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

Report thru Dec 31, 2002

(1) Participants:(1.1)Principal Investigators:

PI: John H. Reif (leader of research project)Title: ProfessorSurface address: D223 LSRC, Duke Univ., Durham, NC 27708-0129Phone number: 919-660-6568Fax number: 919-660-6519Email address: reif@cs.duke.eduHomepage URL: www.cs.duke.edu/~reif/HomePage.htmlPapers in DNA Nanostructures:http://www.cs.duke.edu/~reif/vita/topics/biomolecular.htmlProject URL: http://www.cs.duke.edu/~reif/BMCProject Report URL:http://www.cs.duke.edu/~reif/BMC/reports/NSF.NANO.ITR.report/NSF.NANO.ITR.report.html

Natasha JonoskaTitle: Associate ProfessorSurface address: Department of Mathematics, University of South Florida, 4202 E.Fowler Av., PHY 114, Tampa Fl, 33620-5700Phone number: 813-974-9566Fax number: 813-974-2700Email address: jonoska@math.usf.eduHomepage URL: www.math.usf.edu/~jonoskaProject URL: http://www.math.usf.edu/~jonoska/bio-comp

Nadrian C. SeemanTitle: ProfessorSurface address: Department of Chemistry, New York University, New York, NY 10003Phone number: 212-998-8395Fax number: 212-260-7905Email address: ned.seeman@nyu.eduHomepage URL: http://seemanlab4.chem.nyu.edu/Project URL: http://seemanlab4.chem.nyu.edu/nanotech.html

(1.2) Collaborating Scientists: Research Assistant Professors:Thom LaBeanTitle: Research Assistant Professor

Surface address: D230 LSRC, Duke University, Durham, NC 27708-0129Phone number: 919-660-6553Fax number: 919-660-6519Email address: thl@cs.duke.eduHomepage URL: www.cs.duke.edu/~thl

Hao YanTitle: Research Assistant ProfessorSurface address: D230 LSRC, Duke University, Durham, NC 27708-0129Phone number: 919-660-6553Fax number: 919-660-6519Email address: hy1@cs.duke.eduHomepage URL: http://www.cs.duke.edu/~hy1

Training and DevelopmentThe PI and subcontract PIs have trained numerous Postdoctoral Assistants in thetechniques of DNA nanotechnology and DNA-based computation. These people areamong the few individuals in the world possessing these skills. We expect that theywill 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-currentSang Jung Ahn (jointly supervised with Thom LaBean), 2003- currentDage 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 Universitywww.cs.duke.edu/~thl/)Thom LaBean, 1998-2001 (currently Research Assistant Professor, CS Dept, DukeUniversity http://www.cs.duke.edu/~hy1/)

NYU Postdoctoral Assistants supervised:Lisa Wenzler SavinYariv Pinto

(1.4) Graduate students:

The PI and subcontract PIs have trained and graduated numerous graduate students in thetechniques of DNA nanotechnology and DNA-based computation. These people areamong the few individuals in the world possessing these skills. We expect that they willbe 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 nonuniformrandomized 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 ofPhysics), Ph.D. thesis topic: Conductivity of Metalized DNA Nanostructures. ProjectedDate 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 ofGraduation: Spring '2004.Duke University Graduate Student Supervision (Completed Degrees):Guo Bo, Master Thesis “Computing by DNA Self-Assembly”. Oct, 2001 (currentlyResearch 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 SavinYariv PintoNYU Graduate students supervised:Pamela ConstantinouHao YanPhiset Sa-ArdyenBaoquan DingXiaoping YangFurong LiuRoujie ShaChengde MaoWeiqiong SunZhiyong ShenHao 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 massiveparallel computing at the molecular scale. This involves the development of experimental proof-of-concept demonstrations of the application of DNA self-assembly to various basiccomputational tasks, such as sequences of arithmetic and logical computations executed inmassively parallel fashion, and the application of this method to hard computational problemssuch as integer factorization. Ongoing research includes the development of novel DNA tileswith properties that facilitate the self-assembly and their visualization by imaging devices suchas atomic force microscopes and electron microscopes, the testing of various input/outputmethods, and methods to minimize errors in self- assembly. The self assembly of junctionmolecules 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 DNAcrossover molecules (tiles). These DNA tiles have sticky ends that preferentially matchthe sticky ends of certain other DNA tiles, facilitating the further assembly into tilinglattices. The self-assembly of large 2D lattices consisting of up to thousands of tiles havebeen recently demonstrated by Seeman and Winfree. DNA self-assembly can, using onlya small number of component tiles, provide arbitrarily complex assemblies. It can be usedto execute computation, using tiles that specify individual steps of the computation. Inthis emerging new methodology for computation: (i) input is provided by sets of singlestranded DNA that serve as nucleation sites for assemblies, and (ii) output can be madeby the ligation of reporter strands of DNA that run though the resulting assembly, andthen released by denaturing. Moreover, DNA self-assembly can be executed in massivelyparallel fashion, with concurrent assemblies that may execute computationsindependently. Due to the very compact form of DNA molecules, the degree ofparallelism (due to distinct tiling assemblies) may be 1016 or possibly 018. In the case ofjunction molecules and 3D structures, the output is the graph structure itself, since thecoding 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 ExperimentalDemonstrations, 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-AssembledDNA Nanostructures, Sixth International Workshop on DNA-Based Computers, DNA2000, 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 forComputation and Nanofabrication”. in CBGI 2001, Proceedings from ComputationalBiology 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 EngineeringMagazine, 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-BasedComputers, 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-assemblyof computational structures. The nano-structures constructed consist of DNA crossovermolecules (tiles) that have sticky ends that match the sticky ends of other DNA tiles. TheDNA tiles self assemble into large lattices that can execute computations. We areexecuting experimental tests of computation by self-assembly of DNA nanostructuretilings. The key advantage of this approach was that the self-assembly sidesteps timeconsuming laboratory steps required by other methods for DNA computation. Theseassembly methods are executed in massively parallel fashion, with concurrent assemblies,each with a (possibly) distinct input strand. We are testing our approach by doingmassively parallel arithmetic operations by this self-assembly method. We are engaged invarious steps required to achieve this goal, including (i) construction of trial inputs byself-assembly of dsDNA (double stranded DNA) segments from ssDNA (single strandedDNA), (ii) design and construction of DNA tiles, and (iii) design and construction ofDNA tilings for massively parallel arithmetic computations. Massively parallel DNAassemblies for integer addition are being demonstrated tested and published in Nature.This will be followed by massively parallel DNA assemblies for integer multiplicationwith random inputs, which will give solution of integer factorization problems (used fordecryption of the RSA crypto-system).Also, Natasa Jonoska is investigating the use of three dimensional structures for solvingcomputational problems with DNA molecules. For example, building blocks of k-armedbranched junction molecules can be used to form graphs to solve the Hamiltonian Cycleproblem, the 3-vertex colorability problem, and the satisfiability problem, potentiallyreducing the number of laboratory (computational) steps.

