Structural Studies Bibliography from
Ned Seeman's Laboratory

* Indicates listing on more than one bibliography.

N.C. Seeman, MIND3: A FORTRAN Patterson Superposition Program for the IBM 1130. In: Crystallographic Computing, F.R. Ahmed, ed., Munksgaard, Copenhagen (1970), pp. 87-89.

B. Berking and N.C. Seeman, The Crystal and Molecular Structure of 1,6;2,3-Dianhydro-b-D-gulopyranose. Acta Crystallographica B27,1752-1760 (1971).

N.C. Seeman, J.L. Sussman, H.M. Berman and S.-H. Kim, Nucleic Acid Conformation: The Crystal Structure of a Naturally Occurring Dinucleoside Phosphate (UpA). Nature New Biology 233, 90-92 (1971).

N.C. Seeman, E.L. McGandy and R.D. Rosenstein, The Crystal and Molecular Structure of Pyrazole-3-L-Alanine. Journal of the American Chemical Society 94, 1717-1720 (1972).

J.J. Madden, E.L. McGandy and N.C. Seeman, The Crystal Structure of the Orthorhombic Form of L-(+)-Histidine. Acta Crystallographica B28, 2377-2382 (1972).

J.J. Madden, E.L. McGandy, N.C. Seeman, M.M. Harding and A. Hoy, The Crystal Structure of the Monoclinic Form of L-(+)-Histidine. Acta Crystallographica B28, 2382-2389 (1972).

J.L. Sussman, N.C. Seeman, S.-H. Kim and H.M. Berman, The Crystal Structure of a Naturally Occurring Dinucleoside Phosphate: Uridylyl-3',5'-adenosine. Model for RNA Chain Folding. Journal of Molecular Biology 66, 403-421 (1972).

N.C. Seeman, Determinata la Struttura Cristallina di un Dinucleosidofosfato Naturale (UpA). In: Enciclopedia Della Scienze E Della Tecnica, Annuario Della EST, Mondadori, Milano (1972), pp. 68-69 (in Italian).

S.-H. Kim, H.M. Berman, N.C. Seeman and M.D. Newton, Seven Basic Conformations of Nucleic Acid Structural Units. Acta Crystallographica B29, 703-710 (1973).

J.M. Rosenberg, N.C. Seeman, J.-J.P. Kim, F.L. Suddath, H.B. Nicholas and A. Rich, Double Helix at Atomic Resolution. Nature 243, 150-154 (1973).

R.O. Day, N.C. Seeman, J.M. Rosenberg and A. Rich, A Crystalline Fragment of the Double Helix: The Structure of the Dinucleoside Phosphate Guanylyl-3',5'-cytidine. Proceedings of the National Academy of Sciences (USA) 70, 849-853 (1973).

S.-H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, J.L. Sussman, A.H.-J. Wang, N.C. Seeman and A. Rich, The Three Dimensional Tertiary Structure of Transfer RNA. Science 185, 435-440 (1974).

S.-H. Kim, J.L. Sussman, G.J. Quigley, F.L. Suddath, A. McPherson, A.H.-J. Wang, N.C. Seeman and A. Rich, A Generalized Structure for Transfer RNA. Proceedings of the National Academy of Sciences (USA) 71, 4970-4974 (1974).

N.C. Seeman, R.O. Day and A. Rich, Nucleic Acid-Mutagen Interactions: The Crystal Structure of Adenylyl-3',5'-uridine Plus 9-Aminoacridine. Nature 253, 324-326 (1975).

G.J. Quigley, A.H.-J. Wang, N.C. Seeman, F.L. Suddath, A. Rich, J.L. Sussman and S.-H. Kim, Hydrogen Bonding in Yeast Phenylalanine Transfer RNA. Proceedings of the National Academy of Sciences (USA) 72, 4866-4870 (1975).

G.J. Quigley, N.C. Seeman, A.H.-J. Wang, F.L. Suddath and A. Rich, Yeast Phenylalanine Transfer RNA: Atomic Coordinates and Torsion Angles. Nucleic Acids Research 2, 2329-2341 (1975).

