ITR/RC: Self-Assembly of DNA Nano-Scale Structures for Computation

Report thru Dec 31, 2002

(1) Participants: (1.1)Principal Investigators:

PI: John H. Reif (leader of research project) Title: Professor Surface address: D223 LSRC, Duke Univ., Durham, NC 27708-0129 Phone number: 919-660-6568 Fax number: 919-660-6519 Email address: [email protected] Homepage URL: www.cs.duke.edu/~reif/HomePage.html Papers in DNA Nanostructures: http://www.cs.duke.edu/~reif/vita/topics/biomolecular.html Project URL: http://www.cs.duke.edu/~reif/BMC Project Report URL: http://www.cs.duke.edu/~reif/BMC/reports/NSF.NANO.ITR.report/NSF.NANO.ITR.rep ort.html

Natasha Jonoska Title: Associate Professor Surface address: Department of Mathematics, University of South Florida, 4202 E. Fowler Av., PHY 114, Tampa Fl, 33620-5700 Phone number: 813-974-9566 Fax number: 813-974-2700 Email address: [email protected] Homepage URL: www.math.usf.edu/~jonoska Project URL: http://www.math.usf.edu/~jonoska/bio-comp

Nadrian C. Seeman Title: Professor Surface address: Department of Chemistry, New York University, New York, NY 10003 Phone number: 212-998-8395 Fax number: 212-260-7905 Email address: [email protected] Homepage URL: http://seemanlab4.chem.nyu.edu/ Project URL: http://seemanlab4.chem.nyu.edu/nanotech.html

(1.2) Collaborating Scientists: Research Assistant Professors: Thom LaBean Title: Research Assistant Professor Surface address: D230 LSRC, Duke University, Durham, NC 27708-0129 Phone number: 919-660-6553 Fax number: 919-660-6519 Email address: [email protected] Homepage URL: www.cs.duke.edu/~thl

Hao Yan Title: Research Assistant Professor Surface address: D230 LSRC, Duke University, Durham, NC 27708-0129 Phone number: 919-660-6553 Fax number: 919-660-6519 Email address: [email protected] Homepage URL: http://www.cs.duke.edu/~hy1

Training and Development The PI and subcontract PIs have trained numerous Postdoctoral Assistants in the techniques of DNA nanotechnology and DNA-based computation. These people are among the few individuals in the world possessing these skills. We expect that they will be successful in using these methods in their future careers.

(1.3) Postdoctoral Assistants: Duke Postdoctoral Assistants supervised by John Reif: Xiaoju Guan (jointly supervised with Hao Yan), 2003-current Sang Jung Ahn (jointly supervised with Thom LaBean), 2003- current Dage Liu, Research Associate http://www.cs.duke.edu/~liu , 2002- current

Prior Duke Postdoctoral Assistants: Hao Yan, 2001-2002 (currently Research Assistant Professor, CS Dept, Duke University www.cs.duke.edu/~thl/) Thom LaBean, 1998-2001 (currently Research Assistant Professor, CS Dept, Duke University http://www.cs.duke.edu/~hy1/)

NYU Postdoctoral Assistants supervised: Lisa Wenzler Savin Yariv Pinto

(1.4) Graduate students:

The PI and subcontract PIs have trained and graduated numerous graduate students in the techniques of DNA nanotechnology and DNA-based computation. These people are among the few individuals in the world possessing these skills. We expect that they will be successful in using these methods in their future careers.

Duke University Graduate Students supervised by John Reif: (Ph.D. candidates) Zhung(Robert) Sun, Ph.D. thesis topic: Complexity of Robotic Movement Problems. Projected Date of Graduation: Spring 2002. Tingting Jiang, Ph.D. thesis topic: Molecular simulation algorithms and nonuniform randomized path planning. Projected Date of Graduation: Spring '2004. Peng Yin, Ph.d thesis topic: DNA Nanorobotics. Projected Date of Graduation: Spring '2004. Sung Ha Park (jointly supervised with Thom LaBean and Gleb Finkelstein, Dept of Physics), Ph.D. thesis topic: Conductivity of Metalized DNA Nanostructures. Projected Date of Graduation: Spring '2004. Hanging Li (jointly supervised with Hao Yan and Dan Kenan, Medical School), Ph.D. thesis topic: Laboratory Demonstration of Molecular Robotics. Projected Date of Graduation: Spring '2004. Duke University Graduate Student Supervision (Completed Degrees): Guo Bo, Master Thesis “Computing by DNA Self-Assembly”. Oct, 2001 (currently Research Scientist, Mitsubishi Electric, Japan). Yuan Guangwei, Master Thesis “Simulation of DNA Self-Assembly”, Fall 2000 (currently Research Scientist, China). Christopher Butler, Master Thesis “Simulations of Molectronics architectures”, 2000. May 2000, Xavier Berni: MS Thesis, DNA tagging.

NYU Graduate Student Supervision by Ned Seeman(NYU): NYU Postdoctoral Assistants supervised: Lisa Wenzler Savin Yariv Pinto NYU Graduate students supervised: Pamela Constantinou Hao Yan Phiset Sa-Ardyen Baoquan Ding Xiaoping Yang Furong Liu Roujie Sha Chengde Mao Weiqiong Sun Zhiyong Shen Hao Yan

Natasha Jonoska (USF): USF PhD graduate students current: Kalpana Mahalingam (projected graduation 2003) Danieal Filipov (projected graduation 2003) Joni Pirno (starting) David Kephart (starting)

(2) Major Project Activities and Findings (2.1) Major research and education ACTIVITIES: Summary of Goals. This research is a collaboration between: John Reif at Duke University (PI), Nadrian Seeman at New York University, and Natasha Jonoska at the University of South Florida. The overall goal was to develop and demonstrate DNA self-assembly to do massive parallel computing at the molecular scale. This involves the development of experimental proof- of-concept demonstrations of the application of DNA self-assembly to various basic computational tasks, such as sequences of arithmetic and logical computations executed in massively parallel fashion, and the application of this method to hard computational problems such as integer factorization. Ongoing research includes the development of novel DNA tiles with properties that facilitate the self-assembly and their visualization by imaging devices such as atomic force microscopes and electron microscopes, the testing of various input/output methods, and methods to minimize errors in self- assembly. The self assembly of junction molecules and construction of three dimensional structures such as graphs

Overview of computation by DNA self-assembly. DNA self-assembly is a methodology for the construction of molecular scale structures. In this method, artificially synthesized single stranded DNA self-assembles into DNA crossover molecules (tiles). These DNA tiles have sticky ends that preferentially match the sticky ends of certain other DNA tiles, facilitating the further assembly into tiling lattices. The self-assembly of large 2D lattices consisting of up to thousands of tiles have been recently demonstrated by Seeman and Winfree. DNA self-assembly can, using only a small number of component tiles, provide arbitrarily complex assemblies. It can be used to execute computation, using tiles that specify individual steps of the computation. In this emerging new methodology for computation: (i) input is provided by sets of single stranded DNA that serve as nucleation sites for assemblies, and (ii) output can be made by the ligation of reporter strands of DNA that run though the resulting assembly, and then released by denaturing. Moreover, DNA self-assembly can be executed in massively parallel fashion, with concurrent assemblies that may execute computations independently. Due to the very compact form of DNA molecules, the degree of parallelism (due to distinct tiling assemblies) may be 1016 or possibly 018. In the case of junction molecules and 3D structures, the output is the graph structure itself, since the coding of the problem is such that the solution exists iff the structure is assembled.

For surveys of recent work in this area see: J. H. Reif, Molecular Assembly and Computation: From Theory to Experimental Demonstrations, plenary paper, 29-th International Colloquium on AutomataLanguages, and Programming(ICALP), Málaga, Spain (July 8, 2002).

J.H. Reif, T.H. LaBean & N.C. Seeman, Challenges and Applications for Self-Assembled DNA Nanostructures, Sixth International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, (June, 2000) ed. A. Condon, G. Rozenberg. Springer- Verlag, Berlin Heidelberg, Lecture Notes in Computer Science 2054, 173-198, (2001).

T.H. LaBean (in press, 2003) “Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication”. in CBGI 2001, Proceedings from Computational Biology and Genome Informatics, held 3/2001 Durham, NC, World Scientific Publishing.

Talk Slides: J. H. Reif, DNA Lattices: A Programmable Method for Molecular Scale Patterning and Computation, special issue on Bio-Computation, Computer and Scientific Engineering Magazine, IEEE Computer Society. February 2002, pp 32-41.

For more details, see: J.H. Reif, T.H. LaBean, and N.C. Seeman, “Challenges and Applications for Self- Assembled DNA Nanostructures,” Proc. Sixth International Workshop on DNA-Based Computers, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Edited by A. Condon and G. Rozenberg. Lecture Notes in Computer Science, Springer- Verlag, Berlin Heidelberg, vol. 2054, 2001, pp. 173-198:. .

