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

[Journals List]  [Group Meetings]  [Group Pictures]  [CV & Contact Info]

[SKS Lab Home]  [SKS Lab People]  [SKS Lab Publications]

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.

Overview of Silverman lab research

DNA as a catalyst DNA as a constraint DNA as a sensor

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

Defense Threat Reduction Agency (DTRA, part of Department of Defense)

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]  [Click here for a list of reviews and other publications]

75. "Deoxyribozymes: Selection Design and Serendipity in the Development of DNA Catalysts", S. K. Silverman, Acc. Chem. Res. 2009, 42, in press (invited review).

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

73. "Use of Deoxyribozymes in RNA Research", S. K. Silverman and D. A. Baum, Methods Enzymol. 2009, in press (invited review).

72. "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. [pdf] [Supp Info] [PubMed entry]

71. "Efficient Control of Group I Intron Ribozyme Catalysis By DNA Constraints", E. Zelin and S. K. Silverman, Chem. Commun. 2009, 767-769. [pdf] [Supp Info] [Chem. Commun. "Hot Article" feature story]

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, Org. Biomol. Chem. 2008, 6, 4391-4398. [pdf] [Supp Info] [PubMed entry]

69. "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. [pdf] [Supp Info] [PubMed entry]

68. "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. [pdf] [Supp Info] [PubMed entry]

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

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

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

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

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

55. "Artificial Functional Nucleic Acids: Aptamers, Ribozymes and Deoxyribozymes Identified by In Vitro Selection", S. K. Silverman, in Functional Nucleic Acids for Analytical Applications, Y. Li and Y. Lu, eds.; Springer Science + Business Media, LLC: New York, 2009. [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] [PubMed entry]

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] [PubMed entry]

52. "In Vitro Selection and Application of Nucleic Acid Enzymes (Ribozymes and Deoxyribozymes)", S. K. Silverman, in Wiley Encyclopedia of Chemical Biology, T. P. Begley, ed.; John Wiley & Sons,  2008. [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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

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

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

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] [PubMed entry]

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

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

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] [PubMed entry]

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] [PubMed entry]

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] [PubMed entry]

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

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] [PubMed entry]

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] [PubMed entry]

Publications listing last updated May 22, 2009