Single-Stranded Nucleic Acid Topology
Bibliography from Ned Seeman's Laboratory.

* Indicates listing on more than one bibliography.

*N.C. Seeman, Physical Models for Exploring DNA Topology. Journal of Biomolecular Structure and Dynamics 5, 997-1004 (1988).

J.E. Mueller, S. M. Du and N.C. Seeman, The Design and Synthesis of a Knot from Single-Stranded DNA, Journal of the American Chemical Society 113, 6306-6308 (1991).

J. Chen and N.C. Seeman, The Electrophoretic Properties of a DNA Cube and its Sub-Structure Catenanes Electrophoresis 12, 607-611 (1991).

S.M. Du and N.C. Seeman, The Synthesis of a DNA Knot Containing both Positive and Negative Nodes, Journal of the American Chemical Society 114, 9652-9655 (1992).

*S.M. Du, S. Zhang and N.C. Seeman, DNA Junctions, Antijunctions and Mesojunctions, Biochemistry 31, 10955-10963 (1992).

N.C. Seeman, The Design of Single-Stranded Nucleic Acid Knots, Molecular Engineering 2, 297-307 (1992).

H. Wang, S.M. Du and N.C. Seeman, Tight Single-Stranded DNA Knots, Journal of Biomolecular Structure and Dynamics 10, 853-863 (1993).

*N.C. Seeman, J. Chen, S.M. Du, J.E. Mueller, Y. Zhang, T.-J. Fu, H. Wang, Y. Wang, and S. Zhang, Synthetic DNA Knots and Catenanes, New Journal of Chemistry 17, 739-755 (1993).

*N.C. Seeman and N.R. Kallenbach, DNA Branched Junctions, Annual Review of Biophysics and Biomolecular Structure 23, 53-86 (1994).

S.M. Du and N.C. Seeman, The Construction of a Trefoil Knot from a DNA Branched Junction Motif, Biopolymers 34, 31-37 (1994).

*T-J. Fu, Y.-C. Tse-Dinh, and N.C. Seeman, Holliday Junction Crossover Topology, Journal of Molecular Biology 236, 91-105 (1994).

*N.C. Seeman, Y. Zhang, T.-J. Fu, S. Zhang, Y. Wang and J. Chen, Chemical Synthesis of Nanostructures, Biomolecular Materials by Design: Materials Research Society Symposium Proceedings 330, 45-56 (1994).

*N.C. Seeman, Y. Zhang, S.M. Du, H. Wang, J.E. Mueller, Y. Wang, B. Liu, J. Qi and J. Chen, The Control of DNA Structure and Topology: An Overview., Molecularly Designed Ultrafine/Nanostructured Materials: Materials Research Society Symposium Proceedings 351 57-66 (1994).

S.M. Du, H. Wang, Y.C. Tse-Dinh and N.C. Seeman, Topological Transformations of Synthetic DNA Knots, Biochemistry 34, 673-682 (1995).

H. Wang and N.C. Seeman, Structural Domains of DNA Mesojunctions, Biochemistry 34, 920-929 (1995).

S.M. Du, B.D. Stollar, and N.C. Seeman, A Synthetic DNA Molecule in Three Knotted Topologies, Journal of the American Chemical Society 117, 1194-1200 (1995).

*N.C. Seeman, Molecular Craftwork with DNA, The Chemical Intelligencer 1(3), 38-47 (1995).

*N.C. Seeman, Y. Zhang, S.M. Du and J. Chen, Construction of DNA Polyhedra and Knots Through Symmetry Minimization, In: Supramolecular Stereochemistry, ed. by J. Siegel, NATO Advanced Research Workshops Series, Kluwer, Dordrecht, 27-32 (1995).

E. Flapan and N.C. Seeman, A Topological Rubber Glove Obtained from a Synthetic Single Stranded DNA Molecule, Journal of the Chemical Society, Chemical Communications, 2249-2250 (1995).