Summary of Research Activities. We are developing new methods for nano-assembly of computational structures. The nano-structures constructed consist of DNA crossover molecules (tiles) that have sticky ends that match the sticky ends of other DNA tiles. The DNA tiles self assemble into large lattices that can execute computations. We are executing experimental tests of computation by self-assembly of DNA nanostructure tilings. The key advantage of this approach was that the self-assembly sidesteps time consuming laboratory steps required by other methods for DNA computation. These assembly methods are executed in massively parallel fashion, with concurrent assemblies, each with a (possibly) distinct input strand. We are testing our approach by doing massively parallel arithmetic operations by this self-assembly method. We are engaged in various steps required to achieve this goal, including (i) construction of trial inputs by self-assembly of dsDNA (double stranded DNA) segments from ssDNA (single stranded DNA), (ii) design and construction of DNA tiles, and (iii) design and construction of DNA tilings for massively parallel arithmetic computations. Massively parallel DNA assemblies for integer addition are being demonstrated tested and published in Nature. This will be followed by massively parallel DNA assemblies for integer multiplication with random inputs, which will give solution of integer factorization problems (used for decryption of the RSA crypto-system). Also, Natasa Jonoska is investigating the use of three dimensional structures for solving computational problems with DNA molecules. For example, building blocks of k-armed branched junction molecules can be used to form graphs to solve the Hamiltonian Cycle problem, the 3-vertex colorability problem, and the satisfiability problem, potentially reducing the number of laboratory (computational) steps.

List of Main activities undertaken by the project. We are conducting experiments to evaluate the speed and error rates of the various types of self-assembly reactions. • Experimental Demonstrations of Massively Parallel Computations by DNA Tiling Assemblies.: We are experimentally testing massively parallel DNA self-assembly on particular computational problems, such as the simultaneous execution of many arithmetic or Boolean vector operations. The degree of parallelism in these experiments is intended to range from 1016 or possibly 018. • Error Control in DNA Assemblies: We are executing experiments with the goal of developing methods for improved error control in self-assemblies. As a secondary tasks, • We developed improved software for the design of DNA tiles and for simulations of the kinetics of self-assembly (with the goal of developing a more fundamental understanding of self-assembly processes). • We are also developing software for the design of DNA encoding of the sticky ends to avoid mismatched pairing. • We are making theoretical investigations into the complexity of DNA assemblies and their computations.

Presentations: The PI and subcontract PIs also gave numerous national and international presentations on DNA computing.

Reif Invited Lectures:

Software Design for Molectronics, DARPA Molectronics Meeting, Arlington, VI, (Feb 26,2000). Self-Assembled DNA Nanostructures, ADT Novel Technologies for Information: DNA/Biological SRC meeting, San Jose CA, (March 26, 2000). Self-Assembled DNA Nanostructures, NSF workshop on nano-scale molecular based electronics, Arlington, VI, (May 18, 2000). An Efficient Approximation Algorithm for Weighted Region Optimal Path Problem, Workshop on Foundations of Robotics (WFR2000), Dartmouth, NH, (March 2000). Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization, Invited Talk, Sixth International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands, (June, 2000) "Challenges and Applications for Self-Assembled DNA Nanostructures", Invited paper, Sixth International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands, (June, 2000) Algorithmic self-assembly of DNA tilings, City University of Hong Kong, Kowloon, Hong Kong, Oct 2, 2000. Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization, City University of Hong Kong, Kowloon, Hong Kong, Oct 3, 2000. On the Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, City University of Hong Kong, Kowloon, Hong Kong, Oct 4. A Biomolecular System for Ultra-Scale Associative Search, Invited Talk, National Reconnaissance Office, Chantilly, VA, November, 2000. A Biomolecular System for Ultra-Scale Associative Search, Theory Seminar, CS Dept, Duke University, November 16, 2000. Programmable Assembly at the Molecular Scale: Self-Assembly of DNA Lattices, Invited talk, 2001 IEEE International Conference on Robotics and Automation (ICRA2001), Seoul, Korea, May 26, 2001 J.H. Reif and Zheng Sun, An Efficient Approximation Algorithm for Weighted Region Optimal Path Problem, Workshop on Foundations of Robotics (WFR2000), Dartmouth, NH, (March 2000). Molecular Computing via Programmed Self-Assembly of Patterned Molecules, Plenary Talk, 2001 Congress on Evolutionary Computation (CEC2001), Seoul, Korea, May 28, 2001 Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability, Seventh International Meeting on DNA Based Computers (DNA7), Tampa, FL, June 11-13, 2001. Molecular Database Systems for Storage, Processing & Retrieval of Genetic Information & Material, Invited Talk, MiniSymposium “On Interfaces among Information Technology, sensing sciences, and Biological Systems”, organized by Jagdish Chandra and Srikanta Kumar, SIAM Annual Meeting, San Diego, California, July 9-13, 2001 Movement Planning in the Presence of Flows, Workshop on Algorithms and Data Structures (WADS2001), Brown University, Providence, RI, August 8-10, (2001). Computations & patterned structures via DNA self-assembly, Invited talk, Max Planck Institute for the Physics of Complex Systems, Dresden, Germany, August 20-24,2001. DNA in NanoScience, Invited talk, Department of Computer Science Seminar Series, October 22, 2001 DNA Computation by Self-Assembly of DNA Nano-Scale Structures, Symposium on New Approaches toward Computing, Plenary Talk, National Academy of Arts and Sciences, Brussels, Belguim, November 9, 2001 Programmable DNA Lattices: Design, Synthesis and Applications, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 – 30, 2001. Self-Assembly of DNA Nano-Scale Structures for Computation, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 – 30, 2001. Self-Assembly of DNA Nano-Scale Structures, Invited Talk, DARPA ITO BioComp PI Meeting, Washington, DC, May 22-24, 2002. The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA, The 8th International Meeting on DNA Based Computers (DNA 8), Sapporo, Japan, June 10-13, 2002. Molecular Assembly and Computation: From Theory to Experimental Demonstrations, plenary talk, 29th International Colloquium on Automata, Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002). Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations, distinguished lecture, Computer Science Department, John Hopkins University, Baltimore, Maryland, October 3, 2002. Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations, invited talk, Workshop on Alternative Computing, Institute for Pure and Applied Mathematics (IPAM), September , 2002. Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations, invited talk, Alternative Computing Workshop, Mathematics in Nanoscale Science and Engineering, UCLA, September, 2002. Programmable DNA Lattices: Design, Synthesis and Applications, Invited Talk, Department of Computer Science, Boston University, Boston, MA, December 2, 2003. Patterned Molecular Self-Assembly, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, San Deigo, CA. December 7, 2003. Upcoming Keynote Talk,7th Joint Conference on Information Sciences (JCIS 2003). Upcoming Keynote Talk, 5th Conference on Computational Biology and Genome Informatics (CBGI), Cary, North Carolina, September 26-30, 2003. Seeman Invited Lectures:

American Physical Society, Minneapolis, 2000. Interfacing Biology and Polymer Science, Amherst, 2000. NATO ARW on Frontiers of Nano-Optical-Electronic Systems, Kiev, 2000. International Symposium on Nanoscale Science and Technology, Tel Aviv, 2000. Bio-Organic Chemistry Gordon Conference, 2000. Organic Structures and Properties Gordon Conference, 2000. Nanoscience & Technology: Shaping Biomedical Research, BECON 3, Bethesda, 2000. 11th International Symposium on Supramolecular Chemistry, Fukuoka, 2000. Functional Nanostructures, American Chemical Society, Washington DC, 2000. Petersheim Symposium, American Chemical Society, Washington DC, 2000. Second Intl. Conf. on Supramolecular Science and Technology, Leuven, 2000. Eighth Foresight Conference on Molecular Nanotechnology, Washington DC, 2000. National Nanofabrication Users Network Workshop, Washington DC, 2000. Poly Millennial 2000, Waikoloa, HI, 2000. Dartmouth Molecular Materials Symposium, 2001. American Physical Society, Seattle, 2001. Ninth Suddath Memorial Symposium, Atlanta, 2001. ARDA Workshop on Molecular Electronics, College Park, 2001. Strategic Nucleic Acid Research, Stockholm, 2001. National Academy of Sciences, Sackler Colloq. on Nanoscience, Washington, DC, 2001. ACS Symposium on Biological Applications of Nanotechnology, Berkeley, 2001. Seventh Workshop on DNA-Based Computation (Tutorial), Tampa, 2001. Condensed Matter Physics Gordon Conference, 2001. Nucleic Acids Gordon Conference, 2001. Chemistry of Electronic Materials Gordon Conference, 2001. American Crystallographic Association, Los Angeles, 2001. Nano-Physics and BioElectronics, Dresden, 2001. Electron Interactions in DNA, Los Angeles, 2001. Life Sciences and Nanostructured Materials, Philadelphia, 2001. Nanoscience in a Mega-City, New York, 2001. Jeffrey Memorial Symposium, Pittsburgh Diffraction Conference, Covington, KY, 2001. DOE-BES Biomolecular Materials Workshop, Del Mar, CA, 2002. American Association for the Advancement of Science, Boston, 2002.