List of Main activities undertaken by the project. We are conducting experiments toevaluate the speed and error rates of the various types of self-assembly reactions.• Experimental Demonstrations of Massively Parallel Computations by DNA TilingAssemblies.: We are experimentally testing massively parallel DNA self-assembly onparticular computational problems, such as the simultaneous execution of manyarithmetic or Boolean vector operations. The degree of parallelism in these experimentsis intended to range from 1016 or possibly 018.• Error Control in DNA Assemblies: We are executing experiments with the goal ofdeveloping 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 understandingof self-assembly processes).• We are also developing software for the design of DNA encoding of the sticky ends toavoid mismatched pairing.• We are making theoretical investigations into the complexity of DNA assemblies andtheir computations.

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

Reif Invited Lectures:

Software Design for Molectronics, DARPA Molectronics Meeting, Arlington, VI, (Feb26,2000).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 basedelectronics, 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 AssociativeSearch Using Error-Correcting Codes and Vector-Quantization, Invited Talk, SixthInternational 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, TheNetherlands, (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 andVector-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, CityUniversity of Hong Kong, Kowloon, Hong Kong, Oct 4.A Biomolecular System for Ultra-Scale Associative Search, Invited Talk, NationalReconnaissance 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, 2001J.H. Reif and Zheng Sun, An Efficient Approximation Algorithm for Weighted RegionOptimal Path Problem, Workshop on Foundations of Robotics (WFR2000), Dartmouth,NH, (March 2000).Molecular Computing via Programmed Self-Assembly of Patterned Molecules, PlenaryTalk, 2001 Congress on Evolutionary Computation (CEC2001), Seoul, Korea, May 28,

2001Experimental Construction of Very Large Scale DNA Databases with Associative SearchCapability, 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 InformationTechnology, sensing sciences, and Biological Systems”, organized by Jagdish Chandraand Srikanta Kumar, SIAM Annual Meeting, San Diego, California, July 9-13, 2001Movement Planning in the Presence of Flows, Workshop on Algorithms and DataStructures (WADS2001), Brown University, Providence, RI, August 8-10, (2001).Computations & patterned structures via DNA self-assembly, Invited talk, Max PlanckInstitute 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, 2001DNA Computation by Self-Assembly of DNA Nano-Scale Structures, Symposium onNew Approaches toward Computing, Plenary Talk, National Academy of Arts andSciences, Brussels, Belguim, November 9, 2001Programmable DNA Lattices: Design, Synthesis and Applications, Invited Talk, JointDARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 – 30, 2001.Self-Assembly of DNA Nano-Scale Structures for Computation, Invited Talk, JointDARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 – 30, 2001.Self-Assembly of DNA Nano-Scale Structures, Invited Talk, DARPA ITO BioComp PIMeeting, 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, June10-13, 2002.Molecular Assembly and Computation: From Theory to Experimental Demonstrations,plenary talk, 29th International Colloquium on Automata, Languages, andProgramming(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 AppliedMathematics (IPAM), September , 2002.Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations,invited talk, Alternative Computing Workshop, Mathematics in Nanoscale Science andEngineering, 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 PIMeeting, 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 GenomeInformatics (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, 2000University 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, 2001University 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, 2000Sectional 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

