Chemistry at Illinois University of Illinois at Urbana-Champaign

Scott K. Silverman

Professor of Chemistry
associate head of budget and operations
Affiliate, Department of Biochemistry

Professor Silverman received the B.S. degree in chemistry from UCLA in 1991. He obtained the Ph.D. degree in chemistry from Caltech in 1997, working with Dennis Dougherty on physical organic chemistry and molecular neurobiology, and he performed postdoctoral research with Thomas Cech at the University of Colorado at Boulder. He joined the faculty at the University of Illinois in 2000, working in the areas of chemical biology and organic chemistry.

Research

The Silverman lab is a group of researchers who are interested in developing, characterizing, and applying DNA as a catalyst. We use techniques and concepts from chemical biology, organic chemistry, biochemistry, molecular biology, and other disciplines to design our experiments and interpret our results. We have many projects that are suitable for undergraduate research students. Please see www.scs.illinois.edu/silverman/ for more information about research in the Silverman lab.

 

Publications

"A Modular Tyrosine Kinase Deoxyribozyme with Discrete Aptamer and Catalyst Domains", V. Dokukin and S. K. Silverman, Chem. Commun. 2014, 50, 9317-9320.

"DNA-Catalyzed Lysine Side Chain Modification", B. M. Brandsen, T. E. Velez, A. Sachdeva, N. A. Ibrahim, and S. K. Silverman, Angew. Chem. Int. Ed. 2014, 53, 9045-9050.

"A Generalizable DNA-Catalyzed Approach to Peptide-Nucleic Acid Conjugation", C. Chu, O. Wong, and S. K. Silverman, ChemBioChem 2014, 15, 1905-1910.

"DNA-Catalyzed Hydrolysis of Esters and Aromatic Amides", B. M. Brandsen, A. R. Hesser, M. A. Castner, M. Chandra, and S. K. Silverman, J. Am. Chem. Soc. 2013, 135, 16014-16017.

"DNA Catalysts with Tyrosine Kinase Activity", S. M. Walsh, A. Sachdeva, and S. K. Silverman, J. Am. Chem. Soc. 2013, 135, 14928-14931.

"DNA Catalysis of a Normally Disfavored RNA Hydrolysis Reaction", D. J. Parker, Y. Xiao, J. M. Aguilar, and S. K. Silverman, J. Am. Chem. Soc. 2013, 135, 8472-8475.

"Catalytic DNA with Phosphatase Activity", J. Chandrasekar and S. K. Silverman, Proc. Natl. Acad. Sci. USA 2013, 110, 5315-5320.

"Systematic Evaluation of the Dependence of Deoxyribozyme Catalysis on Random Region Length", T. E. Velez, J. Singh, Y. Xiao, E. C. Allen, O. Y. Wong, M. Chandra, S. C. Kwon, and S. K. Silverman, ACS Comb. Sci. 2012, 14, 680-687.

"Shields for Small Molecules", S. K. Silverman, Nat. Chem. 2012, 4, 774-775.

"Covalent Tagging of Phosphorylated Peptides By Phosphate-Specific Deoxyribozymes", A. Sachdeva, M. Chandra, J. Chandrasekar, S. K. Silverman, ChemBioChem 2012, 13, 654-657.

"Lanthanide Ions as Required Cofactors for DNA Catalysts", V. Dokukin, S. K. Silverman, Chem. Sci. 2012, 3, 1707-1714.

"Establishing Broad Generality of DNA Catalysts for Site-Specific Hydrolysis of Single-Stranded DNA", Y. Xiao, R. J. Wehrmann, N. A. Ibrahim, and S. K. Silverman, Nucleic Acids Res. 2012, 40, 1778-1776.

"DNA-Catalyzed Reactivity of a Phosphoramidate Functional Group and Formation of an Unusual Pyrophosphoramidate Linkage", A. Sachdeva and S. K. Silverman, Org. Biomol. Chem. 2012, 10, 122-125.

"DNA-Catalyzed Reductive Amination", O. Y. Wong, A. E. Mulcrone, and S. K. Silverman, Angew. Chem. Int. Ed. 2011, 50, 11679-11684.

"DNA-Catalyzed Covalent Modification of Amino Acid Side Chains in Tethered and Free Peptide Substrates", O. Y. Wong, P. I. Pradeepkumar, and S. K. Silverman, Biochemistry 2011, 50, 4741-4749.

"Merely Two Mutations Switch a DNA-Hydrolyzing Deoxyribozyme from Heterobimetallic (Zn2+/Mn2+) to Monometallic (Zn2+-only) Behavior", Y. Xiao, E. C. Allen, and S. K. Silverman, Chem. Commun. 2011, 47, 1749-1751.

