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Cynthia J. Burrows ORGANIC & BIOLOGICAL CHEMISTRY Distinguished Professor B. A. University of Colorado, 1975 Ph. D. Cornell University, 1982 NSF-CNRS Postdoctoral Fellow, Université Louis Pasteur, Strasbourg 1981-83 Phone: (801) 585-7290 Office: 3152 HEB-N Email: burrows@chem.utah.edu Contact Information Research Group Publications

Activities & Awards

• NSF – CNRS Exchange of Scientists Fellowship, 1981-82
• Japan Soc. for the Promotion of Science Research Fellow, 1989-90
• NSF Creativity Award, 1993-95
• NSF Career Advancement Award, 1993-94
• Bioorganic & Natural Products Study Section, NIH, 1990-94
• NSF Math & Physical Sciences Advisory Committee, 2005-2008
• Assoc. Editor, Organic Letters, 1999 - 2002
• Senior Editor, Journal of Organic Chemistry, 2001-present
• Robert W. Parry Teaching Award, 2002
• ACS Utah Award, 2000
• Bea Singer Award, 2004
• Fellow, AAAS, 2004
• Distinguished Scholarly and Creative Research Award, Univ. of Utah, 2005
• Cope Scholar Award, American Chemical Society, 2008

Research Interests

The heterocyclic bases of nucleic acids are rich targets for both toxins that damage DNA and drugs that interact with DNA and RNA. Our laboratory investigates several different aspects of nucleic acid chemistry ranging from the mechanistic organic chemistry of oxidative DNA damage to biochemical studies of enzymes that act on DNA lesions. Lessons learned in modified DNA bases are also being applied to the design of new siRNAs for applications to therapeutic RNA interference. Tools used in our lab include:

• nucleotide, peptide and ligand synthesis
• organic reaction mechanisms (labeling, kinetics, isotope studies)
• ESI-MS and NMR
• bioinorganic studies of metal ion complexes
• gel electrophoresis, PCR and polymerase assays
• protein expression and purification
• RNA interference and gene silencing

Chemistry and Biochemistry of Guanine Oxidation.  Reactive oxygen species (ROS) in the cell lead to DNA damage including base lesions that are mutagenic if unrepaired.  The molecular events leading to mutagenesis now provide a direct link between oxidative DNA damage and cancer.  An understanding of the molecular basis of carcinogenesis is the foundation of prevention and treatment.  The unusual heterocycles 5-guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), whose structures were recently assigned in this laboratory, are major products of guanosine and 8-oxo-7,8-dihydroguanosine (OG) oxidation by a wide variety of ROS including singlet oxygen and peroxyl radicals.  We have investigated the chemical mechanism of formation of Gh and Sp, developed methods of generating highly pure synthetic oligodeoxynucleotides containing these lesions, studied misinsertion of nucleotides opposite the lesions as well as repair by base excision repair (BER) enzymes, and observed a 99% mutation rate of both lesions in an in vivo assay.  The recent detection of Sp in repair-deficient bacterial cells increases the relevancy of these lesions to oxidative damage and disease.

Currently we seek to understand the molecular basis for the extremely high mutation rates and the unusual G to C mutations observed with Gh and Sp.  Other oxidized purines, including OG, are under study for comparison.  Specifically, we hope to determine the structures of Gh and Sp in duplex DNA using NMR and x-ray crystallographic techniques, examine misinsertion of nucleotides opposite the lesions with Y-family (lesion bypass) DNA polymerases and investigate sequence-dependent frameshift mutagenesis with eukaryotic polymerases.  Structural studies involve collaborations with Prof. Mike Stone (Vanderbilt) and Prof. Sylvie Doublié (U. Vermont).  In collaboration with Prof. Sheila David (UC, Davis) we are studying the molecular mechanisms of repair of Gh and Sp lesions using BER glycosylases, and with Prof. John Essigmann (MIT) we are investigating in vivo mutagenesis using site-specifically incorporated lesions in DNA plasmids.  All of our research goals require continual refinement of our synthetic procedures for generation of nucleoside standards, nucleotide triphosphates and oligonucleotide substrates as well as mass spectrometric characterization of the lesions. 
This research is supported by a grant from the National Institutes of Health, 2R01 CA090689.
Mechanisms of DNA Oxidation and Cross-linking.  DNA strand breaks, base lesions, and DNA-protein cross-links result from oxidative insult to chromatin.  Although detailed mechanistic pathways are being elucidated for the first two of these processes in a number of laboratories, formation of DNA-protein cross-links (DPCs) remains poorly understood at the molecular level.  Studies outlined in this proposal build upon recent results showing that 8-oxo-7,8-dihydroguanosine is sensitive to further oxidation by one-electron oxidants leading to a quinonoid intermediate that is nucleophilically trapped to ultimately generate hydantoin products.

