Department of Medicinal Chemistry and Molecular Pharmacology Personnel - Donald E. Bergstrom

Donald E. Bergstrom, Ph.D.

Walther Professor of Medicinal Chemistry

Medicinal and Bioorganic Chemistry of Nucleic Acids

Research: Medicinal and Bioorganic Chemistry of Nucleic Acids

The fight against cancer requires a broad understanding of the fundamental biochemistry of normal and cancer cells. To achieve this understanding, better molecular tools for probing cellular biochemistry are required. With this goal as a starting point, our laboratory has created a new set of tools consisting of unnatural nucleic acid components useful for studying DNA replication, a process fundamental to cancer cell growth. In collaboration with Dr. V. J. Davisson we are investigating the incorporation of a series of modified nucleosides into DNA primers, and then using these primers in PCR DNA replication experiments to determine the coding properties of the modified nucleosides. Recognition by these analogues provides detailed insight into the mechanism of DNA replication of polymerases. Another important goal of this project is to re-engineer proteins through introduction of controlled mutations using the modified nucleic acid bases. More recently we have begun an investigation of a related set of ribonucleoide analogues to study RNA polymerases. An intimate understanding of RNA replication by RNA polymerases will allow us ultimately to design nucleoside analogue antiviral agents.

A second major research effort in our laboratory is directed towards re-engineering DNA through incorporation of linker molecules. We have developed a novel set of linkers, which stabilize double-stranded DNA (dsDNA) by preventing melting of the duplex ends. This capped dsDNA is being investigated in collaboration with other researchers at Purdue in applications ranging from DNA-protein complex structural studies to immune response modulators. Capped dsDNA is being studied in collaboration with Professor Alan Friedman, Department of Biology, as a component of complexes with nucleases such as Endo VI, and with DNA ligases. Both are of interest as tools for cancer mutation detection. Covalently closed endcapped duplexes containing CpG moieties are under investigation as immunostimulatory agents in collaboration with Professor Philip Low, Department of Chemistry. The endcaps protect against rapid nuclease degradation, an essential property for in vivo application.

In an effort to improve nucleic acid synthesis technology, we have developed a strategy to derivatize oligonucleotides with a biotin conjugate that functions as a traceless purification module. The chemistry was developed so that it can yield either 5'-phosphoylated or 5'-unphosphorylated oligonucleotides. One of the unique features of the methodology is that it should be readily adaptable to a high-throughput automated synthesis of very pure oligonucleotides. This has important implications for applications that require highly purified oligonucleotides, such as automated total gene synthesis.

Another project is underway to develop new strategies for conjugation of biomolecules and synthetic receptors to nano-scale features on silicon derived microelectronic devises. This research involves collaborators in the School of Engineering (micro- and nano-device construction) and Mayo Clinic (cancer biology). In its initial phase the project is based on nano-wires containing a set of antibodies for monitoring proteins over-expressed in prostate cancer. Other studies in our laboratory are seeking to design and develop new kinds of synthetic receptors based on transition metal-mediated cryptand assembly and self-assembly of modified nucleic acids.

In another project, the Bergstrom Laboratory working with researchers in the School of Civil Engineering (Ernest R. Blatchley) has developed a novel nucleoside analogue UV light sensor. This nucleoside analogue has been attached to micro-particles for dosimetry applications that require UV sensor mobility. This research is expected to lead to a method for monitoring UV water disinfection system. These systems are designed to replace conventional water chlorination systems, which may create carcinogenic chlorinated hydrocarbons.

Representative Publications

Pei-Sze Ng and Donald E. Bergstrom, "Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides", Nucleic Acids Research 2004, 32, e107.

Weidong Wu, Donald E. Bergstrom, and V. Jo Davisson "Chemoenzymatic Preparation of Nucleoside Triphosphates", In Current Protocols in Nucleic Acid Chemistry (S.L. Beaucage, D. E. Bergstrom, G.D. Glick and R.A. Jones, eds.) pp.13.2.1-13.2.19. John Wiley and Sons, New York, 2004.

Donald E. Bergstrom, "Orthogonal Base-Pairs Continue to Evolve", Chemistry and Biology, 2004, 11(1), 18-20.

Shiyue Fang and Donald E. Bergstrom, "Reversible Biotinylation of the 5'-Terminus of Oligodeoxyribonucleotides and Its Applicatioin in Affinity Purification", In Current Protocols in Nucleic Acid Chemistry (S.L. Beaucage, D. E. Bergstrom, G.D. Glick and R.A. Jones, eds.) pp.4.20.1-4.20.17. John Wiley and Sons, New York, 2003.

Shiyue Fang, Yousheng Guan, Ernest R. Blatchley III, Lian-Shin Lin, Cheng Yue Shen, Donald E. Bergstrom, "Development of a Nucleoside Analog UV Light Sensor", Nucleosides, Nucleotides and Nucleic Acids 2003, 22(5-8), 703-705.

Pei-Sze Ng, Maneesh R. Pingle, Ganesan Balasundarum, Alan Friedman, Xiaolin Zu, Donald E. Bergstrom, " Endcaps for Stabilizing Short DNA Duplexes," Nucleosides, Nucleotides and Nucleic Acids 2003, 22(5-8), 1635-1637.

Natasha Paul, Vishal C. Nashine, Geoffrey Hoops, Peiming Zhang, Jie Zhou, Donald E. Bergstrom, and V. Jo Davisson, "DNA Polymerase Template Interactions Probed by Degenerate Isosteric Nucleobase Analogs," Chemistry and Biology 2003, 10(9),815-825.

H. McNally, M. Pingle, S. W. Lee, D. Guo, D. E. Bergstrom, and R. Bashir. "Self-Assembly of Micro and Nano-Scale Particles using Bio-Inspired Events," Applied Surface Science 2003, 214(1-4) 109-119.

Weidong Wu, Donald E. Bergstrom, and V. Jo Davisson, ":A Combination Chemical and Enzymatic Approach for the Preparation of Azolecarboxamide Nucleoside Triphosphate," J. Org. Chem. 2003, 68(10), 3860-3865.

Shiyue Fang and Donald E. Bergstrom, "Reversible Biotinylation Phosphoramidite for 5'-End Labeling, Phosphorylation and Affinity Purification of Synthetic Oligonucleotides," Bioconjugate Chemistry 2003, 14, 80-85.