ACCOMPLISHMENTSMain Results to Date.Summary of Main Results:(a) As our main result, we have performed the first successful computation using DNAalgorithmic assembly. This DNA algorithmic assembly was of DNA triple crossovermolecules in one dimension. We have extended this work to massively parallel integerarithmetic.(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 basedon a new 4 x 4 tile.(c)We have made a robust sequence-dependent nanomechanical device and we haveworked up a motif for embedding it in a 2D array, preparatory to a nanorobotic approachto DNA circuit formation. We have designed and are testing a device to enable amultiplicity of structural states in a DNA lattice. We have designed a DNAnanomechanical device whose conformation is sequence driven.(d) We (NYU) have established conditions that promote PX-form association as a meansof replacing sticky-ends with paranemic, topologically closed cohesion. We have alsodeveloped edge-sharing cohesion. We have also established the cohesion of Bowtiejunction 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 nanomechanicaldevice into an array. This will allow us to make molecular pegboards for nanoscalecircuit experimentation.(f) We have prototyped the first covalent assembly of an irregular graph, where the helixaxes correspond to the edges of the graph.(g) We have assembled a number of tiles for 3D motifs, whose 3D self-assembly we areexploring actively. We developed methods for executing computation using three-dimensional DNA nanostructures and begun testing these in the laboratory. Recentsuccessful 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 nanotechnologyand DNA computation. LaBean taught a graduate level course on Molecular Computingduring Spring semesters 2001 and 2002. In addition to the annual class on nucleic acidstructure, symmetry, design and nanotechnology, Seeman gave a tutorial on nucleic acidbasics was presented to the 7th and 8th Workshop on DNA-Based Computationconcerning non-standard base-pairing and backbone structures and was programchairman 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 bySeeman 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 DNAnanotechnology. She spent a sabbatical at Seeman’s laboratory learning the basictechniques used in the work described, and is teaching these techniques to students atUniversity of Florida. Natasha Jonosk taught a PhD level graduate course in DNAcomputingDetails of Main Results: (a) The major outcome of this project during this period is the first successfulcomputation using DNA algorithmic assembly(Duke & NYU). We have made asuccessful experimental demonstration of a cumulative XOR calculation, which appearedin:C. Mao, T. LaBean, J.H. Reif and N.C. Seeman, Logical Computation Using AlgorithmicSelf-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 inputstrings, leading to two different output strings that correctly associated to produce theXOR result. This calculation was performed by using triple crossover (TX) DNAmolecules 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 itsneighbors. 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 contentsof those strands would have been re-used in a later calculation calling on those strands asthough they constituted a look-up table. This would have been done by using input tilescapable of assembling randomly in all 16 possible permutations. However, thiscalculation was the first calculation ever done in this fashion, so we did two specificcalculations, 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 somewhatlonger sticky ends (7 nucleotides) than the answer tiles (5 nucleotides). Thus, they, andthe two initialization tiles were able to assemble during the cooling protocol before any ofthe four answer tiles, and they thereby created a 'frame' superstructure into which theanswer tiles could fit. The answer tiles contained the four possible XOR options, inputsof 0 and 0 or 1 and 1 leading to a tile value of 0, and inputs of 1 and 0 or 0 and 1 leadingto a tile value of 1. Both input tile and output tile values (0 or 1) were encrypted on thereporter strands as restriction sites, one enzyme representing 0 and a second representing1. After the tiles had assembled, the reporter strands were ligated, thus establishing aconnection between the input and output values. The reporter strands were then purifiedand amplified by PCR treatment. The PCR product was then partially digested by one orthe 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-Gilbertsequencing gel (with, of course, much greater separations between the bands). Theanswers 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 incorrecttiles for positions within an array. However, in this case, correct tiles are competing withpartially correct tiles. For example, the same sticky end is used in the same position tosignify 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 onecannot 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 integerarithmetic (Duke & NYU). We are testing the execution of integer arithmetic via selfassembly 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 TAEcomputational 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 leftand RC to the right) of a growing tile complex and terminate the complex since they donot display additional sticky-ends exposed for further tile binding.• Structure of tiles tested by PAGE and OH-radical cleavage footprinting. Stoichiometryof strand association as well as observation of cleavage protection at crossover points andsites 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 involvingbook-end tiles and computational tiles. Autoradiograms of test ligations have recentlyimplicated the joint on the central helix between the right-most computational tile and theright book-end tile as the problem ligation.

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

DX XOR and Adder. We have constructed and tested a single layer computationalstring tile system capable of simultaneously calculating all possible XOR or additionsums (up to some length) using double crossover complexes. DX (DAE) tiles providecontinuous oligonucleotide strands running from one side of the tile to the other on boththe top and bottom helices (see figure below). Sites on these transverse strands are usedto record input (top helix) and output (bottom helix) bits for the four possible pairs ofinputs. Four tile types are required for XOR and eight tile types for addition since wemust 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 DXXOR calculation: a). a drawing of a DAE tile where red strands carry bit-valueinformation and will become part of the reporter strand; b). truth table for XOR showingbit values on each of the four computational tiles and also a sketch of the three tile typesrequired for valid superstructure assembly; c). drawing of a simple three tile complexwith reporter strand segments in blue, red and green; d). geometric representation of a sixtile complex which performs a 4-bit computation. The right figure shows an AFM image(600x600 nm) demonstrating the formation of the computational complexes. AFMimaging is used in the project to monitor the formation and final lengths of thecomputational complexes in order to evaluate annealing protocols and other experimentalconditions. 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 usingSelf-Assembly of DNA Double Crossover Complexes, manuscript in preparation].