Experiments underway include NMR and LC/MS characterization of amino acid and polyamine adducts to nucleosides and to DNA oligomers, and investigation of their mechanisms of formation and chemical stability.  Methods are being developed to understand the chemical structures responsible for DNA-protein cross-linking via both DNA oxidation and protein oxidation.  Adducts of phenols and catechols to guanosine in DNA have been prepared and analyzed for their ability to mediate further oxidative damage to DNA.  The intellectual merit of this work is the formation of a detailed molecular picture of how DNA is oxidized in the presence of reactive species such as protein and polyamine nucleophiles.
Students working on this project are well versed in mechanistic organic chemistry, and gain biotechnical skills in the manipulation of nucleic acids and proteins.  Their overall contribution is to our molecular understanding of DNA damage which underlies processes leading to aging, cancer, and neurological disorders.
This project is funded by the National Science Foundation, CHE-0514612.

Chemical Modifications of siRNA Bases.  Selective nuclease digestion of messenger RNAs inside living cells via the short interfering RNA (siRNA)-triggered RNA interference pathway has become a mainstay in molecular biology to study gene function, and it holds promise for the development of new therapeutics.  However, gaps in our understanding of the basic RNA interference mechanism and ability of siRNAs to interact with intracellular RNA-binding proteins, particularly those involved in the innate immune response, limit the application of this promising new technology.  Our laboratory is developing new synthetic approaches to modified RNA oligonucleotides that carry out gene silencing with reduced undesirable off-target effects.  Specifically, we are engaged in the study of alkylated RNA bases that change the shape of the minor or major groove of double-stranded RNA while maintaining Watson-Crick-like base pairing.  These siRNA duplexes are being used to determine the effect of steric blocks in gene silencing.  The modifications are also expected to block sequence-dependent off-target ettects mediated by Toll-like receptors and sequence-independent effects from dsRBM proteins.

Secondly, we are developing modified bases capable to switching their steric blockades from the minor groove to the major groove (see figure).  These modifications will be placed in the antisense strand using a Watson-Crick-paired sense strand for delivery; the antisense strand will be designed to target a complementary mRNA sequence via Hoogsteen base pairing in which a conformational change hides the steric blockade in the major groove.
This project is being conducted in collaboration with Professor Peter Beal (UC, Davis) and is supported by the NIH, R01 GM080784.