S.-H Kim, F.L. Suddath, G.J. Quigley, A. McPherson, J.L. Sussman, A.H.-J. Wang, N.C. Seeman and A. Rich, The Tertiary Structure of Yeast Phenylalanine Transfer RNA. In: Structure and Conformations of Nucleic Acids and Protein-Nucleic Acid Interactions, ed by M. Sundaralingam and S.T. Rao, University Park Press, Baltimore, (1975) pp. 7-14.

N.C. Seeman, J.M. Rosenberg and A. Rich, Sequence Specific Recognition of Double Helical Nucleic Acids by Proteins. Proceedings of the National Academy of Sciences (USA) 73, 804-808 (1976).

J.M Rosenberg, N.C. Seeman, R.O. Day and A. Rich, RNA Double Helices Derived from Studies of Small Fragments. Biochemical and Biophysical Research Communications 69, 979-987 (1976).

A. Rich and N.C. Seeman, RNA Double Helices at Atomic Resolution. In: Handbook of Biochemistry and Molecular Biology, vol II, 3rd edition, ed. by G. Fasman, CRC Press, Cleveland (1976), pp. 413-419.

N.C. Seeman, J.M Rosenberg, F.L. Suddath, J.-J.P. Kim and A. Rich, RNA Double Helical Fragments at Atomic Resolution I: The Crystal and Molecular Structure of Adenylyl-3',5'-uridine Hexahydrate. Journal of Molecular Biology 104, 109-144 (1976).

J.M. Rosenberg, N.C. Seeman, R.O. Day and A. Rich, RNA Double Helical Fragments at Atomic Resolution II: The Crystal and Molecular Structure of Guanylyl-3',5'-cytidine Nonahydrate. Journal of Molecular Biology 104, 145-167 (1976).

A. Rich, N.C. Seeman and J.M. Rosenberg, Protein Recognition of Base Pairs in a Double Helix. In: Nucleic Acid-Protein Recognition, ed. by H.G. Vogel, Academic Press, New York (1977), pp. 361-374.

N.H. Woo, N.C. Seeman and A. Rich, The Crystal Structure of Putrescine Diphosphate: A Model for Amine-Nucleic Acid Interactions. Biopolymers 18, 539-552 (1979).

N.C. Seeman, Single Crystal Crystallography. In: Stereodynamics of Molecular Systems, ed. by R.H. Sarma, Pergamon Press, New York (1979), pp. 75-109.

N.C. Seeman, Single Crystal Crystallography for Nucleic Acid Structural Studies. In: Geometry and Dynamics of Nucleic Acids, ed. by R.H. Sarma, Pergamon Press, New York (1980), pp. 47-82.

N.C. Seeman, Crystallographic Investigation of Oligonucleotide Structure. In: Geometry and Dynamics of Nucleic Acids, ed. by R.H. Sarma, Pergamon Press, New York (1980), pp. 109-142.

J.F. Hyde, J.A. Zubieta and N.C. Seeman, The Crystal and Molecular Structure of ((Mo(S-CH2-CH2-S-CH2-CH2-S)2)2Ag)PF6.1/2 DMF, A Thiolate-Bridged Mixed Metal Cluster. Inorganica Chemica Acta 54, L137-L139 (1981).

J.A. DiVerdi, S.J. Opella, R.-I. Ma, N.R. Kallenbach and N.C. Seeman, 31P NMR of DNA in Eukaryotic Chromosomal Complexes. Biochemical and Biophysical Research Communications 102, 885-890 (1981).

R.D. Rosenstein, M. Oberding, J. Hyde, J.A. Zubieta, K.D. Karlin and N.C. Seeman, The Crystal Structure of Hypoxanthinium Nitrate Monohydrate: Intercalation of Water Between Purines. Crystal Structure Communications 11, 1507-1513 (1982).

R.D. Sheardy and N.C. Seeman, The Construction of an Oligonucleotide Containing 5-Iodo-Deoxyuridine. Journal of Organic Chemistry 51, 4301-4303 (1986).

J.-H. Chen, N.C. Seeman and N.R. Kallenbach, Tracts of A-T Nucleotide Pairs Retard the Electrophoretic Mobility of Short DNA Duplexes. Nucleic Acids Research 16, 6803-6812 (1988).