TX XOR and Adder with Visual Readout. In order to streamline the readout ofstring tile computations and avoid the need for ligation, we have implemented a TX tilesystem with AFM visible topographical markers recording the bit values. The presenceor 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 stickingout of the tile plane is used to indicate an output value of 1.

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

(c) We have begun studies to extend this work from one dimension to twodimensions and we have designed and begun to prototype a two dimensionalalgorithmic assembly(Duke & NYU). In further work involving algorithmic assembly,now in two dimensions, we have designed a DNA array that contains a specific structuralfeature in the middle and on its edges, but the bulk of the array contains filler. This typeof assembly prototypes the key feature of algorithmic assembly when applied to layingthe basis of simple designs: The use of one particular tile as filler. We have producedthe border and the central structural feature, but have encountered problems in getting thefiller to work as intended.We have explored a large number of potential 3D motifs with the aim of extendingassembled lattices from 2D to 3D. These lattices may be periodic or aperiodic, but forthe present we are emphasizing periodic lattices, because their assembly can beestablished by the X-ray diffraction experiment. We have begun from the 2D TX latticesthat 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 thesystem. 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 nucleotidepairs, 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 thehairpins on the helical domains above and below the plane with sticky ends. [2] Wehave replaced the filler helix D* with a fourth TX molecule, D, also containing stickyends above and below the plane. The sticky ends of the bottom domain of the Cmolecule complement those of the upper domain of the D molecule; the sticky ends ofthe top domain of the C molecule complement those of the lower domain of the Dmolecule, so the arrangement is designed to fill space. Many crystals have been

600 nm AFM image of visual readout TXcomputation performing XOR on randomlyassembled input strings. The brighter spots locatedalong the complexes show pair-wise computationswith output values of 1. In this image the inputvalues are not readable, however we have designedbiotin containing oligos such that binding ofstreptavidin to the biotin should be visible as bulgesoff the sides of the tiles. This image was collected byLaBean and Yan during a recent visit to Winfree’s labat CalTech.

obtained, but so far diffraction has not been achieved. We are working on a number ofsimplifications (one or two tiles) and helicity variants (10.0, 10.2, 10.5 fold helices) ofthe system.

A second motif is to design a DX molecule that connects to other DX molecules with a120˚ angles. This leads to a 31 axis, and a trigonal crystal. The predicted cell dimensionsfor this system are a = b = 33.75 Å vs. observed 34.5 Å and c = 355 Å vs. 360 Åobserved. The presence of the screw axis is confirmed by the systematic extinctioncondition of l = 3n along 001. The key disappointment of this experiment is the poorresolution of the crystal, and we are working to improve it. We have used the same motifwith DNA parallelogram tiles, and they have been grown quite large, although we havenot 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 forthe near future.

(d) We have designed and are testing a device to enable a multiplicity of structuralstates in a DNA lattice and we have designed a DNA nanomechanical device whoseconformation is sequence driven(NYU). We have prototyped previously a DNAnanomechanical device that utilized the ability of a small molecule to induce the B-Ztransition of DNA. The disadvantage of this type of device is that if incorporated into aDNA array, all of the devices would be in either the B-state or the Z-state, at least towithin the limits of chemical nuances dependent on the Z-forming proclivities of varioussequences. A more fruitful approach is to produce a device that is driven by the presenceof 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 devicebased 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 throughparanemic PX cohesion. This type of association is likely to prove much more robustthan sticky-ended cohesion, because the units that are involved can be topologicallyclosed. Hence, molecules and motifs can be purified by denaturing conditions, and theextend of cohesion and recognition can be quite large. Purifying topologically closedmolecules under denaturing conditions and then restricting them leads to sticky ends thatare only four or fewer nucleotides long. However, with PX cohesion, the extend ofcohesion is unlimited. We have also developed edge-sharing cohesion.

(f) We have developed a motif to embed a robust sequence-dependent nanomechanicaldevice into an array. This will allow us to make molecular pegboards for nanoscalecircuit 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 thehelix axes correspond to the edges of the graph.Natasha Jonoska developed new methods for using three-dimensional DNAnanostructures to do computation and began testing these in Seeman’s laboratory. Mostof the past year was spent by Jonoska in collaboration with Nadrian Seeman at New YorkUniversity trying to investigate the possibility to construct three dimensional graph

structures with DNA and the feasibility that they are used as a computational tool. Quitesome time was spent in encoding and designing the structure to be made and most of theFall was used in performing the experiments. The main idea is to use DNA duplexes asedges and k-armed junction molecules as k-degree vertices as building blocks such thatby joining and ligating the building blocks the intended graph structure is obtained. Thestructure was designed such that the final structure, if obtained, forms one single strandedcircular molecule. The final analysis of the 3D graph structure self assembled by DNA isdone and we have a solid confirmation of formation of this structure, this was done atNYU.On a theoretical level, several investigations have been initiated. Using linear DNAsegments and branched junction molecules many different three-dimensional DNAstructures (i.e. graphs) could be self-assembled. We investigate maximum and minimumnumbers of circular DNA that form these structures. For a given graph G, we considercompact orientable surfaces, called thickened graphs of G, that have G as a deformationretract. The number of boundary curves of a thickened graph G corresponds to thenumber of circular DNA strands that assemble into the graph G. We investigate how thisnumber changes by recombinations or edge additions and relate to some results fromtopological graph theory. This work is in collaboration with Masahico Saito fromUniversity of South Florida. Two dimensional (Wang) tiling systems were investigatedfrom the symbolic dynamics point of view. This work was done in collaboration withEthan Coven from Wesleyan University. We identified certain systems, which we calluniformly transitive, that are entropy minimal i.e. they do not contain any subsystemswith same topological (which happens to be the same as the informational Shannon)entropy. We showed that uniformly transitive systems also have their periodic pointsdense.Other theoretical results by Jonoska include: (a) we have a proof that the self assemblyof graphs using junction molecules is computational universal (still a draft), (b) westarted investigating languages that may be taken as DNA code words (which wouldavoid hairpin structures and other intermolecular interactions) and have characterizedtheir properties to remain unchanged when such codes are ligated (software developmenthas 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 itscharacteristics.