Cornell Medical College, Genetic Medicine Department, 2000. Polytechnic University, Chem. Eng., Chem. & Mat. Sci. Department, 2000. University of Virginia, Department of Chemistry, 2000. University of Minnesota, Department of Chemistry, 2000 University of Massachusetts, Department of Chemistry, 2000. Texas A&M, Biochemistry Department (2), 2000. University of Texas Health Science Center, San Antonio, Inst. of Biotechnology, 2000. Cornell University, Department of Chemistry & Chemical Biology, 2000. University of Wisconsin, Madison, Department of Chemistry, 2000. University of Toronto, Department of Pharmaceutical Sciences, 2000. Columbia University, Genome Center, Biochemistry Department, 2000. University of Tokyo, Department of Chemistry, 2000. National Institute of Standards and Technology, Biomolecular Materials Group, 2000. Polytechnic University of Catalonia, Department of Chemical Engineering, 2000. University of Delft, Department of Applied Physics, 2000. University of Leiden, Institute of Advanced Computer Science, 2000. University of Maryland, Department of Chemistry & Biochemistry, 2000. Naval Research Laboratory, 2000. Hunter College, CUNY, Chemistry Department, 2000. University of Washington, Chemistry Department, 2000. University of Pennsylvania, Physics Department, 2001. Brookhaven National Laboratory, Structural Biology Department, 2001 University of California, Berkeley, Chemistry Department, 2001. University of British Columbia, Computer Science Department, 2001. Simon Fraser University, Chemistry Department, 2001. University of Notre Dame, Chemical Engineering Department, 2001. Princeton University, Physics Department, 2001. Bryn Mawr College, Chemistry Department, 2001. University of Utah, Biology Department, 2001. Institut Haute Études Scientifique, 2001. University of South Florida, Chemistry Department, 2001. Clemson University (Irix Pharmaceutical Lecturer), Chemistry Department, 2001. Avon, Inc., Suffern Research and Development, 2001. Duke University, Computational Biology Series, 2001. North Carolina State University, Department of Chemistry, 2001. University of Amsterdam, Organic Chemistry Department, 2001. Johns Hopkins Univ., Chem. Dept. (Ephraim & Wilma Shaw Roseman Lecturer), 2001. University of California at Santa Barbara, California Nanosystems Institute, 2001. Callistogen, AG, 2002. Brandeis University, Biochemistry Department, 2002.

Jonoska invited lectures:

3rd Int. Meeting on Informatics Comp. and Techn. (plenary) Macedonia, December 2002. Genetic and Evolutionary Computing Meeting, New York, July 2002. 8th Int. Meeting on DNA Based Computers, Hokkaido University, Japan, June 2002. Florida Southern College, (university lecture) Lakeland FL, April 2002. Department of Biochemistry and Mol. Biology, Col. of Medicine, USF March 20, 2002. Symposium on nanotechnology, College of Arts and Sciences, USF January 2002. National AMS meeting San Diego, CA January 6-9 2002. 7th International Meeting on DNA Based Computers, USF Tampa FL June, 2001. Math. Dept. Binghamton University, SUNY, April 2001. Combinatorics of New England meeting at Smith College, MA, April 2001. Sectional AMS meeting San Francisco,CA, October 21-22, 2000. Theorietag, University of Technology, Vienna, Austria, September, 2000. Faculty of Math. and Nat. Sci., Cyril and Methodius Univ., Skopje, Macedonia, 2000 Sectional AMS meeting at Notre Dame University, April 8-9, 2000. Math. Dept. Wesleyan University, Middletown CT, 2000. Sonia Kovalevski High Sch. Math Day: Women in Math., USF New College, 2000 (Numerous seminars within the Math Department at USF)

(2.2) FINDINGS AND RESULTS from Jan 1, 2000 thru Dec 31, 2002

ACCOMPLISHMENTS Main Results to Date. Summary of Main Results: (a) As our main result, we have performed the first successful computation using DNA algorithmic assembly. This DNA algorithmic assembly was of DNA triple crossover molecules in one dimension. We have extended this work to massively parallel integer arithmetic. (b) We have begun studies to extend this work from one dimension to two dimensions. We have designed and begun to prototype a two dimensional algorithmic assembly based on a new 4 x 4 tile. (c)We have made a robust sequence-dependent nanomechanical device and we have worked up a motif for embedding it in a 2D array, preparatory to a nanorobotic approach to DNA circuit formation. We have designed and are testing a device to enable a multiplicity of structural states in a DNA lattice. We have designed a DNA nanomechanical device whose conformation is sequence driven. (d) We (NYU) have established conditions that promote PX-form association as a means of replacing sticky-ends with paranemic, topologically closed cohesion. We have also developed edge-sharing cohesion. We have also established the cohesion of Bowtie junction lattices, a new motif that we expect to be of use in 2D aperiodic assembly. (e) We have developed a motif to embed a robust sequence-dependent nanomechanical device into an array. This will allow us to make molecular pegboards for nanoscale circuit experimentation. (f) We have prototyped the first covalent assembly of an irregular graph, where the helix axes correspond to the edges of the graph. (g) We have assembled a number of tiles for 3D motifs, whose 3D self-assembly we are exploring actively. We developed methods for executing computation using three- dimensional DNA nanostructures and begun testing these in the laboratory. Recent successful design and assembly of 3D graph structure with DNA. (h) We have developed improved software for DNA tile design and sequence selection. Educational Activities: In 2000, Reif taught a graduate course on DNA nanotechnology and DNA computation. LaBean taught a graduate level course on Molecular Computing during Spring semesters 2001 and 2002. In addition to the annual class on nucleic acid structure, symmetry, design and nanotechnology, Seeman gave a tutorial on nucleic acid basics was presented to the 7th and 8th Workshop on DNA-Based Computation concerning non-standard base-pairing and backbone structures and was program chairman of that workshop. In addition to the annual class on nucleic acid structure, symmetry, design and nanotechnology, a tutorial on nucleic acid basics was presented by Seeman to the Seventh Workshop on DNA-Based Computation concerning non-standard base-pairing and backbone structures. NCS was program chairman of that workshop. Natasha Jonoska gave a number of seminars on theoretical aspects of DNA nanotechnology. She spent a sabbatical at Seeman’s laboratory learning the basic techniques used in the work described, and is teaching these techniques to students at University of Florida. Natasha Jonosk taught a PhD level graduate course in DNA computing Details of Main Results: (a) The major outcome of this project during this period is the first successful computation using DNA algorithmic assembly(Duke & NYU). We have made a successful experimental demonstration of a cumulative XOR calculation, which appeared in: C. Mao, T. LaBean, J.H. Reif and N.C. Seeman, Logical Computation Using Algorithmic Self-Assembly of DNA Triple Crossover Molecules, Nature 407, 493-496 (2000); Erratum: Nature 408, 750-750 (2000). This calculation was performed as a prototype calculation, with two different input strings, leading to two different output strings that correctly associated to produce the XOR result. This calculation was performed by using triple crossover (TX) DNA molecules or tiles, previously prototyped in the early phases of this research program. Each of the TX molecules contained a reporter strand capable of being ligated to its neighbors. In an actual calculation involving 4 input bits and, consequently, four output bits, sixteen (24) different strands would have been produced in parallel, and the contents of those strands would have been re-used in a later calculation calling on those strands as though they constituted a look-up table. This would have been done by using input tiles capable of assembling randomly in all 16 possible permutations. However, this calculation was the first calculation ever done in this fashion, so we did two specific calculations, using special sets of input tiles that led to two specific calculations. The calculation was arranged so that the four input tiles were assembled with somewhat longer sticky ends (7 nucleotides) than the answer tiles (5 nucleotides). Thus, they, and the two initialization tiles were able to assemble during the cooling protocol before any of the four answer tiles, and they thereby created a 'frame' superstructure into which the answer tiles could fit. The answer tiles contained the four possible XOR options, inputs of 0 and 0 or 1 and 1 leading to a tile value of 0, and inputs of 1 and 0 or 0 and 1 leading to a tile value of 1. Both input tile and output tile values (0 or 1) were encrypted on the reporter strands as restriction sites, one enzyme representing 0 and a second representing 1. After the tiles had assembled, the reporter strands were ligated, thus establishing a connection between the input and output values. The reporter strands were then purified and amplified by PCR treatment. The PCR product was then partially digested by one or the other of the enzymes. The results were then run on a denaturing polyacrylamide gel, producing a series of bands in the '1's lane or '0's lane, much like a Maxim-Gilbert sequencing gel (with, of course, much greater separations between the bands). The answers were readily read off the gel, and they were essentially correct.This type of self- assembly was much more difficult than the self-assemblies reported by our group earlier, when producing periodic arrays. In those assemblies, correct tiles compete with incorrect tiles for positions within an array. However, in this case, correct tiles are competing with partially correct tiles. For example, the same sticky end is used in the same position to signify an input of '1' both on the XOR tile whose input is '1' and '0' (leading to a tile value of '1') and on the XOR tile whose input is '1' and '1' (leading to a tile value of '0'). Very small errors were detected, but it was not possible to quantitate them, because one cannot compare restriction cleavage intensities across sites on either the same strand or (as needed here) on different strands.

(b) Promising progress toward extending this work to massively parallel integer arithmetic (Duke & NYU). We are testing the execution of integer arithmetic via self assembly of a linear sequence of a special subclass of TX DNA tiles known as TAE tiles. • Design, construction and testing of TAE tiles. We have successfully built TAE computational tiles with three sticky-ends on each side of the tile as well as "book-end" tiles with sticky-ends on only one side. Book-end tiles anneal to one end (LC to the left and RC to the right) of a growing tile complex and terminate the complex since they do not display additional sticky-ends exposed for further tile binding. • Structure of tiles tested by PAGE and OH-radical cleavage footprinting. Stoichiometry of strand association as well as observation of cleavage protection at crossover points and sites design to lie between helices indicated TAE structures formed as designed. • TEM and AFM imaging indicate tile complexes are forming as designed. (see Figure). • Reporter strand ligation results in full-length product from two-tile complex. • Reporter strand ligation results in partial product formation for complex involving book-end tiles and computational tiles. Autoradiograms of test ligations have recently implicated the joint on the central helix between the right-most computational tile and the right book-end tile as the problem ligation.

