[Univ. of Illinois]  [School of Chemical Sciences]  [Dept. of Chemistry]  [Organic Chemistry]  [Chemical Biology]

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The Silverman laboratory studies fundamental and applied aspects of the nucleic acids, DNA and RNA. In these efforts, we use concepts and techniques from organic chemistry, chemical biology, and biochemistry. We study DNA as a catalyst (deoxyribozyme) for bioorganic chemical reactions; we apply double-stranded DNA as a conformational constraint for other macromolecules; and we develop allosteric nucleic acid enzymes (aptazymes) as sensors for practical detection of environmental toxins, pollutants, and other compounds. We also investigate fundamental features of RNA folding and catalysis. Please click on the images below for brief descriptions of our research projects.

Research links:  [DNA as a catalyst]  [DNA as a constraint]  [DNA as a sensor]  [RNA folding & catalysis]

The Silverman laboratory has received research funding from the following sources:

National Institutes of Health

National Science Foundation

The David and Lucile Packard Foundation

Burroughs Wellcome Fund

The March of Dimes Birth Defects Foundation

American Chemical Society (Petroleum Research Fund)

University of Illinois at Urbana-Champaign Research Board

University of Illinois at Urbana-Champaign Department of Chemistry

Publications from the Silverman laboratory

[Click here for a full publications list with graphics]

70. "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, 2008, submitted for publication.

69. "Selective Stabilization of Natively Folded RNA Structure by DNA Constraints", J. P. Gerdt, C. V. Miduturu, and S. K. Silverman, 2008, submitted for publication.

68. "Convergent and General DNA-Catalyzed One-Step Synthesis of Multiply Branched DNA", T. P. Mui and S. K. Silverman, 2008, submitted for publication.

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

66. "A Forced March Across an RNA Folding Landscape", S. K. Silverman, Chem. Biol. 2008, 15, 211-213 (invited commentary). [pdf]

65. "Deoxyribozymes: Useful DNA Catalysts In Vitro and In Vivo", D. A. Baum and S. K. Silverman, Cell. Mol. Life Sci. 2008, 65, 2156-2174 (invited review). [pdf]

64. "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. [pdf] [Supp Info]

63. "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. [pdf] [Supp Info]

62. "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. [pdf]

61. "Recent Advances in DNA Catalysis", C. Höbartner and S. K. Silverman, Biopolymers 2007, 87, 279-292 (invited review). [pdf]

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

59. "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. [pdf] [Supp Info]

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

57. "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. [pdf]

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

55. "Artificial Functional Nucleic Acids: Aptamers, Ribozymes and Deoxyribozymes Identified by In Vitro Selection", S. K. Silverman, in Functional Nucleic Acids for Sensing and Other Analytical Applications, Y. Lu and Y. Li, eds.; Springer: New York, 2007. [preprint pdf]

54. "A Simple Molecular Model for Thermophilic Adaptation of Functional Nucleic Acids", J. M. Blose, S. K. Silverman, and P. C. Bevilacqua, Biochemistry 2007, 46, 4232-4240. [pdf] [Supp Info]

53. "Control of Macromolecular Structure and Function Using Covalently Attached Double-Stranded DNA Constraints", S. K. Silverman, Mol. Biosyst. 2007, 3, 24-29 (invited review). [pdf]

52. "In Vitro Selection and Application of Nucleic Acid Enzymes (Ribozymes and Deoxyribozymes)", S. K. Silverman, Wiley Encyclopedia of Chemical Biology 2006, in press (invited review). [preprint pdf]

51. "Tools for Molecular Diversification and Their Applications in Chemical Biology", S. K. Silverman and P. J. Hergenrother, Curr. Opin. Chem. Biol. 2006, 10, 185-187 (editorial overview of June 2006 special issue on combinatorial chemistry & molecular diversity). [pdf]

50. "Experimental Tests of Two Proofreading Mechanisms for 5′-Splice Site Selection", Y. Wang and S. K. Silverman, ACS Chem. Biol. 2006, 1, 316-324. [pdf] [Supp Info]

