SELECTED PUBLICATIONS
(PROF. JUNGHUEI CHEN )

1. J. Chen, M.E.A. Churchill, T.D. Tullius, N.R. Kallenbach and N.C. Seeman. “Construction and Analysis of Mono-Mobile DNA Junctions” Biochemistry  27, 6032-6038 (1988).

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

3. N. C. Seeman, J. Chen and N. R. Kallenbach. “Gel Electrophoretic Analysis of DNA Branched Junctions”  Electrophoresis 10, 345-354. (1989).

4. J. Chen, N.R. Kallenbach and N.C. Seeman. “A Specific Quadrilateral Synthesized from DNA Branched Junctions” J. Am. Chem. Soc., 111, 6402-6407 (1989).

5. N.C. Seeman, J.E. Mueller, J. Chen, M. E.A. Churchill, A. Kimball, T.D. Tullius, B. Kemper, R.P. Cunningham and N.R. Kallenbach. “Immobile Junctions Suggest New Features of the Structural Chemistry of Recombination” in R. H. Sarma & M. H. Sarma (eds.) Structure & Methords, Volume 1: Human genome initiative & DNA recombination, pp 137-156 (1990).

6. J. Chen and N. C. Seeman. “The Electroophoretic Properties of a DNA Cube and its Substructure Catenanes”  Electrophoresis 12,607-611. (1991).

7. J. Chen and N.C. Seeman.  “Synthesis from DNA of a Molecule with the Connectivity of a Cube”  Nature  350, 631-633 (1991).

8. N. C. Seeman, J. Chen, Y. Zhang, T-J Fu, J. E. Mueller, Y. Wang, and S. Zhang. “Synthetic DNA Knots and Catenanes” New. J. Chem. 17,739-755. (1993).

9. N. C. Seeman, Y. Zhang, T-J Fu, S. Zhang, Y. Wang, and J. Chen. “Chemical Synthesis of Nanostructures” Mat. Res. Soc. Symp. Proc. 330, 45-56. (1994).

10. N. C. Seeman, Y. Zhang, H. Wang, J. E. Mueller, B. Liu, and J. Chen. “The Control of DNA Structure and Topology; An Overview” Mat. Res. Soc. Symp. Proc. 351, 57-66. (1994).

11. N. C. Seeman, Y. Zhang, and J. Chen. “DNA Nanoconstructions” J. Vac. Sci. Technol. A.  12(4), 1895-1903 (1994).

12. J. Chen, R. Kannar, and N. R. Cozzarelli. “The Sep1 strand exchange protein from Saccharomyces cerevisiae promotes a paranemic joint between homologous DNA molecules” Genes & Development 8, 1356-1365 (1994).

13. J. Chen, C. A. Rauch, J. H. White, P. T. Englund, and N. R. Cozzarelli. “The topology of the kinetoplast DNA network” Cell  80, 61-69 (1995).

14. J. Chen, P. T. Englund, and N. R. Cozzarelli. “Changes in network topology during the replication of kinetoplast DNA” EMBO J. 14, 6339-6347 (1995).

15. N. C. Seeman, Y. Zhang, S. Du, and J. Chen. “Construction of DNA Polyhedra and Knots Through Symmetry Minimization” in Supramolecular Stereochemistry, 27-32. J. S. Siegel (ed.) (Kluwer Academic Publishers) (1995).

16. N. C. Seeman, H. Wang, J. Chen, J. E. Mueller, and S. Zhang. “DNA Nanotechnology and Topology” in Biological Structure and Dynamics, Vol. 9, 319-339. R. H. Shama & M. H. Sarma (eds.) (Adenine Press) (1996).

17. 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).

18. N. C. Seeman, J. Qi, X. Li, X. Yang, N. B. Leontis, S., Du and J. Chen. “The Control of DNA Structure: From Topological Modules to Geometrical Modules” in J. Michl (ed.; Kluwer Academic Publishers) Modular Chemistry, 95-104 (1997).

19. N.C. Seeman, J. Chen, Y. Zhang, , L.A. Wenzler, S, Du, J.E. Mueller, H. Wang, C. Mao, W. Sun, Z. Shen, M.H. Wong, H, Yan and R. Sha “A Bottom-Up Approach to Nanotechnology Using DNA”  in: Biological Molecules in Nanotechnology, ed. by S.C. Lee, IBC Libraries, Southborough, MA, Chapter 8 (1998).

20. Z. Zhang, A. M. Simons, V. P. Prabhu, and J. Chen. “Strand Exchange Protein 1 (Sep1) from Saccharomyces cerevisiae does not promote branch migration in vitro”. J. Biol. Chem.  273, 4950-4956. (1998).

21. N. C. Seeman, H. Wang, X. Yang, and J. Chen. “New Motifs in DNA Nanotechnology” Nanotechnology 9, 257-273 (1998).

22. N. C. Seeman, H. Wang, B. Liu, X. Yang,W. Sun, Z. Shen, and J. Chen. “ The Perils of Polynucleotides: The Experimental Gap Between The Design and Assembly of Unusual DNA Structures” DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 44, 215-233. (1998).

23. J. Chen and D. H. Wood. “A New DNA Separation Technique with a Low Error Rate” DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 48, 47-56. (1999).