Parallel integer arithmetic (Duke). A large number of unsuccessful design iterations on the TX computational assembly convinced us that ligation of the reporter strand in that system was too problematic. We moved to a DX (DAE) tiling system and met with better success. We have now shown XOR calculating complex with ligated reporter strand of at least 15 bits, and have PCR amplified, cloned, and read by sequencing several examples of 4 bit computations. A tile set containing ten tile types which encodes n-bit addition has also been successfully implemented; readout of example problems is underway.

DX XOR and Adder. We have constructed and tested a single layer computational string tile system capable of simultaneously calculating all possible XOR or addition sums (up to some length) using double crossover complexes. DX (DAE) tiles provide continuous oligonucleotide strands running from one side of the tile to the other on both the top and bottom helices (see figure below). Sites on these transverse strands are used to record input (top helix) and output (bottom helix) bits for the four possible pairs of inputs. Four tile types are required for XOR and eight tile types for addition since we must allow for the carry-in bits to be 1 or 0. The left figure shown above illustrates the design of DNA structures used in the DX XOR calculation: a). a drawing of a DAE tile where red strands carry bit-value information and will become part of the reporter strand; b). truth table for XOR showing bit values on each of the four computational tiles and also a sketch of the three tile types required for valid superstructure assembly; c). drawing of a simple three tile complex with reporter strand segments in blue, red and green; d). geometric representation of a six tile complex which performs a 4-bit computation. The right figure shows an AFM image (600x600 nm) demonstrating the formation of the computational complexes. AFM imaging is used in the project to monitor the formation and final lengths of the computational complexes in order to evaluate annealing protocols and other experimental conditions. These results are currently being written up for publication [Yan, H., Feng, L., LaBean, T.H., Reif, J.H. “String Tile” Parallel Computation of Pair-Wise XOR using Self-Assembly of DNA Double Crossover Complexes, manuscript in preparation].

TX XOR and Adder with Visual Readout. In order to streamline the readout of string tile computations and avoid the need for ligation, we have implemented a TX tile system with AFM visible topographical markers recording the bit values. The presence or absence of a particular bump or bulge on each tile indicates a value of 1 or 0, respectively. In the current incarnation, an extra stem-loop on the middle helix sticking out of the tile plane is used to indicate an output value of 1. 600 nm AFM image of visual readout TX computation performing XOR on randomly assembled input strings. The brighter spots located along the complexes show pair-wise computations with output values of 1. In this image the input values are not readable, however we have designed biotin containing oligos such that binding of streptavidin to the biotin should be visible as bulges off the sides of the tiles. This image was collected by LaBean and Yan during a recent visit to Winfree’s lab at CalTech.

Details of the tile sets and information encodings are similar to those described for the DX system, above. Four types of computational tiles are required for XOR calculation while eight types are needed for executing addition (i.e. one computational tile type for each row in the truth table). We are currently preparing a manuscript describing these findings [LaBean, T.H., Yan, H., Reif, J.H. (2003) “Parallel Computation by Self- Assembling Triple Crossover Complexes with Visual Readout”, manuscript in preparation.

(c) We have begun studies to extend this work from one dimension to two dimensions and we have designed and begun to prototype a two dimensional algorithmic assembly(Duke & NYU). In further work involving algorithmic assembly, now in two dimensions, we have designed a DNA array that contains a specific structural feature in the middle and on its edges, but the bulk of the array contains filler. This type of assembly prototypes the key feature of algorithmic assembly when applied to laying the basis of simple designs: The use of one particular tile as filler. We have produced the border and the central structural feature, but have encountered problems in getting the filler to work as intended. We have explored a large number of potential 3D motifs with the aim of extending assembled lattices from 2D to 3D. These lattices may be periodic or aperiodic, but for the present we are emphasizing periodic lattices, because their assembly can be established by the X-ray diffraction experiment. We have begun from the 2D TX lattices that we have reported previously. Those lattices contain an A and a B tile in one plane, connected in a 1-3 fashion. This leaves two different types of single-helix gaps in the system. In previous work we have taken one of these gaps and inserted a third TX tile (C) within it. Of course, one cannot put a triple crossover molecule directly into single- helix gap, unless one rotates it. We have rotated our TX molecules by three nucleotide pairs, roughly 103˚. In previous work, we filled the other gap with a simple helix (D*). For 3D assembly, we have made the following changes: [1] We have replaced the hairpins on the helical domains above and below the plane with sticky ends. [2] We have replaced the filler helix D* with a fourth TX molecule, D, also containing sticky ends above and below the plane. The sticky ends of the bottom domain of the C molecule complement those of the upper domain of the D molecule; the sticky ends of the top domain of the C molecule complement those of the lower domain of the D molecule, so the arrangement is designed to fill space. Many crystals have been obtained, but so far diffraction has not been achieved. We are working on a number of simplifications (one or two tiles) and helicity variants (10.0, 10.2, 10.5 fold helices) of the system.

A second motif is to design a DX molecule that connects to other DX molecules with a 120˚ angles. This leads to a 31 axis, and a trigonal crystal. The predicted cell dimensions for this system are a = b = 33.75 Å vs. observed 34.5 Å and c = 355 Å vs. 360 Å observed. The presence of the screw axis is confirmed by the systematic extinction condition of l = 3n along 001. The key disappointment of this experiment is the poor resolution of the crystal, and we are working to improve it. We have used the same motif with DNA parallelogram tiles, and they have been grown quite large, although we have not yet characterized them. Likewise, we have used this motif a third time with TX tiles, and have also recently obtained crystals. Diffraction analyses have been scheduled for the near future.

(d) We have designed and are testing a device to enable a multiplicity of structural states in a DNA lattice and we have designed a DNA nanomechanical device whose conformation is sequence driven(NYU). We have prototyped previously a DNA nanomechanical device that utilized the ability of a small molecule to induce the B-Z transition of DNA. The disadvantage of this type of device is that if incorporated into a DNA array, all of the devices would be in either the B-state or the Z-state, at least to within the limits of chemical nuances dependent on the Z-forming proclivities of various sequences. A more fruitful approach is to produce a device that is driven by the presence of a DNA sequence in solution, thereby producing a diversity of states: For N devices incorporated into an array, there could be 2N states. We have designed such a device based on a new motif of DNA, and are in the process of demonstrating its functionality. (e) We have learned how to promote the intermolecular cohesion of DNA objects through paranemic PX cohesion. This type of association is likely to prove much more robust than sticky-ended cohesion, because the units that are involved can be topologically closed. Hence, molecules and motifs can be purified by denaturing conditions, and the extend of cohesion and recognition can be quite large. Purifying topologically closed molecules under denaturing conditions and then restricting them leads to sticky ends that are only four or fewer nucleotides long. However, with PX cohesion, the extend of cohesion is unlimited. We have also developed edge-sharing cohesion.

(f) We have developed a motif to embed a robust sequence-dependent nanomechanical device into an array. This will allow us to make molecular pegboards for nanoscale circuit experimentation.

(g) New Theoretical Results and their Experimental Tests(Univ. of S. Florida & NYU). We have prototyped the first covalent assembly of an irregular graph, where the helix axes correspond to the edges of the graph. Natasha Jonoska developed new methods for using three-dimensional DNA nanostructures to do computation and began testing these in Seeman’s laboratory. Most of the past year was spent by Jonoska in collaboration with Nadrian Seeman at New York University trying to investigate the possibility to construct three dimensional graph structures with DNA and the feasibility that they are used as a computational tool. Quite some time was spent in encoding and designing the structure to be made and most of the Fall was used in performing the experiments. The main idea is to use DNA duplexes as edges and k-armed junction molecules as k-degree vertices as building blocks such that by joining and ligating the building blocks the intended graph structure is obtained. The structure was designed such that the final structure, if obtained, forms one single stranded circular molecule. The final analysis of the 3D graph structure self assembled by DNA is done and we have a solid confirmation of formation of this structure, this was done at NYU. On a theoretical level, several investigations have been initiated. Using linear DNA segments and branched junction molecules many different three-dimensional DNA structures (i.e. graphs) could be self-assembled. We investigate maximum and minimum numbers of circular DNA that form these structures. For a given graph G, we consider compact orientable surfaces, called thickened graphs of G, that have G as a deformation retract. The number of boundary curves of a thickened graph G corresponds to the number of circular DNA strands that assemble into the graph G. We investigate how this number changes by recombinations or edge additions and relate to some results from topological graph theory. This work is in collaboration with Masahico Saito from University of South Florida. Two dimensional (Wang) tiling systems were investigated from the symbolic dynamics point of view. This work was done in collaboration with Ethan Coven from Wesleyan University. We identified certain systems, which we call uniformly transitive, that are entropy minimal i.e. they do not contain any subsystems with same topological (which happens to be the same as the informational Shannon) entropy. We showed that uniformly transitive systems also have their periodic points dense. Other theoretical results by Jonoska include: (a) we have a proof that the self assembly of graphs using junction molecules is computational universal (still a draft), (b) we started investigating languages that may be taken as DNA code words (which would avoid hairpin structures and other intermolecular interactions) and have characterized their properties to remain unchanged when such codes are ligated (software development has been started), (c) have started theoretical model describing the set of DNA strands (considered as formal language) as a topological space and we are investigating its characteristics.