V.N. Morozov, J. Sherman, N.R. Kallenbach, S.M. Du and N.C. Seeman, A Scanning Tunneling Microscopy Study of the Formation and Chemical Activation of Step Defects on the Basal Plane of Pyrolytic Graphite, Journal of Microscopy 170, pt. 3, 237-245 (1993).

V.N. Morozov, N.C. Seeman and N.R. Kallenbach, New Methods for Depositing and Imaging Molecules in Scanning-Tunneling Microscopy, Scanning Microscopy International 7, 757-779 (1994).

*H. Qiu, J.C. Dewan and N.C. Seeman, A DNA Decamer with a Sticky End: The Crystal Structure of d-CGACGATCGT. J. Mol. Biol. 267, 881-898 (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).

*A. Podtelezhnikov, C. Mao, N.C. Seeman & A. Vologodskii, Multimerization-Cyclization of DNA Fragments as a Method of Conformational Analysis, Biophys. J. 79, 2692-2704 (2000).

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

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

*P. Sa-Ardyen, A.V. Vologodskii and N.C. Seeman, The Flexibility of DNA Double Crossover Molecules. Biophysical Journal 84, 3829-3837 (2003).

*P.S. Lukeman, A. Mittal, & N.C. Seeman, Two Dimensional PNA/DNA Arrays:  Estimating the Helicity of Unusual Nucleic Acid Polymers, Chemical Communications 2004, 1694-1695 (2004).

P. Paukstelis, J. Nowakowski, J.J. Birktoft and N.C. Seeman, The Crystal Structure of a Continuous Three-Dimensional DNA Lattice, Chemistry and Biology 1`1, 1119-1126 (2004).

*W. Shen, M. Bruist, S. Goodman & N.C. Seeman, A Nanomechanical Device for Measuring the Excess Binding Energy of Proteins that Distort DNA, Angew. Chem. Int. Ed. 43, 4750-4752 (2004); Angew.Chem. 116, 4854-4856 (2004).

* W.B. Sherman & N.C. Seeman, Design of Low-Stress Nucleic Acid Nanotubes, Bioiphys. J., 90, 4546-4557 (2006).

P.S. Lukeman, M. Stevenson & N.C. Seeman, Morphology Change of Calcium Carbonate in the Presence of Polynucleotides, Cryst. Growth & Design 8, 1200-1202 (2008).

Y. Liu, R. Wang, L. Ding, R. Sha, P.S. Lukeman, J. W. Canary & N.C. Seeman, Thermodynamic Analysis of Nylon Nucleic Acids, ChemBioChem 9, 1641-1648 (2008).

J. Lin, N.C. Seeman & N. Vaidehi, Molecular Dynamics Simulations of Insertion of Chemically Modified DNA Nanostructures into a Water-Chloroform Interface, Biophys. J. 95, 1099-1107 (2008).

*Y. Liu, R. Sha, R. Wang, L. Ding , J.W. Canary, & N.C. Seeman, 2',2'-Ligation Demonstrates the Thermal Dependence of DNA-Directed Positional Control, Tetrahedron 64, 9417-8422 (2008).

Y. Liu, A. Kuzuya, R. Sha, J. Guillaume, R. Wang, J.W. Canary & N.C. Seeman, Coupling Across a DNA Helical Turn Yields a Hybrid DNA/Organic Catenane Doubly Tailed with Functional Termini, J. Am. Chem. Soc. 130, 10882-10883 (2008).

J. Zheng, P.S. Lukeman, W.B. Sherman, C. Micheel, A. P. Alivisatos, P.E. Constantinou & N.C. Seeman, Metallic Nanoparticles Used to Estimate the Structural Integrity of DNA Motifs, Biophys. J. 95, 3340-3348 (2008).

R. Dreyfus, M.E. Leunissen, R. Sha, A.V. Tkachenko,  N.C. Seeman, D.J. Pine & P.M. Chaikin, A simple quantitative model for the reversible association of DNA coated colloids, Phys. Rev. Lett. 102, Article  048301 (2009).

*N. Jonoska, N.C. Seeman & G. Wu, On the Existence of Reporter Strands in DNA-Based Graph Structures,  Theor. Computer Sci. 410, 1448-1460 (2009).