24. J. Chen, E. Antipov, B. Lemieux, W. Cedeno, and D. H. Wood. “ DNA Computing Implementing Genetic Algorithms” in L. Landweber, E. Winfree, R. Lipton, and S. Freeland (eds.) Proceedings of DIMACS Workshop on Evolution as Computation, pp 39-49 (Piscataway, NJ) (1999).

25. D. H. Wood, E. Antipov, B. Lemieux, W. Cedeno, and J. Chen. “A DNA Implementation of the Max 1s Problem ” in W. Banzhaf, A. Eiben, M. Garzon, V. Honavar, M. Jakiela, and R. E. Smith (eds.) GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference pp1835-1842 (Morgan Kaufman, San Francisco) (1999).

26. D. H. Wood, and J. Chen. “ Toward Large Populations for Royal Road Problems via DNA” in P. Angeline, Z. Michalewicz, M Schoenauer, X. Yao, and A. Zalzaza (eds.) 1999 Congress on Evolutionary Computation. (IEEE Computer Society Press, New York) (1999).

27. J. Chen, E. Antipov, B. Lemieux, W. Cedeno, and D. H. Wood. “In vitro Selection for a Max 1s DNA Genetic Algorithm” D. K. Gifford & E. Winfree (eds.) in press DNA based Computer V (1999).

28. D. H. Wood. J. Chen, E. Antipov, B. Lemieux, W. Cedeno “ A Design for DNA Computation of OneMax Problem”. Special issue on Biomolecular Approaches to Soft Computing. Soft Computing, to appear (2000).

29. N. C. Seeman, F. Liu, C. Mao, X. Yang, J. Chen and E. Winfree. “ Two Dimensions and Two states in DNA Nanotechnology”. J. Biomolecular Structure & Dynamics. 11, 253-262. (2000).

30. J-T. Oh, Y. Cajal, E. M. Skowronska, S. Belkin, J. Chen, T. K. Van Dyk, M. Sasser, M. K. Jain. “ Cationic Peptide Antimicrobials Induce Selective Transcription of micF and osmY in Escherichia coli” Biochimica et Biophysica Acta. 1463, 43-54. (2000).

31. A. Liechty, J. Chen, and M. K. Jain. “Origin of Antibacterial Stasis by Polymyxin B in Escherichia coli”. Biochimica et Biophysica Acta. 1463, 55-64. (2000).

32. J. Chen and D. H. Wood. “Computation with Biomolecules”. Proc. Nat. Acad. Sci. USA. 97, 1328-1330. (2000).

33. N. C. Seeman, C. Mao, F. Liu, R. Sha, X. Yang, L. Wenzler, X. Li, Z. Shen, H. Yan, P. Sa-Ardyen, Y. Pinto, J. Qi, B. Liu, H. Qiu, S. Du, H. Wang, W. Sun, Y. Wang, T-J Fu, Y. Zhang, J. E. Mueller and J. Chen. “Nicks, Nodes, and New Mortifs for DNA Nanotechnology. In L. Pavesi and E. Buzaneva (eds.), Fromtiers of Nano-Optoelectronic Systems, 177-197. (2000) Kluwer Academic Publishers.

34. E. Goode, D. H. Wood, and J. Chen. “DNA Implementation of a Royal Road Fitness Evolution” in G. Rozenberg & H. J. Hoogeboom (eds.), DNA Based Computers VI accepted (2000).

35. L. Cai, U. Marquardt, Z. Zhang, M. J. Taisey and J. Chen “Influences of DNA Topology on Synaptic Complex Formation Promoted by RecA Protein of E. coli” Nucleic Acids Research 29, 1389-1398 (2001).

36. Z. Zhang, D. Yoon, J. R. LaPorte, and J. Chen. “Appropriate Initiation of Strand Exchange Reaction Promoted by RecA Protein Requires ATP Hydrolysis” J. Mol. Biol.  309, 29-43 (2001).

37. J. Lukes, J. C. Hines, C. J. Evans, N. K. Avliyakulov, V. P. Prabhu, J. Chen and D. S. Ray  “Disruption of the Crithidia fasciculata KAP1 gene results in structural rearrangement of the kinetoplast disc” Molecular & Biochemical Parasitology 117, 179-186. (2001).

38. V. P. Prabhu, A. M. Simons, H. Iwasaki, D. Gai, D. T. Simmons, and J. Chen. “The Effect of p53 on the Rate of Spontaneous Branch Migration and Resolution of the Holliday Junction by RuvC”
  J. Mol. Biol.  316, 1023-1032  (2002).

39.    R. Deaton, J. Chen, H. Bi, M. Garzon, H. Rubin, and D. H. Wood “A PCR-based Protocol for In Vitro Selection of Non-crosshybridzing Oligonucleotides” in M. Hagiya & A. Ohuchi (eds.), DNA Computing VIII  pp. 196-204. (2002).

40.    R. Deaton, J. Chen, H. Bi, and J. A. Rose “ASoftware Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides” in M. Hagiya & A. Ohuchi (eds.), DNA Computing VIII  pp. 252-261. (2002).


41.    R. Deaton, J-W, Kim, and J. Chen. “Design and test of noncrosshybridizing oligonucleotide building blocks for DNA computers and nanostructures” Appl. Phys. Lett., 82, 1305-1307 (2003).


42.    D. Yoon, Y. Wang, K. Stapleford, L.  Wiesmüller, and J. Chen.” P53 Inhibits Strand Exchange and Replication Fork Regression Promoted by Human Rad51”. J. Mol. Biol.  336, 639–654 (2004).