49. "Synthesis and Application of a 5′-Aldehyde Phosphoramidite for Covalent Attachment of DNA to Biomolecules", C. V. Miduturu and S. K. Silverman, J. Org. Chem. 2006, 71, 5774-5775. [pdf] [Supp Info]

48. "Efficient RNA 5'-Adenylation By T4 DNA Ligase To Facilitate Practical Applications", Y. Wang and S. K. Silverman, RNA 2006, 12, 1142-1146. [pdf]

47. "Adenosine is Inherently Favored as the Branch-Site RNA Nucleotide in a Structural Context that Resembles Natural RNA Splicing", E. Zelin, Y. Wang, and S. K. Silverman, Biochemistry 2006, 45, 2767-2771. [pdf] [Supp Info]

46. "Fluorescence of Covalently Attached Pyrene as a General RNA Folding Probe", M. K. Smalley and S. K. Silverman, Nucleic Acids Res. 2006, 34, 152-166. [pdf] [Supp Info]

45. "Modulation of DNA Constraints that Control Macromolecular Folding", C. V. Miduturu and S. K. Silverman, Angew. Chem. Int. Ed. 2006, 45, 1918-1921. [pdf] [Supp Info]

44. "A General Two-Step Strategy to Synthesize Lariat RNAs", Y. Wang and S. K. Silverman, RNA 2006, 12, 313-321. [pdf]

43. "In Vitro Selection, Characterization, and Application of Deoxyribozymes that Cleave RNA", S. K. Silverman, Nucleic Acids Res. 2005, 33, 6151-6163 (review). [pdf]

42. "Modulation of RNA Tertiary Folding by Incorporation of Caged Nucleotides", C. Höbartner and S. K. Silverman, Angew. Chem. Int. Ed. 2005, 44, 7305-7309. [pdf] [Supp Info]

41. "General Deoxyribozyme-Catalyzed Synthesis of Native 3'–5' RNA Linkages", W. E. Purtha, R. L. Coppins, M. K. Smalley, and S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 13124-13125. [pdf] [Supp Info]

40. "Mimicking the First Step of RNA Splicing: An Artificial DNA Enzyme Can Synthesize Branched RNA Using an Oligonucleotide Leaving Group as a 5’-Exon Analogue", R. L. Coppins and S. K. Silverman, Biochemistry 2005, 44, 13439-13446. [pdf] [Supp Info]

39. "DNA Constraints Allow Rational Control of Macromolecular Conformation", C. V. Miduturu and S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 10144-10145. [pdf] [Supp Info]

38. "Efficient One-Step Synthesis of Biologically Related Lariat RNAs by a Deoxyribozyme", Y. Wang and S. K. Silverman, Angew. Chem. Int. Ed. 2005, 44, 5863-5866. [pdf] [Supp Info]

37. "A Deoxyribozyme That Synthesizes 2’,5’-Branched RNA With Any Branch-Site Nucleotide", E. D. Pratico, Y. Wang, and S. K. Silverman, Nucleic Acids Res. 2005, 33, 3503-3512. [pdf] [Supp Info]

36. "Zn²⁺-Dependent Deoxyribozymes That Form Natural and Unnatural RNA Linkages", K. A. Hoadley, W. E. Purtha, A. C. Wolf, A. Flynn-Charlebois, and S. K. Silverman, Biochemistry 2005, 44, 9217-9231. [pdf] [Supp Info]

35. "Synthesis of Amine- and Thiol-Modified Nucleoside Phosphoramidites for Site-Specific Introduction of Biophysical Probes into RNA", S. Jin, C. V. Miduturu, D. C. McKinney, and S. K. Silverman, J. Org. Chem. 2005, 70, 4284-4299. [pdf] [Supp Info]

34. "A Deoxyribozyme That Forms a Three-Helix-Junction Complex With Its RNA Substrates and Has General RNA Branch-Forming Activity", R. L. Coppins and S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 2900-2907. [pdf] [Supp Info]