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

(4) Next Steps Planned.Primary Tasks: We plan to experimentally test DNA self-assembly on further arithmeticand Boolean vector computations.

(i) Experimental Demonstrations of Parallel Integer Multiplication by DNA TilingAssemblies (Duke). We intend to extend our DNA tiling assembly methods from integeraddition to integer multiplication, and to experimentally demonstrate these methods. Themost 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. Weare designing for this two dimensional tiling assemblies.(ii) Experimental Demonstrations of Massively Parallel Logical Computations byDNA Tiling Assemblies (Duke). We [Lagoudakis and LaBean, 99] have recentlydeveloped (but not yet experimentally tested) a 2D DNA self-assembly for Booleanvariable satisfiability, which uses parallel construction of multiple self-assembling 2DDNA lattices to solve the problem. Such methods for solving combinatorial searchproblems do not scale well with the input size (the number of parallel tiling assembliesgrows exponentially with the number of Boolean variables of the formula). However,similar constructions may be used for evaluating Boolean formulas and circuits inmassively parallel fashion, for multiple input settings of the input Boolean variable. Weare developing an experimental demonstration of this application.(iii) Error Control in DNA Assemblies (Duke & NYU). We are conduct experiments toevaluate the speed and error rates of the various types of self-assembly reactions and areinvestigating and comparing error control by free versus step-wise assembly. Self-assembly may be restricted such that certain assembly reactions can proceed only afterothers have been completed (serial self-assembly). Alternatively, self-assembly reactionsmay be limited by no such restrictions (free self-assembly). As examples, BCA tilesutilize local parallelism and serial self-assembly [Winfree95]; DHHP tiles utilize bothlocal and global parallism and serial self-assembly [Winfree96]; and self-assembly oflinear, 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 notyet known if free self-assembly is faster, and more robust than serial self-assembly or if itis less error-prone. We are making careful experimental studies of these two possiblemethods 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). DXcomplexes and lattices have been used successfully as substrate for enzymatic reactionsincluding cleavage and ligation [Liu99a]. We would like to investigate the use of DNAlattices to execute a broader class of reactions. We are working to modify the topologyand geometry of the DNA lattice using restriction enzymes that operate on exposedportions of the DNA lattices. This will aid in the DNA tiling computations describedabove, for example by providing mechanisms for error repair in DNA tilingcomputations.-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 computationalprocess and possibly solve another instance of a computational problem. Theoretically weneed to characterize the graph structures that can be designedsuch that after self-assembly the structure is only one cyclic molecule. Also algorithmicprocedure 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 partof this is theoretical characterization of DNA languages that represent good encodings.Topological investigation of the space of formal languages (sets of DNA strands)continuesSecondary Tasks: We will also devote a portion of our resources to the following:-Use of DNA Lattices as a Substrate for Surface Chemistry. One intriguingapplication for DNA lattices is there use as an attachment substrate for an array of DNAstrands, using hybridization with single stranded DNA on individual tiles. This has anumber of applications that impact DNA computations (e.g., see Brockman,et al98][Smith,98]): (i) It may provide a dramatically miniaturization of the DNA chiptechnology (a technology that might be used for I/O in DNA computations, among otherapplications), to molecular scale aspect widths. (ii) It may provide a dramaticminiaturization 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. incollaboration with Reed at Yale (in a DARPA funded contract of which Reif is asubcontractor) have designed and demonstrated [Chen et al 99] organic molecules that actas conducting wires [Reed et al.97],[Zhou99] and also organic molecules that act asrectifying diodes. A key remaining problem is to develop method for assembling thesemolecular electronic components into a circuit. We propose to investigate the possibleapplication of self-assembled DNA 2D lattices for the layout of nano-scale circuitcomponents (organic polymers)on the lattices. This might be done by designing amodified chemistry for these organic molecules for attachment to DNA. This would thenallow for the selective attachment of the molecular electronic components to particulartiles of the DNA tiling array. There are known molecular probe devices (developed inthat same project) may be used to test the electrical properties of the resulting molecularcircuit attached to the DNA tiling array.-Construction of 3D DNA lattices. We also intend to begin an investigation of a numberof possible methods for constructing 3D DNA lattices. This would allow us to extend ourproposed DNA lattice computations to 3D, providing computations with (implicit) datamovement 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 extendingthe construction of periodic matter to three dimensions. Also, we are considering variousclass 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 ofcontrolled movement [Mao, et al 99a]. In addition to these static constructs, we have builta prototype DNA nanomechanical device. This device consists of two DX moleculesconnected by a DNA double helix that contains a segment of DNA that can be convertedto the left-handed Z-DNA structure. In B-promoting conditions, the two unconnectedhelices of the device are on the same side of the connecting helix, but they are onopposite sides in Z-promoting conditions. This results in an apparent rotary motion ofabout 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. Thismotion has been demonstrated by fluorescent resonance energy transfer (FRET).