(f) We also developed improved software for DNA tile design using an evolutionary search algorithm to optimize this search (Duke). It improved on prior software by Eric Winfree which had used a greedy approach to constructing the design. This software was developed as part of the Masters Thesis of Bo Guo (who graduated in the fall of 2001) at Duke University, under the supervision of John Reif. The software also incorporated a Java front end developed by a senior undergraduate Tina Belmore, under the supervision of John Reif. A software for DNA strand design has been started by Jonoska at USF based on the theoretical findings for codes

(4) Next Steps Planned. Primary Tasks: We plan to experimentally test DNA self-assembly on further arithmetic and Boolean vector computations. (i) Experimental Demonstrations of Parallel Integer Multiplication by DNA Tiling Assemblies (Duke). We intend to extend our DNA tiling assembly methods from integer addition to integer multiplication, and to experimentally demonstrate these methods. The most direct way to do this is to do the multiplication by repeated additions and bit shifts, mimicking known VLSI systolic array architecture designs for integer multiplication. We are designing for this two dimensional tiling assemblies. (ii) Experimental Demonstrations of Massively Parallel Logical Computations by DNA Tiling Assemblies (Duke). We [Lagoudakis and LaBean, 99] have recently developed (but not yet experimentally tested) a 2D DNA self-assembly for Boolean variable satisfiability, which uses parallel construction of multiple self-assembling 2D DNA lattices to solve the problem. Such methods for solving combinatorial search problems do not scale well with the input size (the number of parallel tiling assemblies grows exponentially with the number of Boolean variables of the formula). However, similar constructions may be used for evaluating Boolean formulas and circuits in massively parallel fashion, for multiple input settings of the input Boolean variable. We are developing an experimental demonstration of this application. (iii) Error Control in DNA Assemblies (Duke & NYU). We are conduct experiments to evaluate the speed and error rates of the various types of self-assembly reactions and are investigating and comparing error control by free versus step-wise assembly. Self- assembly may be restricted such that certain assembly reactions can proceed only after others have been completed (serial self-assembly). Alternatively, self-assembly reactions may be limited by no such restrictions (free self-assembly). As examples, BCA tiles utilize local parallelism and serial self-assembly [Winfree95]; DHHP tiles utilize both local and global parallism and serial self-assembly [Winfree96]; and self-assembly of linear, hairpin, and branched DNA molecules to generate regular, bilinear, and context- free languages makes use of global parallelism and free self-assembly [Winfree96,Eng97], as do the proposals of Jonoska et al [Jonoska97, Jonoska98]. It is not yet known if free self-assembly is faster, and more robust than serial self-assembly or if it is less error-prone. We are making careful experimental studies of these two possible methods for self-assembly, to particular determine which method provides the least error. -Use of DNA Lattices as a Reactive Substrate for Error Repair(Duke & NYU). DX complexes and lattices have been used successfully as substrate for enzymatic reactions including cleavage and ligation [Liu99a]. We would like to investigate the use of DNA lattices to execute a broader class of reactions. We are working to modify the topology and geometry of the DNA lattice using restriction enzymes that operate on exposed portions of the DNA lattices. This will aid in the DNA tiling computations described above, for example by providing mechanisms for error repair in DNA tiling computations. -3D Selfassembling Graph Structures from DNA Nanostructures (Univ S Florida & NYU). Plans for 2002. Our plans are to use the 3D DNA structure assembled in a computational process and possibly solve another instance of a computational problem. Theoretically we need to characterize the graph structures that can be designed such that after self-assembly the structure is only one cyclic molecule. Also algorithmic procedure in designing such graph and their computational power has to be characterize. Algorithms to generate good DNA strands for self assembly are also on agenda, and part of this is theoretical characterization of DNA languages that represent good encodings. Topological investigation of the space of formal languages (sets of DNA strands) continues Secondary Tasks: We will also devote a portion of our resources to the following: -Use of DNA Lattices as a Substrate for Surface Chemistry. One intriguing application for DNA lattices is there use as an attachment substrate for an array of DNA strands, using hybridization with single stranded DNA on individual tiles. This has a number of applications that impact DNA computations (e.g., see Brockman,et al 98][Smith,98]): (i) It may provide a dramatically miniaturization of the DNA chip technology (a technology that might be used for I/O in DNA computations, among other applications), to molecular scale aspect widths. (ii) It may provide a dramatic miniaturization of DNA computation methods using surface chemistry [Corn, et al 99], again to molecular scale aspect widths. -Use of DNA Lattices as a Substrate for Layout of Nano-Scale Circuit Components ([Petty et al 95] [Aviram,Ratner98] ). Recently Tour’s group at Rice Univ. in collaboration with Reed at Yale (in a DARPA funded contract of which Reif is a subcontractor) have designed and demonstrated [Chen et al 99] organic molecules that act as conducting wires [Reed et al.97],[Zhou99] and also organic molecules that act as rectifying diodes. A key remaining problem is to develop method for assembling these molecular electronic components into a circuit. We propose to investigate the possible application of self-assembled DNA 2D lattices for the layout of nano-scale circuit components (organic polymers)on the lattices. This might be done by designing a modified chemistry for these organic molecules for attachment to DNA. This would then allow for the selective attachment of the molecular electronic components to particular tiles of the DNA tiling array. There are known molecular probe devices (developed in that same project) may be used to test the electrical properties of the resulting molecular circuit attached to the DNA tiling array. -Construction of 3D DNA lattices. We also intend to begin an investigation of a number of possible methods for constructing 3D DNA lattices. This would allow us to extend our proposed DNA lattice computations to 3D, providing computations with (implicit) data movement in three dimensions. The TX tiling array that we constructed [LaBean et al, 99] have well-defined helices that come out of the plane and suggest ways of extending the construction of periodic matter to three dimensions. Also, we are considering various class of more complex (but still stable) tiles that may provide 3D tiling assemblies. -DNA Motors and their Possible Application to DNA computations. Recently, Seeman’s group made a DNA construction of a nanomechanical device capable of controlled movement [Mao, et al 99a]. In addition to these static constructs, we have built a prototype DNA nanomechanical device. This device consists of two DX molecules connected by a DNA double helix that contains a segment of DNA that can be converted to the left-handed Z-DNA structure. In B-promoting conditions, the two unconnected helices of the device are on the same side of the connecting helix, but they are on opposite sides in Z-promoting conditions. This results in an apparent rotary motion of about a half-revolution, leading to atomic displacements ranging from 2 to 6 nm, depending on the location of the atom relative to the axis of the stationary helix. This motion has been demonstrated by fluorescent resonance energy transfer (FRET). We are working to build on this work in several directions. We intend to combine the nanomolecular device with the 2-D arrays, so that we can achieve an array of devices. This has not been possible to do with the DX system, but the advantages of the TX system are likely to render it feasible; this because it is not necessary for the pivoting part of the system to point normal to the array in the TX system, as it must in the DX system. It is important to point out that the device based on the B-Z transition is only a prototype that we have used to learn how to characterize motion in DNA systems. It lacks programmability, except to the limited extent that one can orient the two DX molecules at a variety of relative torsion angles in the B-state. Thus, all of the molecules must be in either the B-state or in the Z-state, assuming one has robust chemical control. The polycrossover (PX) system we have recently designed leads to sequence-specific motion. Thus, there are two discrete states, PX or JX, in which the helices at one end of the molecule are in reversed positions. Thus, an array of these molecules would contain individually programmed molecules whose conformational state would be amenable to specific reversal (or not, depending on the program) from cycle to cycle. This system would lead to the ability to 'nanofacture' specific molecules, a capability not available today. We intend that this system would ultimately permit us to do chemistry at chemically identical but spatially distinct sites. This system offers a direct route to nanorobotics, because it couples a series of distinct structural states with programmability. A DNA array with programmability of this sort offers a mechanism to do DNA computation of arrays whose elements(the tiles) hold state. That is, the DNA assemblies may be able to simulate a parallel computing model known as cellular automata, which consist of arrays of finite state automata, each which holds state. The transitions of these automata and communication of values to their neighbors might be done by conformal (geometry) changes, again using this programmability. There are numerous examples of 1 D (2 D, respectively) cellular automata that can do computations that tiling assemblies would have required a further dimension (for example, integer multiplication in one dimension instead of two). USC is also investigating the possibility of using JX-PX for a potential use in a programmable finite state automaton -Simulation Tools. In addition to software for the design of DNA tiles, we are working to develop software simulation tools of the kinetics of self-assembly for self-assembly, providing a more fundamental understanding of self-assembly processes. These will improve upon the software simulations [Winfree,98] (which allowed tiling assemblies only to be constructed from individual tiles appending to tiling assemblies), to provide for assembly processes that include the combination of distinct tiling assemblies. (5) Key Open Research Issues. (a) To what extant can we, in practice, scale the parallelism of DNA self-assembly computations? Potentially, DNA self-assembly assemblies and computations can scale up to can be up to 1016 or possibly 018 molecules. However, there may be critical barriers that we need to overcome. Defect errors, self-assembly kinetics and other processes may limit this scale. We do not yet know what are the optimal settings of the key parameters (time, solution concentrations, etc.) and which error resilient techniques provide the best avenue to scale to assemblies with extremely large numbers of molecules. (b) To what degree can we, in practice, scale the complexity of computations using DNA self-assembly? To date, the computations we have demonstrated via DNA self-assembly have been simple Boolean XOR operations executed in one dimension. Prior theoretical results have establishing the potential power of tiling assembles to arbitrary complex assemblies in two and three dimensions. Extending this work to two and three dimensions thus provides many further opportunities. Potentially, we can also have multiple distinct DNA self-assembly computations occurring simultaneously and asynchronously, and these may interact with each other.

