Donald E. Bergstrom, Ph.D. Walther Professor of Medicinal Chemistry Phone: (765) 494-6275 Fax: (765) 494-1414 E-mail: bergstrom@purdue.edu Full directory listing

Specialization: Medicinal and Bioorganic Chemistry of Nucleic Acids

Education

Research: Medicinal and Bioorganic Chemistry of Nucleic Acids

Our research is directed towards the construction of modified nucleic acids for use as biochemical tools, diagnostic probes, and therapeutics. This research requires the design and synthesis of nucleic acid components as well as novel molecular probes. For example, we are engaged in the development of a new generation of molecular end-caps designed to stabilize short double-stranded DNA segments (dsDNA). Capped dsDNA facilitates crystallization of protein-DNA complexes. In addition, endcaps are being investigated as structural elements for directing the folding and stabilizing G-quadruplexes and as components of therapeutic oligonucleotides, including decoy oligonucleotides directed towards STAT3, a transcription factor of significance to the etiology of head and neck cancer.

Carbon nanotubes have been shown to function as water-soluble carriers for biological molecules. These are taken up into cells and have been proposed as cell-targeting therapeutic-delivery platforms. In collaboration with Professors Ron Reifenberger (Physics) and David Riese (Medicinal Chemistry and Molecular Pharmacology), we have prepared DNA conjugated single wall carbon nanotubes and are studying the potential of these as siRNA carriers specific for EGF receptor, which is over-expressed in cancer cells.

Working in collaboration with Ernest R. Blatchley III (School of Civil Engineering) and J. Paul Robinson (School of Veterinary Medicine), we have developed a microsphere coated with the compound (E)-5-[2-(methoxy-carbonyl)ethenyl]cytidine for UV dosimetry. On UV irradiation the coated microspheres become fluorescent. This attribute allows their application as a Lagrangian actinometer for estimation of dose distributions and process performance in polychromatic UV disinfection system

Working with Professor Rashid Bashir (School of Electrical and Computer Engineering) we are developing nanowires for quantifying microRNAs and proteins overexpressed in cancer. Our segment of the project is focused on the development of methodology for the functionalization of silicon nanowires with peptide nucleic acids (PNA). In addition, we are building PNA derived nanoparticles as components of cancer therapeutic agents with Professor James Leary (Weldon School of Biomedical Engineering).

Representative Publications

Shiyue Fang, Yousheng Guan, Ernest R. Blatchley III, Chengyue Shen, and Donald E. Bergstrom, "Conjugation of (E)-5-[2-(Methoxycarbonyl)ethenyl]cytidine to Hydrophilic Microspheres: Development of a Mobile Microscale UV Light Actinometer", Bioconjugate Chemistry, 2008, 19, 592-597.

Roman V. Rozhkov, V. Jo Davisson, Donald E. Bergstrom, "Fluorogenic Transformations Based on Formation of CC Bonds Catalyzed by Palladium: An Efficient Approach for High Throughput Optimizations and Kinetic Studies", Advanced Synthesis & Catalysis 2008, 350, 71-75.

E. R. Blatchley III, C. Shen , O.K. Scheible, J.P. Robinson, K. Ragheb, D.E. Bergstrom and D. Rokjer, "Validation of large-scale, monochromatic UV disinfection systems for drinking water using dyed microspheres", Water Research 2008, 42, 677-688.

Roya R. Lahiji, Bridget D. Dolash, Donald E. Bergstrom, and Ronald Reifenberger, "Oligonucleotide Association with Single-Walled Carbon Nanotubes Studied by SPM", Small 2007, 3, 1912-1920.

Ernest R. Blatchley III, Chengyue Shen, Zorana Naunovic, Lian-Shin Lin, Dennis A. Lyn, J. Paul Robinson, Katherine Ragheb, Gerald Gregon, Donald E. Bergstrom, Shiyue Fang, Yousheng Guan, Kristofer Jennings, Nilupa Gunaratna, "Dyed Microspheres for Quantificatiion of UV Dose Distributions: Photochemical Reactor Characterization by Lagrangian Actinometry", Journal of Environmental Engineering 2006, 132, 1390-1403.

Olga Adelfinskaya, V. Jo Davisson, and Donald E. Bergstrom, " Synthesis and structural analysis of oxadiazole carboxamide deoxyribonucleoside analogs", Nucleosides, Nucleotides, and Nucleic Acids 2005, 24, 1919-1945.

Olga Adelfinskaya, Vishal C. Nashine, Donald E. Bergstrom, V. Jo Davisson, "Efficient Primer Strand Extension beyond Oxadiazole Carboxamide Nucleobases", J. Amer. Chem. Soc. 2005, 127 (46) 16000-16001.

Samir M. Iqbal, G. Balasundaram, Subhasis Ghosh, D. E. Bergstrom and R. Bashir, "Direct current electrical measurement of dsDNA in nanogap junctions", Applied Physics Letters 2005, 86, 153901.

Chengyue Shen, Shiyue Fang, Donald E. Bergstrom, and Ernest R. Blatchley. "(E)-5-[2-Methoxycarbonyl)ethenyl]cytidine as a Chemical Actinometer for Germicidal Radiation, Environmental Science & Technology, 2005, 39, 3826-3832.

Pei-Sze Ng and Donald E. Bergstrom, "Alternative Nucleic Acid Analogues for Programmable Assembly: Hybridization of LNA to PNA," Nano Letters 2005, 5, 107-111.