"Improved Deoxyribozymes for Synthesis of Covalently Branched DNA and RNA", C. S. Lee, T. P. Mui, and S. K. Silverman, Nucleic Acids Res. 2011, 39, 269-279.

"Functional Compromises Among pH Tolerance, Site Specificity, and Sequence Tolerance for a DNA-Hydrolyzing Deoxyribozyme", Y. Xiao, M. Chandra, and S. K. Silverman, Biochemistry 2010, 49, 9630-9637.

"DNA-Catalyzed Serine Side Chain Reactivity and Selectivity", A. Sachdeva and S. K. Silverman, Chem. Commun. 2010, 46, 2215-2217.

"DNA as a Versatile Chemical Component for Catalysis, Encoding, and Stereocontrol&quot, S. K. Silverman, Angew. Chem. Int. Ed. 2010, 49, 7180-7201.

"Multivector Fluorescence Analysis of the xpt Guanine Riboswitch Aptamer Domain and the Conformational Role of Guanine", M. D. Brenner, M. S. Scanlan, M. K. Nahas, T. Ha, and S. K. Silverman, Biochemistry 2010, 49, 1596-1605.

"Deoxyribozymes: Selection Design and Serendipity in the Development of DNA Catalysts", S. K. Silverman, Acc. Chem. Res. 2009, 42, 1521-1531.

"DNA-Catalyzed Sequence-Specific Hydrolysis of DNA", M. Chandra, A. Sachdeva, and S. K. Silverman, Nat. Chem. Biol. 2009, 5, 718-720.

"Use of Deoxyribozymes in RNA Research", S. K. Silverman and D. A. Baum, Methods Enzymol. 2009, 469, 95-117.

"Multimodal Optical Sensing and Analyte Specificity Using Single-Wall Carbon Nanotubes", D. A. Heller, H. Jin, B. M. Martinez, D. Patel, B. M. Miller, T.-K. Yeung, P. V. Jena, C. Höbartner, T. Ha, S. K. Silverman, and M. S. Strano, Nat. Nanotechnol. 2009, 4, 114-120.

"Efficient control of group I intron ribozyme catalysis by DNA constraints", E. Zelin and S. K. Silverman, Chem. Commun., 2009, 767-769.

"Controlling the Direction of Site-Selectivity and Regioselectivity in RNA ligation by Zn2+-Dependent Deoxyribozymes That Use 2',3'-Cyclic Phosphate RNA Substrates", D. M. Kost, J. P. Gerdt, P. I. Pradeepkumar, and S. K. Silverman, Org. Biomol. Chem 2008, 6, 4391-4398.

"Selective Stabilization of Natively Folded RNA Structure by DNA Constraints", J. P. Gerdt, C. V. Miduturu, and S. K. Silverman, J. Am. Chem. Soc. 2008, 130, 14920-14921.

"Convergent and General DNA-Catalyzed One-Step Synthesis of Multiply Branched DNA", T. P. Mui and S. K. Silverman, Org. Lett. 2008, 10, 4417-4420.

"Catalytic DNA (Deoxyribozymes) for Synthetic Applications — Current Abilities and Future Prospects", S. K. Silverman, Chem. Commun. 2008, 3467-3485.

"A Forced March Across an RNA Folding Landscape", S. K. Silverman, Chem. Biol. 2008, 15, 211-213.

"Deoxyribozymes: Useful DNA Catalysts In Vitro and In Vivo", D. A. Baum and S. K. Silverman, Cell. Mol. Life Sci. 2008, 65, 2156-2174.

"DNA and RNA Can Be Equally Efficient Catalysts for Carbon-Carbon Bond Formation", M. Chandra and S. K. Silverman, J. Am. Chem. Soc. 2008, 130, 2936-2937.

"DNA-Catalyzed Formation of Nucleopeptide Linkages", P. I. Pradeepkumar, C. Höbartner, D. A. Baum, and S. K. Silverman, Angew. Chem. Int. Ed., 2008, 47, 1753-1757.

"Improvement of DNA Adenylation Using T4 DNA Ligase with a Template Strand and a Strategically Mismatched Acceptor Strand", M. P. Patel, D. A. Baum, and S. K. Silverman, Bioorg. Chem. 2008, 36, 46-56.

"Recent Advances in DNA Catalysis", C. Höbartner and S. K. Silverman, Biopolymers 2007, 87, 279-292.

"Allosteric Control of Ribozyme Catalysis by Using DNA Constraints", E. Zelin and S. K. Silverman, ChemBioChem 2007, 8, 1907-1911.

"Engineering a Selective Small-Molecule Substrate Binding Site into a Deoxyribozyme", C. Höbartner and S. K. Silverman, Angew. Chem. Int. Ed. 2007, 46, 7420-7424.