*N.C. Seeman, H. Wang, J. Qi., X.J. Li, X.P. Yang, Y. Wang, H. Qiu, B. Liu, Z. Shen, W. Sun, F. Liu, J.J. Molenda, S.M. Du, J. Chen, J.E. Mueller., Y. Zhang, T.-J. Fu, and S. Zhang, DNA Nanotechnology and Topology. In: Biological Structure and Dyinamics, ed. by R.H. Sarma and M.H. Sarma, Adenine Press, New York, vol. 2, pp. 319-341 (1996).

*J.A. Sekiguchi, N.C. Seeman and S. Shuman, Asymmetric Resolution of Holliday Junctions by Eukaryotic DNA Topoisomerase I. Proceedings of the National Academy of Sciences (USA) 93, 785-789 (1996).

H. Wang, R.J. Di Gate, and N.C. Seeman, An RNA Topoisomerase, Proceedings of the National Academy of Sciences (USA) 93, 9477-9482 (1996).

*C. Mao, W. Sun and N.C. Seeman, Construction of Borromean Rings from DNA, Nature 386, 137-138 (1997).

*N.C.Seeman, J. Chen, Y. Zhang, T.-J. Fu, X. Li, X. Yang, Y. Wang, J. Qi, B. Liu and F. Liu, Control of Structure and Topology in DNA Nanotechnology. In: Molecular Nanotechnology: Biological Approaches and Novel Applications, ed. by S.A. Minden, IBC Libraries, Southborough, MA, Chapter 2.2 (31 pages) (1997).

*A. V. Vologodskii, X. Yang and N.C. Seeman, Non-Complementary DNA Helical Structure Induced by Positive Torsional Stress, Nucleic Acids Resesrch 26, 1503-1508 (1998).

H. Wang, R.J. Di Gate and N.C. Seeman, E. coli DNA The Construction of an RNA Knot and its Role in Demonstrating that Topoisomerase III is an RNA Topoisomerase. Structure, Motion, Interaction and Expression of Biological Macromolecules, ed by R.H. Sarma and M.H. Sarma, Adenine Press, New York, pp. 103-116 (1998).

*N.C. Seeman, H. Wang, B. Liu, J. Qi, X. Li, X. Yang, F. Liu, W. Sun, Z. Shen, Y. Wang, R. Sha, C. Mao, S. Zhang, T.-J. Fu, S. M. Du, J.E. Mueller, Y. Zhang and J. Chen, The Perils of Polynucleotides: The Experimental Gap Between the Design and Assembly of Unusual DNA Structures, In: DNA Based Computers II, L.F. Landweber and E.B. Baum, Am. Math. Soc., Providence, pp. 215-233 (1998).

*N.C. Seeman, Nucleic Acid Nanostructures and Topology. Angewandte Chemie. 110, 3408-3428 (1998); Angewandte Chemie International Edition 37, 3220-3238 (1998).

*N.C. Seeman, Synthetic DNA Topology, Molecular Catenanes, Rotaxanes and Knots, ed. by J.-P. Sauvage and C. Dietrich-Buchecker, Wiley-VCH, Weinheim pp. 323-356 (1999).

*N.C. Seeman, DNA Engineering and its Application to Nanotechnology, Trends in Biotechnology 17, 437-443 (1999).

*W. Sun, C. Mao, H. Iwasaki, B. Kemper and N.C. Seeman, No Braiding of Holliday Junctions in Positively Supercoiled DNA Molecules, Journal of Molecular Biology 294, 683-699 (1999).

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

*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).

*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).

*Z. Shen, H. Yan, T. Wang and N.C. Seeman, Paranemic Crossover DNA:  A Generalized Holliday Structure with Applications in Nanotechnology J. Am. Chem. Soc. 126, 1666-1674 (2004).

* J.J. Birac, W.B. Sherman, J. Kopatsch, P.E. Constantinou and N.C. Seeman, GIDEON, A Program for Design in Structural DNA Nanotechnology, J. Mol. Graphics & Modeling 25, 470-480 (2006).