M. Leunissen, R. Dreyfus, R. Sha, T. Wang, N.C. Seeman, D.J. Pine, & P.M. Chaikin, Towards Self-Replicating Materials of DNA-Functionalized Colloids, Soft Matter (2009).

M.E. Leunissen, R.Dreyfus, F.C. Cheong, D.G. Grier, R. Sha, N.C. Seeman & P.M. Chaikin, Switchable Self-Protected Attractions in DNA-Functionalized Colloids, Nature Materials, 8, 590-595 (2009).

*C.H. Spink, L. Ding, Q. Yang, R.D. Sheardy & N.C. Seeman, Thermodynamics of Forming a Parallel Holliday Crossover, Biophys. J. 97, 528-538 (2009).

*J. Zheng, J.J. Birktoft, Y. Chen, T. Wang, R. Sha, P.E. Constantinou, S.L. Ginell, C. Mao, & N.C. Seeman, From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal, Nature 461, 74-77 (2009).

M.E. Leunissen, R. Dreyfus, R. Sha, N.C. Seeman & P. M Chaikin, A quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes, J. Am. Chem. Soc. 132, 1903-1913 (2010).

*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).

*H. Gu, W. Yang & N.C. Seeman, A DNA Scissors Device Used to Measure MutS Binding to DNA Mis-Pairs, J. Am. Chem. Soc. 132, 4352-4357 (2010).

R. Dreyfus, M.E. Leunissen, R. Sha, A. Tkachenko, N.C. Seeman, D.J. Pine, P.M. Chaikin, Aggregation-disaggregation transition of DNA-coated colloids:  Experiments and theory, Phys. Rev. E. 81, 041404 (2010).

* M.I. Lvovska, N.C. Seeman, R. Sha, T.R. Globus, T.B. Khromova & T.S. Dorofeeva, THz Characterization of DNA Four-Way Junctions and its Components, IEEE Trans. Nanotech. 9, 610-617 (2010).

* T. Wang, R. Sha, J.J. Birktoft, J. Zheng, C. Mao & N.C. Seeman, A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit, J. Am. Chem. Soc. 132, 15471-15473 (2010).

* Q. Xu, L. Feng., R. Sha, N.C. Seeman & P.M. Chaikin, Subdiffusion of a Sticky Particle on a Surface, Phys. Rev. Lett. 106, 228102 (2011).

* A. Lehmuskero, N. Hakulinen, H. Lajunen, B. Bai, L. Huang, J. Turunen, J. Zheng, R. Sha, P. Vahimaa & N. C. Seeman, Linear Birefringence Magnitude of Artificial DNA Crystals, Optical Materials Express 1, 936-942 (2011).

* T. Wang, R. Sha, R. Dreyfus, M.E. Leunissen, C. Maass, D. Pine, P.M. Chaikin & N.C. Seeman, Self-Replication of Information-Bearing Nanoscale Patterns, Nature, 478, 225-228 (2011).

* T. Wang, D. Schiffels, S. M. Cuesta, D. K. Fygenson & N. C. Seeman, Design and Characterization of 1D Nanotubes and 2D Periodic Arrays Self-Assembled From DNA Multi-Helix Bundles, J. Am. Chem. Soc. 134, 1606-1616 (2012).

* N. Nguyen,  J.J. Birktoft, R. Sha, T. Wang, J. Zheng, P.E. Constantinou, S.L. Ginell, Y. Chen, C. Mao & N.C. Seeman, The Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure, J. Mol. Recognition 25, 234-237 (2012).

* N. Jonoska & N.C. Seeman, Computing by Molecular Self-Assembly, Interface Focus 2, 504-511 (2012).

* K.-T. Wu, L. Feng, R. Sha, R. Dreyfus, A.Y. Grosberg, N.C. Seeman & P.M. Chaikin, Polygamous Particles, Proc. Nat. Acad. Sci. (USA) 109, 18731-18736 (2012).

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

* R. Sha, J.J. Birktoft, N. Nguyen, A.R. Chandrasekaran, J. Zheng, X. Zhao, C. Mao, N.C. Seeman, Self-Assembled DNA Crystals:  The Impact on Resolution of 5'-Phosphates and the DNA Source, NanoLett. 13, 793-797 (2013).

 

 

 

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