(3) Publications and Products in 2000-2002

(3.1) Journal Publications in 2000-2002:

Duke University Journal Publications:

LaBean, T. H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H. & Seeman, N.C., The construction, analysis, ligation and self-assembly of DNA triple crossover complexes, Journal of American Chemestry Society 122, 1848-1860 (2000).

C. Mao, LaBean, T.H. Reif, J.H., Seeman, Logical Computation Using Algorithmic Self- Assembly of DNA Triple-Crossover Molecules, Nature, vol. 407, Sept. 28 2000, pp. 493–495; C. Erratum: Nature 408, 750-750(2000).

J.H. Reif and S. Tate, Fast spatial decomposition and closest pair computation for limited precision input, Journal of Algorithmica, Volume 28, Number 3, 2000, pp. 271-287.

J.H. Reif, On the Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, Information and Computation, Jan 2000, pp. 1-20.

J.H. Reif and H. Wang, Nonuniform discretization approximation for Kinodynamic motion planning and its applications, Siam Journal of Computing (SICOMP), Volume 30, No. 1, pages 161-190, (2000).

J.H. Reif, Parallel Output Sensitive Algorithms for Combinatorial and Linear Algebra Problems, Journal of Computer and System Sciences, Vol. 62(3), 2001, pp 398-412.

J.H. Reif, Efficient Parallel Computation of the Characteristic Polynomial of a Sparse, Separable Matrix, Algorithmica, 29(3): 487-510 (2001).

G.L. Peterson, J.H. Reif, and S. Azhar, Lower Bounds for Multiplayer Non-Cooperative Games of Incomplete Information. in Computers and Mathematics with Applications, Volume 41, pp 957-992 (2001)

J.H. Reif and J. A. Storer, Optimal Encoding of Non-stationary Sources, Special Issue of Information Sciences, Volume 135, pp. 87-105 (2001).

J. H. Reif, DNA Lattices: A Programmable Method for Molecular Scale Patterning and Computation, special issue on Bio-Computation, Computer and Scientific Engineering Magazine, IEEE Computer Society. February 2002, pp 32-41.

H. Reif, The Emergence of the Discipline of Biomolecular Computation in the US, invited paper to the special issue on Biomolecular Computing, New Generation Computing, edited by Masami Hagiya, Masayuki Yamamura, and Tom Head, 2002.

G.L. Peterson, J.H. Reif, and S. Azhar, Decision Algorithms for Multiplayer Non- Cooperative Games of Incomplete Information. Computers and Mathematics with Applications, Vol. 43, 2002, pp 179-206.

J.H. Reif, Efficient Parallel Factorization and Solution of Structured and Unstructured Linear Systems, to appear in Journal of Computer and System Sciences, 2002.

John H. Reif, Perspectives: Successes and Challenges, Science, 296: 478-479, April 19, 2002.

J. H. Reif, The Emergence of the Discipline of Biomolecular Computation in the US, invited paper to the special issue on Biomolecular Computing, New Generation Computing, edited by Masami Hagiya, Masayuki Yamamura, and Tom Head, 2002.

J. H. Reif, The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA, To appear in Natural Computing, DNA8 special issue, 2003.

Dage Liu, John H. Reif, and Thomas H. LaBean, DNA Nanotubes: Construction and Characterization of Filaments, To appear in Natural Computing, DNA8 special issue, 2003.

NYU Journal Publications:

T. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, J.H. Reif and N.C. Seeman, The Construction, Analysis, Ligation and Self- Assembly of DNA Triple Crossover Complexes, Journal of the American Chemical Society 122, 1848-1860 (2000).

Sha, F. Liu and N.C. Seeman, Direct Evidence for Spontaneous Branch Migration in Antiparallel DNA Holliday Junctions, Biochemistry 39, 11514-11522 (2000).

R. Sha, H. Iwasaki, F. Liu, H. Shinagawa and N.C. Seeman, Cleavage of Symmetric Immobile DNA Junctions by Ruv C, Biochemistry 39, 11982-11988 (2000).

R. Sha, F. Liu, D.P. Millar N.C. Seeman, Atomic Force Microscopy of Parallel DNA Branched Junction Arrays, Chemistry & Biology 7, 743- 751 (2000). A. Podtelezhnikov, C. Mao, N.C. Seeman & A. Vologodskii, Multimerization- Cyclization of DNA Fragments as a Method of Conformational Analysis, Biophys. J. 79, 2692-2704 (2000).

C. Mao, T. LaBean, J.H. Reif and N.C. Seeman, Logical Computation Using Algorithmic Self-Assembly of DNA Triple Crossover Molecules, Nature 407, 493-496 (2000); Erratum: Nature 408, 750-750 (2000).

N.C. Seeman, In the Nick of Space: Generalized Nucleic Acid Complementarity and the Development of DNA Nanotechnology, Synlett 2000, 1536-1548 (2000).

8. N.C. Seeman, DNA Nicks and Nodes and Nanotechnology, NanoLetters 1, 22-26 (2001).

H. Yan, X. Zhang, Z. Shen and N.C. Seeman, A Robust DNA Mechanical Device Controlled by Hybridization Topology, Nature 415, 62- 65 (2002).

N.C. Seeman, It Started with Watson and Crick, But it Sure Didn't End There: Pitfalls and Possibilities beyond the Classic Double Helix, Natural Computing 1, 53-84 (2002)..

N.C. Seeman & A.M. Belcher, Emulating Biology: Nanotechnology from the Bottom Up, Proceedings of the National Academy of Sciences (USA) 99 (supp. 2), 6451-6455 (2002).

R. Sha, F. Liu and N.C. Seeman, Atomic Force Measurement of the Interdomain Angle in Symmetric Holliday Junctions, Biochemistry 41, 5950-5955 (2002).

N.C. Seeman, DNA Nanotechnology: Life's Central Performer in a New Role, Biological Physics Newsletter 2 (1) 2-6 (2002).

R. Sha, F. Liu, H. Iwasaki and N.C. Seeman, Parallel Symmetric Immobile DNA Junctions as Substrates for E. coli RuvC Holliday Junction Resolvase. Biochemistry 41, 10985-10993 (2002).

A. Carbone and N.C. Seeman, Circuits and Programmable Self-Assembling DNA Structures, Proc. Nat. Acad. Sci. (USA) 99 12577-12582 (2002).

X. Zhang, H. Yan, Z. Shen and N.C. Seeman, Paranemic Cohesion of Topologically-Closed DNA Molecules, J Am. Chem. Soc.124, 12940-12941 (2002). S. Xiao, F. Liu, A. Rosen, J.F. Hainfeld, N.C. Seeman, K.M. Musier-Forsyth & R.A. Kiehl, Self-Assembly of Nanoparticle Arrays by DNA Scaffolding, J. Nanoparticle Research 4, 313-317 (2002).

A. Carbone and N.C. Seeman, Fractal Designs Based on DNA Parallelogram Structures, Natural Computing 1, 469-480 (2002).

L. Zhu, O. dos Santos, N.C. Seeman and J.W. Canary, Reaction of N3- Benzoyl-3’, 5’-O-(di-tert-butylsilanediyl)uridine with Hindered Electrophiles: Intermolecular N3 to 2'-O Protecting Group Transfer, Nucleosides, Nucleotides & Nucleic Acids 21, 723-735 (2002)..

N.C. Seeman, DNA in a Material World, Nature 421, 33-37 (2003).

N.C. Seeman, Structural DNA Nanotechnology: A New Organizing Principle for Advanced Nanomaterials, Materials Today 6 (7), 24-29 (2003).

H. Yan and N.C. Seeman, Edge-Sharing Motifs in DNA Nanotechnology. Journal of Supramolecular Chemistry, in press (2003).

University of South Florida Journal Publications (some are joined with NYU):

D. & U. Fiebig, N. Jonoska, Multiplicities of covers of sofic shifts, Theoretical Computer Science, vol. 262 (2001) 349-375.

E. Coven, A. Johnson, N. Jonoska, K. Madden, The symbolic dynamics of multidimensional tiling systems, to appear in Ergodic Theory and Dynamical Systems, (2002).

N. Jonoska, P. Sa-Ardyen, N.C. Seeman, Self-assembly of graphs represented by DNA Helix Axis Topology, to appear , Journal of Natural Computing.

N. Jonoska, D. Kephart, K. Mahalingam, Generating codes for DNA computing, (to appear) Congressus Numerantium. (Also published in the book of late breaking papers GECCO'02.)

N. Jonoska, P. Sa-Ardyen, N.C. Seeman, Computation by self-assembly of DNA graphs, (to appear) Journal of Genetic Programming And Evolvable Machines.

