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  • Junghuei Chen, Associate Professor

    Associate Professor
    University of Delaware
    105A Drake Hall
    Newark, DE 19716
    (302) 831-1035


    (b. 1960) B.S., 1983, National Taiwan University; Ph.D., 1990, New York University

    Current Research

    The mechanism of homologous recombination:

    Our long-term research objective is to study the mechanisms of homologous recombination in eukaryotic systems. Genetic recombination is the molecular process by which new combinations of the genetic material are generated. While homologous recombination is one of the most important biochemical processes in cell, its molecular mechanism, especially in eukaryotes, is still largely unknown. We are interested in homologous recombination not only because of the intellectual challenges it presents, but also on the insights it may bring to the mechanism of the repair of double strand breaks in DNA. Basic understanding of recombination process may lead to the development of new antibacterial and anticancer agents. Currently, we are focusing on two related areas: (1) the mechanism of DNA homology search and strand transfer promoted by the human recombinational proteins, Rad51 and Rad54. (2) The purification and characterization of human Rad51 paralogs, Rad51 B, C, D, and XRCC 2, 3. Our ultimate goal is to understand the function and mechanism of each of these human proteins in homologous recombination.

    Large scale genomic monitoring and profiling using a dna-based matrix:

    We are developing a new method consisting of separating large library of oligonucleotide DNA in a 2-D matrix that is capable of monitoring or profiling the existence of any input DNA or RNA samples. This 2-D matrix would be sensitive enough that provides unprecedented capacity, and sensitivity. For example, human genomic DNA can be used as the input, and the hybridization signatures of these DNA to these matrixes are the output that represents the genomic “signature” of this individual. Due to the high sensitivity of the matrix, this would detect minor differences of two closely related input DNAs. Therefore, generate genomic and gene expression signatures of specific organism, cell type, or tissue that are indicative of different species, phenotypes, or diseases.

    The structure & function of kinetoplast dna networks:

    Kinetoplast DNA (kDNA) is the mitochondrial DNA of trypanosomatids and related protozoan parasites such as those of the genera Trypanosoma, Leishmania, and Crithidia. The structure of kDNA is unique in nature, consisting of a network of thousands of topologically interlocked circles. The goals of this project are to understand and define the overall topological structure of the unique catenated kinetoplast DNA network to explain its basic biological properties. In addition, we wish to study the enzymatic activities of mitochondrial type II topoisomerases that are essential for the stability and the replication of this unique network structure.

    Representative Publications

    • 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., (2004) 336, 639 – 654.
    • R. Deaton, J-W Kim and J. Chen “Design and Test of Noncrosshybridizing Oligonucleotide Building Blocks for DNA Computers and Nanostructures,” Appl. Phys. Lett., (2003) 82, 1305 – 1307.
    • 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., (2002) 316, 1023 – 1032.
    • 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., (2001) 309, 29 – 43.
    • 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, (2001) 29, 1389 – 1398.
    • J. Chen and D. H. Wood “Computation with Biomolecules,” Proc. Nat. Acad. Sci.USA, (2000) 97, 1328 – 1330.
    • J. Chen, C. A. Rauch, J. H. White, P. T. Englund, and N. R. Caozzarelli “The Topology of the Kinetoplast DNA,” Cell, (1995) 80, 61 – 69.
    • J. Chen and N. C. Seeman “Synthesis from DNA of a Molecule with the Connectivity of a Cube,” Nature, (1991) 350, 631 – 633.



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  • Chemistry and Biochemistry
  • 102 Brown Laboratory
  • University of Delaware
  • Newark, DE 19716, USA
  • Phone: 302-831-1247
  • Undergraduate Program Inquiries 302-831-2465