33. "Parallel Selections in Vitro Reveal a Preference for 2’-5’ RNA Ligation By Deoxyribozyme-Mediated Opening of a 2’,3’-Cyclic Phosphate", D. R. Semlow and S. K. Silverman, J. Mol. Evol. 2005, 61, 207-215. [pdf]

32. "Directing the Outcome of Deoxyribozyme Selections to Favor Native 3'-5' RNA Ligation", Y. Wang and S. K. Silverman, Biochemistry 2005, 44, 3017-3023. [pdf] [Supp Info]

31. "Rational Modification of a Selection Strategy Leads to Deoxyribozymes that Create Native 3’-5’ RNA Linkages", R. L. Coppins and S. K. Silverman, J. Am. Chem. Soc. 2004, 126, 16426-16432. [pdf] [Supp Info]

30. "Deoxyribozymes: DNA catalysts for bioorganic chemistry", S. K. Silverman, Org. Biomol. Chem. 2004, 2, 2701-2706 (invited review). [pdf] [journal color plate] 

29. "Site-Specific Fluorescent Labeling of Large RNAs with Pyrene", M. K. Smalley and  S. K. Silverman, in Current Protocols in Nucleic Acid Chemistry 2004, Unit 11.11 (Wiley). [pdf] 

28. "Practical and General Synthesis of 5'-Adenylated RNA (5'-AppRNA)", S. K. Silverman, RNA 2004, 10, 731-746. [pdf] 

27. "Structure-Function Correlations Derived from Faster Variants of an RNA Ligase Deoxyribozyme", T. K. Prior, D. R. Semlow, A. Flynn-Charlebois, I. Rashid, and S. K. Silverman, Nucleic Acids Res. 2004, 32, 1075-1082. [pdf] [Supp Info]

26. "A DNA Enzyme that Mimics the First Step of RNA Splicing", R. L. Coppins  and S. K. Silverman, Nature Struct. Mol. Biol. 2004, 11, 270-274. [pdf] [Supp Info]

25. "Breaking Up is Easy to Do (If You're a DNA Enzyme that Cleaves RNA)", S. K. Silverman, Chem. Biol. 2004, 11, 7-8 (invited commentary). [pdf] 

24. "Characterization of Deoxyribozymes that Synthesize Branched RNA", Y. Wang and S. K. Silverman, Biochemistry 2003, 42, 15252-15263. [pdf] [Supp Info]

23. "Optimization and Generality of a Small Deoxyribozyme that Ligates RNA", B. L. Ricca, A. C. Wolf, and S. K. Silverman, J. Mol. Biol. 2003, 330, 1015-1025. [pdf] [Supp Info]

22. "Deoxyribozymes that Synthesize Branched and Lariat RNA", Y. Wang and S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 6880-6881. [pdf] [Supp Info] [UIUC Press Release]

21. "In Vitro Evolution of an RNA-Cleaving DNA Enzyme into an RNA Ligase Switches the Selectivity from 3'-5' to 2'-5'", A. Flynn-Charlebois, T. K. Prior, K. A. Hoadley, and S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 5346-5350. [pdf] [Supp Info]

20. "Rube Goldberg Goes (Ribo)nuclear? Molecular Switches and Sensors Made from RNA", S. K. Silverman, RNA 2003, 9, 377-383 (invited review). [pdf]

19. "Deoxyribozymes with 2'-5' RNA Ligase Activity", A. Flynn-Charlebois, Y. Wang, T. K. Prior, K. A. Hoadley, R. L. Coppins, A. C. Wolf, and S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 2444-2454. [pdf] [Supp Info]

18. "The GAAA Tetraloop/Receptor Interaction Contributes Differentially to Folding Thermodynamics and Kinetics for the P4-P6 RNA Domain", B. T. Young and S. K. Silverman, Biochemistry 2002, 41, 12271-12276. [pdf]


Publications listing last updated August 4, 2008