
  • Placement and orientation of individual DNA shapes on lithographically patterned surfaces. *
    RJ Kershner, LD Bozano, CM Micheel, AH Hung, AR Fornof, JN Cha, CT Rettner, M Bersani, J Frommer, PWK Rothemund, GM Wallraff.
    Electrical engineers excel at making things using top-down patterning, such as using lithograph to etch circuits on large wafers of silicon, but it is quite difficult to achieve feature sizes below 20nm. Molecular engineers excel at making things using bottom-up self-assembly, such as using DNA hybridization to fold a virus genome into DNA origami, but it is quite difficult to put all the precisely-constructed molecules in the right places on a large scale. Patterning from 10cm down to 20nm. Patterning from 100nm down to 3Å. A match made in heaven. (Joint Caltech/IBM work.)
    [Nature Nanotechnology, 3: 557-561, 16 August, 2009 (5 pages): paper, 784 KB, supplementary information, 9.9 MB, and supplementary movie, 3.3 MB.]
    (Comments in the press... but please take them with a grain of salt. Working nanoscale circuits are much much further from reality than some of these would suggest. Let's be clear: the work here doesn't attempt to make functional circuits, it just provides a step toward the solution for how to position DNA origami on a lithographically-patterned substrate. We have no idea when or if this approach will pay off for a commercial application. Anyway: Caltech Press Release, IBM Press Release, guardian.co.uk, BBC, CNET, Wired, EE Times, Discover Magazine )
  • An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly. *
    Robert D. Barish, Rebecca Schulman, Paul W. K. Rothemund, and Erik Winfree.
    What is a seed? The tiny seed of a giant sequoia tree, sprouting after the fire. The invisible seed of an idea, from which a thousand possibilities grow. A crystal seed, determining the order of all that grows from it. The seed of man and woman, carrying with it the future of humanity. Clearly, it's important stuff. Why? The seed carries the information, the creative part, the inspiration -- and what follows is mere mechanism, the consequences, the algorithm. In this work, we use DNA origami as a highly effective seed for growing DNA tile crystals. Arbitrary information can be put on the seed; it directs the growth of DNA crystals and determines their morphology... much as a genome determines phenotype of an organism... or even, as an idea creates the future.
    [PNAS, 106: 6054-6059, 2009 (6 pages): .pdf, 1.7 MB, supplementary information, 2.6 MB, and appendix, 124 KB. ]
    (Comments in the press: Caltech Press Release, New Scientist, Foresight )
  • An autonomous polymerization motor powered by DNA hybridization. *
    Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.
    Can a DNA molecule walk? Can we design a molecular motor from scratch? If so, how could it work? Consider macroscopic motors for a minute: they come in all varieties, using all sorts of principles -- internal combustion engines, steam engines, Wankel rotary engines, electric motors, pneumatic motors, solenoids, rockets, jets... each best suited to different tasks. The molecular world has similar diversity. In biology, we see rotary motors like ATPase and the flagellar motor, walking motors like kinesin, linear motors like RNA polymerase and the ribosome, and waving motors like cilia. Not to mention muscle. Among the most mind-bending are the polymerization motors of pathogenic bacteria, such as Rickettsia and Listeria, that live inside eukaryotic host cells. By displaying proteins that catalyze the polymerization of the host cell's actin, these bacteria create a "comet tail" behind them that pushes them forcefully through the cell and even into neighboring cells. This was the motor principle targeted in our work, which was lead by Niles' group. Perhaps most fascinating is that the DNA polymers grow by insertion between the polymer tail and the DNA catalyst strands anchored on the "surrogate bacterial cell". This insertion takes place by a series of conformational rearrangements without ever the two sides losing their strong attachment to each other. Quite a dance!
    [Nature Nanotechnology, (vol. 2, pp. 490-494, 2007) (5 pages): .pdf, 738 KB and supplementary information, 581 KB. ]
  • Folding DNA to create nanoscale shapes and patterns. *
    Paul W. K. Rothemund