We are working to build on this work in several directions. We intend to combine thenanomolecular 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 TXsystem are likely to render it feasible; this because it is not necessary for the pivoting partof 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 prototypethat we have used to learn how to characterize motion in DNA systems. It lacksprogrammability, except to the limited extent that one can orient the two DX molecules ata variety of relative torsion angles in the B-state. Thus, all of the molecules must be ineither 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-specificmotion. Thus, there are two discrete states, PX or JX, in which the helices at one end ofthe molecule are in reversed positions. Thus, an array of these molecules would containindividually programmed molecules whose conformational state would be amenable tospecific reversal (or not, depending on the program) from cycle to cycle. This systemwould lead to the ability to 'nanofacture' specific molecules, a capability not availabletoday. We intend that this system would ultimately permit us to do chemistry atchemically identical but spatially distinct sites. This system offers a direct route tonanorobotics, because it couples a series of distinct structural states withprogrammability.A DNA array with programmability of this sort offers a mechanism to do DNAcomputation of arrays whose elements(the tiles) hold state. That is, the DNA assembliesmay be able to simulate a parallel computing model known as cellular automata, whichconsist of arrays of finite state automata, each which holds state. The transitions of theseautomata and communication of values to their neighbors might be done by conformal(geometry) changes, again using this programmability. There are numerous examples of1 D (2 D, respectively) cellular automata that can do computations that tiling assemblieswould have required a further dimension (for example, integer multiplication in onedimension instead of two). USC is also investigating the possibility of using JX-PX for apotential use in a programmable finite state automaton-Simulation Tools. In addition to software for the design of DNA tiles, we are workingto develop software simulation tools of the kinetics of self-assembly for self-assembly,providing a more fundamental understanding of self-assembly processes. These willimprove upon the software simulations [Winfree,98] (which allowed tiling assembliesonly to be constructed from individual tiles appending to tiling assemblies), to provide forassembly 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-assemblycomputations? Potentially, DNA self-assembly assemblies and computations can scale upto can be up to 1016 or possibly 018 molecules. However, there may be critical barriersthat we need to overcome. Defect errors, self-assembly kinetics and other processes maylimit 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 bestavenue to scale to assemblies with extremely large numbers of molecules.(b) To what degree can we, in practice, scale the complexity of computations using DNAself-assembly? To date, the computations we have demonstrated via DNA self-assembly

have been simple Boolean XOR operations executed in one dimension. Prior theoreticalresults have establishing the potential power of tiling assembles to arbitrary complexassemblies in two and three dimensions. Extending this work to two and three dimensionsthus provides many further opportunities. Potentially, we can also have multiple distinctDNA self-assembly computations occurring simultaneously and asynchronously, andthese 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 crossovercomplexes, 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 limitedprecision 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/OBandwidth, Information and Computation, Jan 2000, pp. 1-20.

J.H. Reif and H. Wang, Nonuniform discretization approximation for Kinodynamicmotion 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 AlgebraProblems, 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-CooperativeGames 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 ofInformation Sciences, Volume 135, pp. 87-105 (2001).

J. H. Reif, DNA Lattices: A Programmable Method for Molecular Scale Patterning andComputation, 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 GenerationComputing, 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 withApplications, Vol. 43, 2002, pp 179-206.

J.H. Reif, Efficient Parallel Factorization and Solution of Structured and UnstructuredLinear 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 GenerationComputing, edited by Masami Hagiya, Masayuki Yamamura, and Tom Head, 2002.

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

Dage Liu, John H. Reif, and Thomas H. LaBean, DNA Nanotubes: Construction andCharacterization 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 theAmerican Chemical Society 122, 1848-1860 (2000).

Sha, F. Liu and N.C. Seeman, Direct Evidence for Spontaneous BranchMigration in Antiparallel DNA Holliday Junctions, Biochemistry39, 11514-11522 (2000).

R. Sha, H. Iwasaki, F. Liu, H. Shinagawa and N.C. Seeman, Cleavage ofSymmetric 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 ParallelDNA 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 ConformationalAnalysis, Biophys. J. 79, 2692-2704 (2000).

C. Mao, T. LaBean, J.H. Reif and N.C. Seeman, Logical Computation UsingAlgorithmic 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 AcidComplementarity and the Development of DNANanotechnology, 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 MechanicalDevice 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 theBottom 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 theInterdomain 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 ImmobileDNA Junctions as Substrates for E. coli RuvC Holliday JunctionResolvase. Biochemistry 41, 10985-10993 (2002).

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

X. Zhang, H. Yan, Z. Shen and N.C. Seeman, Paranemic Cohesion ofTopologically-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 DNAScaffolding, J. Nanoparticle Research 4, 313-317 (2002).

A. Carbone and N.C. Seeman, Fractal Designs Based on DNA ParallelogramStructures, 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 HinderedElectrophiles: Intermolecular N3 to 2'-O Protecting GroupTransfer, 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 Principlefor Advanced Nanomaterials, Materials Today 6 (7), 24-29(2003).