"Site-Selective Depurination by a Periodate-Dependent Deoxyribozyme", C. Höbartner, P. I. Pradeepkumar, and S. K. Silverman, Chem. Commun. 2007, 2255-2257.

"Ty1 Reverse Transcriptase Does Not Read Through the Proposed 2',5'-Branched Retrotransposition Intermediate In Vitro", E. D. Pratico and S. K. Silverman, RNA 2007, 13, 1528-1536.

"Deoxyribozyme-Catalyzed Labeling of RNA", D. A. Baum and S. K. Silverman, Angew. Chem. Int. Ed. 2007, 46, 3502-3504.

"Control of Macromolecular Structure and Function Using Covalently Attached Double-Stranded DNA Constraints", S. K. Silverman, Mol. Biosyst. 2007, 3, 24-29.

(Click here for full publications list)

Awards

  • Fellow, Royal Society of Chemistry (2012)
  • UIUC Campus Award for Excellence in Guiding Undergraduate Research (2011)
  • LAS Professorial Scholar Award, College of Liberal Arts and Sciences, University of Illinois (2010)
  • Eli Lilly Award in Biological Chemistry, American Chemical Society, Division of Biological Chemistry (2009)
  • Fellow, American Association for the Advancement of Science (2007)
  • Fellow, UIUC Center for Advanced Study (2004)
  • Packard Foundation Fellowship (2003)
  • March of Dimes Basil O'Connor Research Award (2003)
  • Burroughs Wellcome Fund Award (2001)
  • Excellence in Teaching Award, UIUC School of Chemical Sciences (2001 and 2004)

Highlights

"DNA-catalyzed serine side chain reactivity and selectivity" by A. Sachdeva and S. K. Silverman (Chem. Commun. 2010, 46, 2215-2217) was chosen by the journal as a "Hot Article". See http://www.rsc.org/publishing/journals/CC/article.asp?doi=B927317D

"DNA-Catalyzed Sequence-Specific Hydrolysis of DNA" by M. Chandra, A. Sachdeva, and S. K. Silverman (Nat. Chem. Biol. 2009, 5, 1521-1531) was featured in a U of I press release, in a Chemical & Engineering News item, and in a Genetic Engineering & Biotechnology News podcast.  See http://news.illinois.edu/news/09/0817dna.html, http://pubs.acs.org/cen/news/87/i34/8734news12.html, and http://www.genengnews.com/gencasts.aspx?id=278.

"Efficient control of group I intron ribozyme catalysis by DNA constraints" by E. Zelin and S. K. Silverman (Chem. Commun. 2009, 767-769) was featured as a "Hot Article". See http://pubs.rsc.org/en/content/articlelanding/2009/cc/b820676g#!divAbstract.

"DNA-Catalyzed Formation of Nucleopeptide Linkages" by P. I. Pradeepkumar, C. Höbartner, D. A. Baum, and S. K. Silverman (Angew. Chem. Int. Ed. 2008, 47, 1753-1757) was selected as a Research Highlight in the March 2008 issue of Nature Chemical Biology. See http://www.nature.com/nchembio/journal/
v4/n3/full/nchembio0308-167.html
.

"Modulation of DNA Constraints that Control Macromolecular Folding" by C. V. Miduturu and S. K. Silverman (Angew. Chem. Int. Ed. 2006, 45, 1918-1921) was chosen as an RSC Chemistry World highlight and also featured as a U of I College of LAS News highlight. See http://www.rsc.org/chemistryworld/News/2006/February/27020601.asp and http://www.las.uiuc.edu/news/2006/dnatools.

"DNA Constraints Allow Rational Control of Macromolecular Conformation" by C. V. Miduturu and S. K. Silverman (J. Am. Chem. Soc. 2005, 127, 10144-10145) was the focus of a U of I press release and was a feature story in the Champaign (Illinois) News-Gazette. See http://news.illinois.edu/news/05/0628dna.html.

"Efficient One-Step Synthesis of Biologically Related Lariat RNAs by a Deoxyribozyme" by Y. Wang and S. K. Silverman (Angew. Chem. Int. Ed. 2005, 44, 5863-5866) was featured as a Research Highlight in the September 2005 issue of Nature Chemical Biology. See http://www.nature.com/nchembio/journal/v1/n4/full/nchembio0905-195.html.

Prof. Silverman's selection as a 2003 Fellow of the David and Lucile Packard Foundation was featured in a U of I press release. See http://www.news.uiuc.edu/news/03/1007packard.html.

"Deoxyribozymes that Synthesize Branched and Lariat RNA" by Y. Wang and S. K. Silverman (J. Am. Chem. Soc. 2003, 125, 6880-6881) was the focus of a U of I press release and was a U of I College of LAS News highlight. See http://news.illinois.edu/ii/03/0522/lariat_P.html.

Patents

Photo of Scott K. Silverman