    Paul sends a swarm of staple strands to tie viral DNA in knots...thereby self-assembling 100 x 100 nm objects with roughly 6 nm resolution from the 7 kilobase single-stranded genomic DNA of M13mp18. Rectangles. Squares. Triangles. Stars. Even a smiley-face. About 50 billion copies of each, in a typical reaction, and with very high yields. It works like magic. We did some calculations... Paul's smiley faces constitute the most concentrated happiness ever experienced on earth. Each spot in such a structure contains a unique address and can be addressed as such by DNA hybridization, allowing one to "write" on the DNA origami objects. Words. Pictures. Snowflakes. A map of North and South America. We did some more calculations... Paul probably made more maps than have ever been produced in the history of mankind -- we're definitely talking quantity over quality here. The applications of this technology are likely to be less whimsical. For example, it can be used as a "nanobreadboard" for attaching almost arbitrary nanometer-scale components, and there are few other ways to obtain such precise control over the arrangement of components at this scale. You'll never look at M13 phage DNA the same way again...
    [Nature 440, 297-302 (16 March 2006). article, .pdf, 575 KB. News and View, .pdf, 300 KB. Supplementary material: .pdf, part 1, 6.3 MB; .pdf, part 2, 193 KB. Caltech's Press Release. ]
  • Design of DNA origami. *
    Paul W. K. Rothemund
    Paul talks a little about the design software and future possibilities.
    [Proceedings of the International Conference on Computer-Aided Design (ICCAD) 2005: .pdf, 646 KB.]
  • Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks. *
    Paul W. K. Rothemund
    Paul makes a DNA origami especially for Ned Seeman, and sketches how polygonal networks and polygonal three-dimensional structures can be created.
    [in Nanotechnology: Science and Computation, pages 3-21, 2006. Preprint (22 pages): .pdf, 1.4 MB.]
  • Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting. *
    Robert D. Barish, Paul W. K. Rothemund, and Erik Winfree
    Here we demonstrate crystals that count and tubes that copy. This is interesting as the second example of algorithmic self-assembly. Counting is a useful primitive for bottom-up fabrication tasks such as constructing a memory chip with address demultiplexers. Copying is a useful primitive for Darwinian evolution. The error rates in this work, however, strongly motivate research into "proofreading" and other methods for fault-tolerant self-assembly.
    [Nano Letters 5(12): 2586-2592, 2005 (7 pages): .pdf, 515 KB. See also the Supplementary Materials (.pdf), 622 KB and our Extra Supplementary Materials page.]
  • Algorithmic Self-Assembly of DNA Sierpinski Triangles. *
    Paul W. K. Rothemund, Nick Papadakis, Erik Winfree.
    Our first demonstration of algorithmic crystals, wherein molecularly-encoded information directs the growth process to create a complex pattern. The DNA crystals are, at the molecular level, a two-dimensional woven fabric of short DNA strands. Both because this programmable growth could be considered a super-simplified toy model of organismal development, and because DNA is the central information molecule in biology, I like to call it "weaving the tapestry of life". This is a substantial personal victory for me: I proposed that this should be possible in 1995 as a graduate student -- nearly 10 years later, Paul's efforts made it actually happen.
    [PLoS Biology 2 (12) e424, 2004, (13 pages): .pdf, 4.6 MB.] See also our Extra Supplementary Materials page. (PLoS Biology has a synopsis and a primer by Chengde Mao for this paper. Also it was highlighted in Nature by Philip Ball. And there's a Caltech Press Release. )
  • Design and Characterization of Programmable DNA Nanotubes. *
    Paul W. K. Rothemund, Axel Ekani-Nkodo, Nick Papadakis, Ashish Kumar, Deborah Kuchnir Fygenson, Erik Winfree.
    DNA tiles designed to make sheets sometimes roll up into tubes that are abstractly analogous to protein microtubules that self-assemble from tubulin. Way cool! Fortuitously discovered during Paul's work on the DNA Sierpinski triangles, DNA nanotubes have opened up a whole host of interesting possibilities that we never dreamed of before...
    [JACS 126(50):16344-16353, 2004, (9 pages): article, 891 KB, supp, 5.5 MB.] See also our Extra Supplementary Materials page.
    [Note added Feb. 2013: We presented a correct equation for the persistence length of a DNA tube but gave an incorrect derivation. Here is the erratum stating changes to the paper and the correction to the supplementary information which gives a valid proof. Remember kids, area moment of inertia is for bending, mass moment of inertia is for spinning ice skaters!]
  • Self-Assembled Circuit Patterns. *
    Matthew Cook, Paul W. K. Rothemund, and Erik Winfree.
    Can DNA self-assembly be used for patterning, as a scaffold for functional devices such as molecular electronic circuits? We show that several circuit patterns, including demultiplexers, random-access memory, and Hadamard matrix transforms, can be self-assembled (in principle) from a small number of tile types.
    [in DNA Computers 9, LNCS volume 2943:91-107, 2004. (17 pages, in color): .pdf, 608 KB, .ps, 3.2 MB]