H. Yan and N.C. Seeman, Edge-Sharing Motifs in DNA Nanotechnology. Journal ofSupramolecular 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 ComputerScience, vol. 262 (2001) 349-375.

E. Coven, A. Johnson, N. Jonoska, K. Madden, The symbolic dynamics ofmultidimensional 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 DNAHelix Axis Topology, to appear , Journal of Natural Computing.

N. Jonoska, D. Kephart, K. Mahalingam, Generating codes forDNA computing, (to appear) Congressus Numerantium. (Also published in thebook 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 BasedComputers V: Cambridge, MA, DIMACS Series in Discrete Mathematics andTheoretical 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, DIMACSSeries in Discrete Mathematics and Theoretical Computer Science, Volume 54, edited byE. 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 shortestpath problem. In Proceedings of the 4th Workshop on Algorithmic Foundations ofRobotics(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 the7th International Workshop on Algorithms and Data Structures (WADS2001), volume2125 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 DNASynthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization, Sixth International Meeting on DNA Based Computers (DNA6), DIMACSSeries in Discrete Mathematics and Theoretical Computer Science, Leiden, TheNetherlands, (June, 2000) ed. A. Condon. Springer-Verlag as a volume in Lecture Notesin 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-BasedComputers, Leiden, The Netherlands, June, 2000. DIMACS Series in DiscreteMathematics 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 theMolecular Scale: Self-Assembly of DNA Lattices", Invited paper, 2001 IEEEInternational 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 pathsthrough pseudo-Euclidean spaces. In Proceedings of the 12th Annual InternationalSymposium 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 SearchCapability, Seventh International Meeting on DNA Based Computers (DNA7), DIMACSSeries in Discrete Mathematics and Theoretical Computer Science, Tampa, FL, June 11-13, 2001.

J. H. Reif, Molecular Assembly and Computation: From Theory to ExperimentalDemonstrations, 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 andRolling 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 andCharacterization 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 MobileRobot, 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 SamplingNarrow Passages with Probabilistic Roadmap Planners, 2003 IEEE InternationalConference 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 BiomolecularStereodynamics, ed. by R.H. Sarma and M.H. Sarma, AdeninePress, New York, 253-262 (2000).

N.C. Seeman, DNA Nanotechnology: From Topological Control to StructuralControl, in Pattern Formation in Biology, Vision and Dynamics,ed. by A.Carbone, M.Gromov, P.Pruzinkiewicz, World ScientificPublishing 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 ofNano-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 Workshopon DNA-Based Computers, DNA 2000, Leiden, TheNetherlands, (June, 2000) ed. A. Condon, G. Rozenberg.Springer-Verlag, Berlin Heidelberg, Lecture Notes in ComputerScience 2054, 173-198, (2001).

N.C. Seeman, Key Experimental Approaches in DNA Nanotechnology,Current Protocols in Nucleic Acid Chemistry, Unit 12.1, JohnWiley & 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 SupramolecularChemistry, in press (2003).

N. Jonoska, P. Sa-Ardyen and N.C. Seeman, Compuatation by Self-Assembly of DNAGraphs, 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 BasedComputers (DNA 8), Springer Verlag, Sapporo, Japan, June 10-13, 2002.

Phiset Sa-Ardyen, Natasa Jonoska, and Nadrian C. Seeman, Self-assembling DNAGraphs, Proceedings of the 8th International Meeting on DNA Based Computers (DNA8), 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 (someare 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 7thInternational DNA Based Computer Meeting, June 10-13, 2001, Tampa FL

Phiset Sa-Ardyen, Natasa Jonoska, and Nadrian C. Seeman, Self-assembling DNAGraphs, Proceedings of the 8th International Meeting on DNA Based Computers (DNA8), Springer Verlag, Sapporo, Japan, June 10-13, 2002. (see also above)

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

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

(3.3) Other products (database, software, instruments, inventions, physicalcollections, educational aids, etc) you have reported earlier as developedor 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 DoubleCrossover 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 designSoftware for the optimized design of DNA tiles was first developed in Mathlab byWinfree, then a PhD student at Caltech (advised in part by Adleman at USC). Thissoftware used a greedy search method to optimize the choice of DNA strands comprisingthe DNA tiles. The software was improved Duke graduate student Guo Bo) [Bo01] toallow for a more sophisticated optimization heuristic (providing improved sequencespecificity of the DNA words used for tile pads, minimizing the likelihood of incorrecthybridizations from non-matching pads), to include more realistic models of DNAhybridization, and to provide a Java interface. (Bo, Guo Master Thesis Computing by

DNA Self-Assembly. Oct, 2001.)

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

(Duke):Simulation Tool for DNA Tile AssembliesWinfree, then a PhD student at Caltech (advised in part by Adleman at USC) developedsoftware for discrete time simulation of the tiling assembly processes, using approximateprobabilities for the insertion or removal individual tiles from the assembly. Thesesimulations gave an approximation to the kinetics of self-assembly chemistry andprovided some validation of the feasibility of tiling self-assembly processes. Using thissoftware as a basis, Duke graduate student Guangwei Yuan [Guangwei00] developedimproved (sped up by use of an improved method for computing on/of likelihoodsuggested by Winfree) simulation software with a Java interfacehttp://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 softwareprovided 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 whichshould help in producing sticky ends of the junctions (tiles) used in self-assembly. Thisis based on the theoretical findings about DNA codes. The firs paper will appear soon andthe second is in prepapration. We plan to have the program available to the public on theweb.