Selected Publications

• X. Xu, J. G. Muller, Y. Ye and C. J. Burrows, “DNA-protein cross-links between guanine and lysine depend on the mechanism of oxidation for formation of C5 vs. C8 adducts,” J. Am. Chem. Soc. 2008, 130, 703-709.
• B. H. Munk, C. J. Burrows, and H. B. Schlegel, “An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroimino-dihydantoin by density functional theory,” J. Am. Chem. Soc. 2008, 130, 0000.
• V. Bandaru, X. Zhao, M. R. Newton, C. J. Burrows, and S. S. Wallace, “Human Endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus,” DNA Repair 2007, 6, 1629-1641.
• N. Krishnamurthy, J. G. Muller, C. J. Burrows, and S. S. David, “Unusual structural features of hydantoin lesions translate into efficient recognition by Escherichia coli Fpg,” Biochemistry 2007, 46, 9355-9365.
• B. H. Munk, C. J. Burrows, and H. B. Schlegel, “An exploration of mechanisms for the transformation of 8-hydroxyguanine radical to FAPy-G by density functional theory,” Chem. Res. Toxicol. 2007, 19, 432-444.
• X. Zhao, J. G. Muller, M. Halasyam, S. S. David, and C. J. Burrows, “In vitro DNA ligation of oligodeoxynucleotides containing oxidized purine lesions by bacteriophage T4 DNA ligase,” Biochemistry, 2007, 46, 3734-3744.
• Y. Ye, J. G. Muller, and C. J. Burrows, “Synthesis and Characterization of the Oxidized dGTP Lesions Spiroiminodihydantoin-2'-deoxynucleoside-5'-triphosphate and Guanidinohydantoin-2'-deoxynucleoside-5'-triphosphate,” J. Org. Chem. 2006, 71, 2181-2184.
• M. E. Johansen, X. Xu, J. G. Muller, and C. J. Burrows, “Oxidatively Induced DNA-Protein Cross-linking between Single-Stranded Binding Protein (SSB) and Oligodeoxynucleotides containing 8-Oxo-7,8-dihydro-2’-deoxyguanosine,” Biochemistry, 2005, 44, 5660-5671.
• O. Kornyushyna, A. J. Stemmler, D. M. Graybosch, I. Bergenthal, and C. J. Burrows, “Synthesis of a Metallopeptide-PNA Conjugate and its Oxidative Cross-linking to a DNA Target,” Bioconj. Chem. 2005, 17, 178-183.
• M. E. Hosford, J. G. Muller, and C. J. Burrows, "Spermine participates in oxidative damage of guanosine and 8-oxoguanosine leading to deoxyribosylurea formation," J. Am. Chem. Soc. 2004, 126 , 9540-9541.
• S. Choi, J. G. Muller, C. J. Burrows, et al., "Mechanism of 2-e- oxidation of 5-dGMP by a Pt(IV) complex," J. Am. Chem. Soc. 2004, 126 , 591.
• Y. Ye, J. G. Muller, W. Luo, C. L. Mayne, A. J. Shallop, R. A. Jones, and C. J. Burrows, "Formation of 13C-, 15N- and 18O-labeled guanidinohydantoin from guanosine oxidation with singlet oxygen. Implications for structure and mechanism," J. Am. Chem. Soc. 2003, 125, 13926.
• O. Kornyushyna and C. J. Burrows, "Effect of the oxidized lesions Sp and Gh on proofreading by Klenow fragment," Biochemistry 2003, 42, 13008.
• W. Luo, J.G. Muller, and C.J. Burrows, "The pH-dependent role of superoxide in riboflavin-catalyzed photooxidation of 8-oxo-7,8-dihydroguanosine," Org . Lett . 2001, 3, 2801-2804.
• W. Luo, J. G. Muller, E. Rachlin, and C. J. Burrows, "Characterization of spiroiminodihydantoin as a product of 7,8-dihydro-8-oxoguanosine oxidation," Org. Lett. 2000, 2, 613-616.
• R. P. Hickerson, C. L. Chepanoske, S. D. Williams, S. S. David, and C. J. Burrows, "Mechanism-based DNA-protein cross-linking of MutY via oxidation of 8-oxoguanosine," J. Am. Chem. Soc. 1999, 121, 9901-9902.
• R. P. Hickerson, F. Prat, J. G. Muller, C. S. Foote, and C. J. Burrows, "Sequence and stacking dependence of 8-oxoguanine oxidation: Comparison of one-electron vs. singlet oxygen mechanisms," J. Am. Chem. Soc. 1999, 121, 9423-9428.
• J. Stemmler and C. J. Burrows, "The Sal-XH motif for metal-mediated oxidative DNA-peptide cross-linking," J. Am. Chem. Soc. 1999, 121, 6956-6957.
• C.J. Burrows and J.G. Muller, "Oxidative nucleobase modifications leading to strand scission," Chem. Rev. 1998, 98, 1109-1152.

Contact Information:

Cynthia J. Burrows, Ph. D., Distinguished Professor

U.S. Mailing address:
Department of Chemistry
University of Utah
315 S. 1400 East, Rm 2020
Salt Lake City, UT 84112-0850

Campus mailing address:  2020 HEB

Physical location:       
3152 Henry Eyring Building
Voice:  801-585-7290
Fax:  801-585-0024
Labs:  801-585-3096
burrows@chem.utah.edu

Administrative Assistant:        
Mrs. Gerry Collins
gerry@chem.utah.edu
3270 HEB; 801-581-8517

JOC Editorial Office:             
Cynthia J. Burrows, Senior Editor, Journal of Organic Chemistry
Mrs. Gerry Collins, Editorial Assistant:  cjb.joc@chem.utah.edu
Voice:  801-585-0077
Toll-free:  866-275-0245
Fax:  801-585-0024