    Paul's PhD Thesis: Theory and Experiments in Algorithmic Self-Assembly.
    *
    283 pages, in black and white. University of Southern California, December 2001.
    Paul W. K. Rothemund. Thesis advisor: Leonard Adleman.
    This thesis describes theory on the uniqueness of self-assembled structures with an expanded account of material in the paper "The Program-Size Complexity of Self-Assembled Squares" (see below), experiments in algorithmic capillary force-based self-assembly as well as capillary force-based assembly of Penrose tilings, and DNA computation for breaking the Data Encryption Standard (DES). It has appendices detailing the frequency of certain tile configurations (vertex stars) in the Penrose tiling and an initial experiment in making capillary force-based gears.
    [pwkr_thesis_nov15.ps, 49.8 MB, or pwkr_thesis_nov15.ps.gz, 8.8 MB, or pwkr_thesis_nov15.pdf, 9.1 MB]


  • The Program-Size Complexity of Self-Assembled Squares. *
    Paul W. K. Rothemund and Erik Winfree.
    Are there small self-assembly programs for building squares of a particular size? Yes! Also contains a nice presentation of our model of self-assembly.
    [in STOC 2000, (10 pages): squares_STOC.ps.gz, 114 KB, squares_STOC.ps, 761 KB, or squares_STOC.pdf, 243 KB]
    [ Erratum: In Figure 5, actually N=50. ]
  • Using lateral capillary forces to compute by self-assembly. *
    Paul W. K. Rothemund.
    Here Paul used macroscopic plastic tiles to test ideas about algorithmic self-assembly. The plastic tiles self-assemble at the interface of oil and water, and hydrophilic and hydrophobic patches on the edges of the tiles mediate the specific binding interactions between them. Tiles in this paper encode binding interactions for creating Sierpinski triangles as well as Penrose tilings. Paul had mild success creating unnucleated patterns with Sierpinski tiles and perhaps created the most complex set of specific capillary bonds ever made.
    [in Proceedings of the National Academy of Sciences, 97(3): 984-989, 2000, (6 pages): Rothemund-PNAS-capillary.pdf, 911KB]
  • A Sticker Based Architecture for DNA Computation. *
    Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman.
    A new representation for encoding bits in DNA is presented and examined, and generally applicable methods for decreasing separation error rates are discussed.
    [in DNA Based Computers II, pgs 1-29, 1998 (26 pages): stickers.pdf, 611 KB, or stickers.ps.gz, 231 KB, or stickers.ps, 1.2 MB]
    This appeared in journal form as two papers:
    A Sticker-Based Model for DNA Computatation.
    Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas V. Chelyapov, Myron F. Goodman, Paul W. K. Rothemund, Leonard M. Adleman.
    [ Journal of Computational Biology, 5(4): 615-29, 1998 .pdf, 1.3 MB]
    and
  • On Applying Molecular Computation to the Data Encryption Standard. *
    Leonard M. Adleman, Paul W. K. Rothemund, Sam Roweis, Erik Winfree.
    An algorithm for breaking DES is designed for the Stickers model. Size, space, and error rates of the resulting machine are considered.
    [in DNA Based Computers II, pgs 31-44, 1998 (21 pages): des.pdf, 185 KB, or des.ps.gz, 77 KB, or des.ps, 211 KB]
    The journal version: [ Journal of Computational Biology, 6(1): 53-63, 1999 .pdf, 771 KB]
  • A DNA and restriction enzyme implementation of Turing Machines. *
    Paul W. K. Rothemund.
    Here Paul gives a construction for simulating Minsky's 4 symbol, 7 state universal Turing machine using DNA, the type IIS restriction enzyme Fok I, and ligase. The encoding of machine state and current symbol used in this paper was later used by Kobi Benenson of Udi Shapiro's group to create DNA finite state machines and hence such machines have been called Rothemund-Shapiro machines.
    [in DNA Based Computers, pgs 75-120, 1996, (29 pages below): dimacs.ps, 578KB, or dimacs.pdf, 330KB]


    Reference details for DNA Computing conference proceedings:

    DNA Based Computers: DIMACS Workshop, held April 4, 1995 (eds Richard J. Lipton and Eric B. Baum) American Mathematical Society, 1996.

    DNA Based Computers II: DIMACS Workshop, held June 10-12, 1996 (eds Laura F. Landweber and Eric B. Baum) American Mathematical Society, 1998.

    DNA Based Computers III: DIMACS Woskhop, held June 23-25, 1997 (eds Harvey Rubin and David H. Wood) American Mathematical Society, 1999.

    Proceedings of the Fourth DIMACS Meeting on DNA Based Computers, held at the University of Pennsylvania, June 16-19, 1998. (never published as a book.)

    DNA Based Computers V: DIMACS Workshop, held June 14-15, 1999. (eds. Erik Winfree and David K. Gifford) American Mathematical Society, 2000.

    DNA Based Computers VI: held June 13-17, 2000. (eds. Anne Condon and Grzegorz Rozenberg) Lecture Notes in Computer Science 2054, Springer, 2001.

    Send comments to

    pwkr@dna.caltech.edu