(4) Contributions within Discipline:

(4.1) How have your findings, techniques you developed or extended, or otherproducts from your project contributed to the principal disciplinary field(s) of theproject?We have performed the first successful DNA algorithmic assembly. We have begunstudies to extend this work from one dimension to two dimensions. We have designedand are testing a device to enable a multiplicity of structural states in a DNA lattice. Wehave proposed a DNA circuit approach involving this new device. We have constructedand demonstrated the first irregular DNA graph. We have proposed a series of fractalassemblies from unusual DNA components.

John Reif and Nadrian Seeman (Duke and NYU): We have prototyped a scalablecomputation by self-assembly. We have produced 2D arrays with deliberately designedpatterns.

Nadrian Seeman (NYU): We have produced DNA-based nanomechanical devices thatwill 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-BasedComputers, 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 itsproceedings.

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

(4.2) Contributions to Other DisciplinesHow have your findings, techniques you developed or extended, or otherproducts 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 establishfeatures of branched DNA molecules. These include branch migration, cleavage, anglesbetween helices and molecular rigidity estimates. These contributions have been to thefields 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 designSoftware for the optimized design of DNA tiles was first developed in MatLab byWinfree, then a PhD student at Caltech (advised in part by Adleman at USC). Thissoftware used a greedy search method to optimize the choice of DNA strands comprisingthe DNA tiles. The software was improved Duke graduate student Guo Bo) [Bo01] toallow for a more sophisticated optimization heuristic (providing improved sequencespecificity of the DNA words used for tile pads, minimizing the likelihood of incorrecthybridizations from non-matching pads), to include more realistic models of DNAhybridization, and to provide a Java interface. (Bo, Guo Master Thesis Computing byDNA Self-Assembly. Oct, 2001.)

(Duke):Simulation Tool for DNA computation

A Duke graduate student Ashish Gehani developed a prototype software simulationsystem for DNA computation. These software tools are expected to be very useful tooptimize the experimental BMC protocols and minimize errors. A simulator was writtenin Java, which implemented the operations of the recombinant DNA model. The softwaremodels recombinant DNA operations at multiple levels of detail from high level down tothe kinetics of reactions. For example, molecular complexes are represented as graphs atthe granularity of nucleotides and have a level of spatial description such that mostinfeasible nucleotide complexes are not allowed to contaminate the data set as thecomputation is simulated. We used thermodynamic and kinetic models to representinteractions between complexes.

(Duke):Simulation Tool for DNA tile AssembliesWinfree, then a PhD student at Caltech (advised in part by Adleman at USC) developedsoftware for discrete time simulation of the tiling assembly processes, using approximateprobabilities for the insertion or removal individual tiles from the assembly. Thesesimulations gave an approximation to the kinetics of self-assembly chemistry andprovided some validation of the feasibility of tiling self-assembly processes. Using thissoftware as a basis, Duke graduate student Guangwei Yuan [Guangwei00] developedimproved (sped up by use of an improved method for computing on/of likelihoodsuggested by Winfree) simulation software with a Java interfacehttp://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 softwareprovided 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 inmolecular biophysics. We have established by means of AFM and parallelogram arraysthe parallel nature of Bowtie junctions. Similarly, we have used similar techniques tocharacterize the inter-helical angle in a symmetric Holliday junction: We settled a disputeabout the potential influence of crystal packing forces in a crystal structure determination;by this orthogonal technique, we showed that crystal packing forces were not acontributor to this system.

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

(4.3) Contributions to Human Resource DevelopmentHow have results from your project contributed to human resource developmentin science, engineering, and technology?

The PI and subcontract PIs have trained and graduated numerous graduate students in thetechniques of DNA nanotechnology and DNA-based computation. These people areamong the few individuals in the world possessing these skills. We expect that they will

be successful in using these methods in their future careers.

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

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

Reif taught a graduate course on DNA nanotechnology and DNA computation. Inaddition to the annual class on nucleic acid structure, symmetry, design andnanotechnology, Seeman gave a tutorial on nucleic acid basics was presented to theSeventh Workshop on DNA-Based Computation concerning non-standard base-pairingand backbone structures and was program chairman of that workshop. Natasha Jonoskagave a number of seminars on theoretical aspects of DNA nanotechnology. She spent asabbatical at Seeman’s laboratory learning the basic techniques used in the workdescribed, 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 BiomolecularC o m p u t a t i o n , s p r i n g , 2 0 0 0 a n d f a l l , 2 0 0 0 .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: Macromolecularchemistry that emphasizes the elements of symmetry, topology and structure that arenecessary for building motifs capable of multidimensional self-assembly. This basiccourse in macromolecular features emphasizing the design of DNA nanostructures hasbeen taught at NYU. Seeman havs given tutorials at DNA VII and DNA VIII. Seemanwas 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 andgraph theory (a course for the Bioinformatics program at USF) Fall 2002. NatashaJonoska gave several lectures in front of high school teachers.

The results produced here also have stimulated a large amount of interest in college andhigh school students. We have received numerous inquiries from students interested inthe systems we have developed and wishing to join these efforts.

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

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

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

Patents(see above).