N.C. Seeman, Synthetic Single-Stranded DNA Topology, Applications of Knot Theory, D. Buck & E. Flapan, Eds, Am. Math. Soc. Proc. Symp. Applied. Math. 66 121-153 (2009).

*X. Wang, X. Zhang, C. Mao & N.C. Seeman, Double-Stranded DNA Homology Produces a Physical Signature, Proc. Nat. Acad. Sci. (USA) 107,  12547-12552 (2010).

T. Ciengshin, R. Sha & N.C. Seeman, Automatic Molecular Weaving Prototyped Using Single-Stranded DNA, Angew. Chemie Int. Ed. 50, 4419-4422 (2011).

N.A. Baas & N. C. Seeman, On the Chemical Synthesis of New Topological Structures, J. Math. Chem. 50, 220-232 (2012).

* Y. Liu, R. Wang, L. Ding, R. Sha, N.C. Seeman & J.W. Canary,   Templated Synthesis of Nylon Nucleic Acids and Characterization by Nuclease Digestion, Chem. Sci., 3, 1930-1937 (2012).

* L. Feng, R. Sha, N.C. Seeman and P.M. Chaikin, Topological Interaction by Entangled DNA Loops, Phys. Rev. Lett. 109, 188301 (2012).

*D.A. Rusling, A.R. Chandrasekaran, Y. Ohayon, T.Brown, K.R. Fox, R. Sha, C. Mao & N.C. Seeman, Functionalizing Designer DNA Crystals with a Triple-Helical Veneer, Angew. Chemie Int. Ed. 53, 4060-4063 (2014), DOI: 10.1002/anie.201309914.

*D.D. Li, X.J. Wang, F. Shi, R. Sha, N.C. Seeman, J.W. Canary, Templated DNA Ligation with Thiol Chemistry, Org. & Biomol. Chem. 12, 8823-8827 (2014).

*N A. Baas, N.C. Seeman, A. Stacey, Synthesizing Topological Links, J. Math. Chem., 53, 183-199 (2015) DOI 10.1007/s10910-014-0420-3.*Y. Ohayon, R. Sha, O. Flint, B. Chakraborty, H.K. Subramanian, J. Zheng, A.R. Chandrasekaran, H.O. Abdallah, T. Wang, X. Wang, X. Zhang, N.C. Seeman, Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion, ACS Nano 9, 10296-10303 (2015).

*Y. Ohayon, R. Sha, O. Flint, A.R. Chandrasekaran, H.O. Abdallah, T. Wang, X. Wang, X. Zhang, N.C. Seeman, Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion, ACS Nano 9, 10304-10312 (2015).

*H.O. Abdallah, Y.P. Ohayon, A.R. Chandrasekaran, R. Sha, K.R. Fox, T. Brown, D.A. Rusling, C. Mao, N.C. *Seeman, Stabilization of Self-Assembled DNA Crystals by Triplex-Directed Photo-Crosslinking, Chem. Comm., 52, 8014-8017 DOI: 10.1039/c6cc03695c (2016).

*J. A. Ellis-Monaghan, G. Pangborn, N.C. Seeman, S. Blakely, C. Disher, M. Falcigno, B. Healy, B. Singh, M. Westland, Design Tools for Reporter Strands and DNA Origami Scaffold Strands, Theor. Computer Sci. 671, 69-78 (2017).

*C. Hernandez, J.J. Birktoft, Y.P. Ohayon, A.R. Chandrasekaran, H. Abdallah, R. Sha, V. Stojanoff, C. Mao & N.C. Seeman, Stressed DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component, Cell Chem. Biol. 24, 1401-1406 (2017).

*M.M. Ferrari, A. Cook, A. Houlihan, R. Rouleau, N.C. Seeman, G. Pangborn, J. Ellis-Monaghan, Design Formalism for DNA Self-Assembly of Polyhedral Skeletons using Rigid Tiles, J. Math. Chem., 56, 1365-1392 (2018), DOI 10.1007/s10910-018-0858-9.







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