(3.2) Books or chapters in Books, and Conference and Workshop Papers in 2000- 2002:

Duke Books or chapters in Books, and Conference and Workshop Papers: Handbook of Randomized Computing (Edited by S. Rajasekaran, P. M. Pardalos, J.H. Reif and J. Rolim), Kluwer Volume I and II, Academic Press, London, 2001

Bo, Guo Master Thesis Computing by DNA Self-Assembly. Oct, 2001.

Gehani, A., T. H. LaBean, and J.H. Reif, DNA-based Cryptography, Proc. DNA Based Computers V: Cambridge, MA, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 54, edited by E. Winfree and D.K. Gifford, American Mathematical Society, Providence, RI, pp. 233-249, (2000).

T. H. LaBean, E. Winfree, and J.H. Reif, Experimental Progress in Computation by Self- Assembly of DNA Tilings, Proc. DNA Based Computers V: Cambridge, MA, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Volume 54, edited by E. Winfree and D.K. Gifford, American Mathematical Society, Providence, RI, pp. 123- 140, (2000).

J.H. Reif and Z. Sun. An efficient approximation algorithm for weighted region shortest path problem. In Proceedings of the 4th Workshop on Algorithmic Foundations of Robotics(WAFR2000),Pub. by A. K. Peters Ltd, Hanover, New Hampshire, pages 191- 203, Mar. 16-18 2000.

J.H. Reif and Z. Sun. Movement planning in the presence of flows. In Proceedings of the 7th International Workshop on Algorithms and Data Structures (WADS2001), volume 2125 of Lecture Notes in Computer Science, pages 450-461, Brown University, Providence, RI, August 8-10, (2001).

J.H. Reif and T. H. LaBean, Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector- Quantization, Sixth International Meeting on DNA Based Computers (DNA6), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Leiden, The Netherlands, (June, 2000) ed. A. Condon. Springer-Verlag as a volume in Lecture Notes in Computer Science, (2001).

J.H. Reif, T.H. LaBean, and N.C. Seeman, Challenges and Applications for Self- Assembled DNA Nanostructures, Proc. Sixth International Workshop on DNA-Based Computers, Leiden, The Netherlands, June, 2000. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Edited by A. Condon and G. Rozenberg. Lecture Notes in Computer Science, Springer-Verlag, Berlin Heidelberg, vol. 2054, 2001, pp. 173-198.

J.H. Reif and T. H. LaBean, and N.C. Seeman. "Programmable Assembly at the Molecular Scale: Self-Assembly of DNA Lattices", Invited paper, 2001 IEEE International Conference on Robotics and Automation (ICRA2001), Seoul, Korea, ed. Lee Beom (May, 2001). Z. Sun and J.H. Reif. BUSHWHACK: An approximation algorithm for minimal paths through pseudo-Euclidean spaces. In Proceedings of the 12th Annual International Symposium on Algorithms and Computation(ISAAC01), Christchurch, New Zealand, Dec 19-21, 2001, Pub. in volume 2223 of Lecture Notes in Computer Science, pages 160- 171, Dec, 2001.

J. H. Reif, T. H. LaBean, M. Pirrung, V. Rana, B. Guo, K. Kingsford, and G. Wickham, Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability, Seventh International Meeting on DNA Based Computers (DNA7), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Tampa, FL, June 11- 13, 2001.

J. H. Reif, Molecular Assembly and Computation: From Theory to Experimental Demonstrations, plenary paper, 29-th International Colloquium on Automata,Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002).

J. H. Reif, The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA, The 8th International Meeting on DNA Based Computers (DNA 8), Springer Verlag, Sapporo, Japan, June 10-13, 2002.

Dage Liu, John H. Reif, and Thomas H. LaBean, DNA Nanotubes: Construction and Characterization of Filaments, The 8th International Meeting on DNA Based Computers (DNA 8), Springer Verlag, Sapporo, Japan, June 10-13, 2002.

Zheng Sun and John H. Reif, On Energy-minimizing Paths on Terrains for a Mobile Robot, 2003 IEEE International Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, May 12-17, 2003.

David Hsu, Tingting Jiang, John H. Reif, and Zheng Sun, The Bridge Test for Sampling Narrow Passages with Probabilistic Roadmap Planners, 2003 IEEE International Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, May 12-17, 2003.

NYU Books or chapters in Books, and Conference and Workshop Papers:

N.C. Seeman, F. Liu, C. Mao, X. Yang, L. A. Wenzler, R. Sha, W. Sun, Z. Shen, X. Li, J. Qi, Y. Zhang, T.-J. Fu, J. Chen and E. Winfree, Two Dimensions and Two States in DNA Nanotechnology, Proceedings of the 11th Conversation in Biomolecular Stereodynamics, ed. by R.H. Sarma and M.H. Sarma, Adenine Press, New York, 253-262 (2000).

N.C. Seeman, DNA Nanotechnology: From Topological Control to Structural Control, in Pattern Formation in Biology, Vision and Dynamics, ed. by A.Carbone, M.Gromov, P.Pruzinkiewicz, World Scientific Publishing Company, Singapore, 271-309 (2000). N.C. Seeman, C. Mao, F. Liu, R. Sha, X. Yang, L. Wenzler, X. Li, Z. Shen, H. Yan, P. Sa-Ardyen, X. Zhang, W. Shen, J. Birac, P. Lukeman, Y. Pinto, J. Qi, B. Liu, H. Qiu, S.M. Du, H. Wang, W. Sun, Y. Wang, T.-J. Fu, Y. Zhang, J.E. Mueller and J. Chen, Nicks, Nodes, and New Motifs for DNA Nanotechnology, Frontiers of Nano-Optoelectronic Systems, ed. by L. Pavesi & E. Buzanova, Kluwer, Dordrecht, 177-198 (2000).

J.H. Reif, T.H. LaBean & N.C. Seeman, Challenges and Applications for Self- Assembled DNA Nanostructures, Sixth International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, (June, 2000) ed. A. Condon, G. Rozenberg. Springer-Verlag, Berlin Heidelberg, Lecture Notes in Computer Science 2054, 173-198, (2001).

N.C. Seeman, Key Experimental Approaches in DNA Nanotechnology, Current Protocols in Nucleic Acid Chemistry, Unit 12.1, John Wiley & Sons, New York (2002).

P. Sa-Ardyen, N. Jonoska and N.C. Seeman, Self-Assembling DNA Graphs, DNA-Based Computers VIII, in press (2003).

N.C. Seeman, DNA Nanotechnology, Encyclopedia of Supramolecular Chemistry, in press (2003).

N. Jonoska, P. Sa-Ardyen and N.C. Seeman, Compuatation by Self-Assembly of DNA Graphs, Genetic Programming and Evolvable Machines, in press (2003).

Alessandra Carbone and Nadrian C. Seeman - Circuits and Programmable Self- Assembling DNA Structures. Proceedings of the 8th International Meeting on DNA Based Computers (DNA 8), Springer Verlag, Sapporo, Japan, June 10-13, 2002.

Phiset Sa-Ardyen, Natasa Jonoska, and Nadrian C. Seeman, Self-assembling DNA Graphs, Proceedings of the 8th International Meeting on DNA Based Computers (DNA 8), Springer Verlag, Sapporo, Japan, June 10-13, 2002. (see also below)

Books Edited: N. Jonoska and N.C. Seeman, DNA Computing, 7th International Workshop on DNA- Based Computers, DNA 2001, Lecture Notes in Computer Science 2340, Tampa, Florida, June 2001, Springer-Verlag, Berlin, ISBN 3-540-43775, 392 pages (2002).

University of South Florida Books, and Conference and Workshop Papers (some are with NYU):

Natasa Jonoska & Masahico Saito, Boundary Components of Thickened Graphs, Seventh International Meeting on DNA Based Computers(DNA7), Tampa FL, June 10-13, 2001. Conference Proceedings, Lecture Notes in Computer Science (N. Jonoska, N.C. Seeman, eds.), in press.

N. Jonoska, M. Saito, Boundary components of thickened graphs. Proceedings of the 7th International DNA Based Computer Meeting, June 10-13, 2001, Tampa FL

N. Jonoska: Computing with Biomolecules, (invited paper), Theorietag 2000: New Computing Paradigms: Molecular Computing and Quantum Computing, (R. Freund editor) University of Technology Vienna, (2000) 35-58.

(3.3) Other products (database, software, instruments, inventions, physical collections, educational aids, etc) you have reported earlier as developed or under development out of your project.

Patents: N.C. Seeman, E. Winfree, F. Liu and L. Wenzler Savin, Periodic Two- and Three- Dimensional Nucleic Acid Structures, U.S. Patent #6,255,469, Issued July 03, 2001. N.C. Seeman, X. Li, X. Yang and J. Qi, Nanoconstructions of Geometrical Objects and Lattices from Antiparallel Nucleic Acid Double Crossover Molecules, U.S. Patent #6,072,044, Issued June 06, 2000. N.C. Seeman, E. Winfree, F. Liu and L. Wenzler Savin, Periodic Two- and Three- Dimensional Nucleic Acid Structures, U.S. Patent #6,255,469, Issued July 03, 2001.

Posted on internet

(Duke): Software for DNA Tile design Software for the optimized design of DNA tiles was first developed in Mathlab by Winfree, then a PhD student at Caltech (advised in part by Adleman at USC). This software used a greedy search method to optimize the choice of DNA strands comprising the DNA tiles. The software was improved Duke graduate student Guo Bo) [Bo01] to allow for a more sophisticated optimization heuristic (providing improved sequence specificity of the DNA words used for tile pads, minimizing the likelihood of incorrect hybridizations from non-matching pads), to include more realistic models of DNA hybridization, and to provide a Java interface. (Bo, Guo Master Thesis Computing by DNA Self-Assembly. Oct, 2001.)

(Duke):Simulation Tool for DNA computation A Duke graduate student Ashish Gehani developed a prototype software simulation system for DNA computation. These software tools are expected to be very useful to optimize the experimental BMC protocols and minimize errors. A simulator was written in Java, which implemented the operations of the recombinant DNA model. The software models recombinant DNA operations at multiple levels of detail from high level down to the kinetics of reactions. For example, molecular complexes are represented as graphs at the granularity of nucleotides and have a level of spatial description such that most infeasible nucleotide complexes are not allowed to contaminate the data set as the computation is simulated. We used thermodynamic and kinetic models to represent interactions between complexes.

(Duke):Simulation Tool for DNA Tile Assemblies Winfree, then a PhD student at Caltech (advised in part by Adleman at USC) developed software for discrete time simulation of the tiling assembly processes, using approximate probabilities for the insertion or removal individual tiles from the assembly. These simulations gave an approximation to the kinetics of self-assembly chemistry and provided some validation of the feasibility of tiling self-assembly processes. Using this software as a basis, Duke graduate student Guangwei Yuan [Guangwei00] developed improved (sped up by use of an improved method for computing on/of likelihood suggested by Winfree) simulation software with a Java interface http://www.cs.duke.edu/~yuangw/project/test.html and gave a number of example tilings, including string tilings for integer addition and XOR computations. This software provided more fundamental understanding of self-assembly processes. (Guangwei,Y. "Simulation of DNA Self-assembly", MS Thesis, Duke University, 2000.)

(USF) In addition to the above: we are developing software for strand design which should help in producing sticky ends of the junctions (tiles) used in self-assembly. This is based on the theoretical findings about DNA codes. The firs paper will appear soon and the second is in prepapration. We plan to have the program available to the public on the web.

(4) Contributions within Discipline:

(4.1) How have your findings, techniques you developed or extended, or other products from your project contributed to the principal disciplinary field(s) of the project? We have performed the first successful DNA algorithmic assembly. We have begun studies to extend this work from one dimension to two dimensions. We have designed and are testing a device to enable a multiplicity of structural states in a DNA lattice. We have proposed a DNA circuit approach involving this new device. We have constructed and demonstrated the first irregular DNA graph. We have proposed a series of fractal assemblies from unusual DNA components. John Reif and Nadrian Seeman (Duke and NYU): We have prototyped a scalable computation by self-assembly. We have produced 2D arrays with deliberately designed patterns.

Nadrian Seeman (NYU): We have produced DNA-based nanomechanical devices that will be of use in molecular computation. Seeman served as program chair for DNA-7 and co-editor of its proceedings.

Program Chair: Nadrian Seeman. The Seventh International Workshop on DNA-Based Computers, University of .South Florida, Tampa, Fl, (2001)

Natasha Jonoska (USF): Organizing Chair of Seventh International Workshop on DNA- Based Computers, University of .South Florida, Tampa, Fl, (2001) and co-editor of its proceedings.

Natasha Jonoska (USF): Program Chair of DNA and molecular computing track of Genetic and Evolutionary Computing Conference ‘02 and ’03.

(4.2) Contributions to Other Disciplines How have your findings, techniques you developed or extended, or other products from your project contributed to disciplines other than your own (or not covered under "Contributions within Discipline")?

So as to establish a number of the results in this work, we have needed to establish features of branched DNA molecules. These include branch migration, cleavage, angles between helices and molecular rigidity estimates. These contributions have been to the fields of genetic recombination and to molecular biophysics.

All the groups are multidisciplinary group (mathematics, computer science, biology, chemistry). Each of us, faculty members and students together, learns from the others.

(Duke): Software for DNA Tile design Software for the optimized design of DNA tiles was first developed in MatLab by Winfree, then a PhD student at Caltech (advised in part by Adleman at USC). This software used a greedy search method to optimize the choice of DNA strands comprising the DNA tiles. The software was improved Duke graduate student Guo Bo) [Bo01] to allow for a more sophisticated optimization heuristic (providing improved sequence specificity of the DNA words used for tile pads, minimizing the likelihood of incorrect hybridizations from non-matching pads), to include more realistic models of DNA hybridization, and to provide a Java interface. (Bo, Guo Master Thesis Computing by DNA Self-Assembly. Oct, 2001.)

(Duke):Simulation Tool for DNA tile Assemblies Winfree, then a PhD student at Caltech (advised in part by Adleman at USC) developed software for discrete time simulation of the tiling assembly processes, using approximate probabilities for the insertion or removal individual tiles from the assembly. These simulations gave an approximation to the kinetics of self-assembly chemistry and provided some validation of the feasibility of tiling self-assembly processes. Using this software as a basis, Duke graduate student Guangwei Yuan [Guangwei00] developed improved (sped up by use of an improved method for computing on/of likelihood suggested by Winfree) simulation software with a Java interface http://www.cs.duke.edu/~yuangw/project/test.html and gave a number of example tilings, including string tilings for integer addition and XOR computations. This software provided more fundamental understanding of self-assembly processes. (Guangwei,Y. "Simulation of DNA Self-assembly", MS Thesis, Duke University, 2000.)

Nadrian Seeman(NYU): We have used parallelogram arrays as an analytical tool in molecular biophysics. We have established by means of AFM and parallelogram arrays the parallel nature of Bowtie junctions. Similarly, we have used similar techniques to characterize the inter-helical angle in a symmetric Holliday junction: We settled a dispute about the potential influence of crystal packing forces in a crystal structure determination; by this orthogonal technique, we showed that crystal packing forces were not a contributor to this system.

Natasha Jonoska(USF): Natasha was rather involved in the development of Bioinformatics Masters Program at USF which is now funded by Sloan Foundation, this program contains collaboration between three colleges and five departments and my familiarity of concepts in mathematics, biology, chemistry and computer science was essential. Last semester I taught a course for this program.

(4.3) Contributions to Human Resource Development How have results from your project contributed to human resource development in science, engineering, and technology?

During the course of this work, Drs. Chengde Mao (now on the faculty at Purdue) and Dr. Yan (now research faculty at Duke) were trained extensively in the areas of this project. They learned to perform many operations new to them. Both are now moving onwards with their careers as scientists. Natasha Jonoska, a computer scientist from the University of South Florida has spent a sabbatical in the laboratory learning the basic techniques used in the work described. Mr. Sa-Ardyen is completing and Ms. Constantinou and Mr. Ding are advancing towards their degrees. Two high school students in the lab, Alex Mittal and John Sadowski are Intel semi-finalists.

(4.4) Contributions to Resources for Research and Education How have results from your project contributed to physical, institutional, and information resources for research and education (beyond producing specific products reported elsewhere)?

Reif taught a graduate course on DNA nanotechnology and DNA computation. In addition to the annual class on nucleic acid structure, symmetry, design and nanotechnology, Seeman gave a tutorial on nucleic acid basics was presented to the Seventh Workshop on DNA-Based Computation concerning non-standard base-pairing and backbone structures and was program chairman of that workshop. Natasha Jonoska gave a number of seminars on theoretical aspects of DNA nanotechnology. She spent a sabbatical at Seeman’s laboratory learning the basic techniques used in the work described, and is teaching these techniques to students at University of Florida.

The following Universities gave courses in DNA Computing:

John Reif, Duke University, CPS 296.2: Computational Biology and Biomolecular Computation, spring, 2000 and fall, 2000. http://www.cs.duke.edu/~reif/courses/cps296.2/cps296.2.html

Thomas H LaBean, Duke University, MOLECULAR COMPUTING, Spring, 2001. Spring, 2002.

Nadrian Seeman: courses in 1998-2002 in DNA nanostructures: Macromolecular chemistry that emphasizes the elements of symmetry, topology and structure that are necessary for building motifs capable of multidimensional self-assembly. This basic course in macromolecular features emphasizing the design of DNA nanostructures has been taught at NYU. Seeman havs given tutorials at DNA VII and DNA VIII. Seeman was program chair at DNA VII.

Natasha Jonoska, USF, MAT 6932, Topics in Theoretical Computer Science: Biomolecular computing, (Spring 2002) , MAT 5930 Special topic in Combinatorics and graph theory (a course for the Bioinformatics program at USF) Fall 2002. Natasha Jonoska gave several lectures in front of high school teachers. The results produced here also have stimulated a large amount of interest in college and high school students. We have received numerous inquiries from students interested in the systems we have developed and wishing to join these efforts.

(4.5) Contributions Beyond Science and Engineering How have results from your project contributed to the public welfare beyond science and engineering (e.g., commercializing the technology)?

The technology of DNA nanoassembly developed by the PI and subcontractors is likely eventually to contribute to molecular electronics.

The PI and subcontractors have had numerous conversations with venture capitalists about the possibilities of licensing our patents (including the one listed above) about commercializing this technology. In addition to these contacts with venture capitalists, we have lectured both at private enterprises and to the military to attempt to increase applications of this technology. A number are planning to be involved actively in such an enterprise within a year or two. In conjunction with NYU, we are working to establish a firm to exploit our technology.

Patents(see above).