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Full publications list — Scott K. Silverman

[Click here for a full publications list WITHOUT 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]
 

Graphic for Publication #71 by Zelin & Silverman



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]
 

Graphic for Publication #70 by Kost, Gerdt, Pradeepkumar & Silverman



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]
 

Graphic for Publication #69 by Gerdt, Miduturu & Silverman



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]
 

Graphic for Publication #68 by Mui & Silverman



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]
 

Click here for a pdf file of Publication #67 by Silverman



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

Click here for a pdf file of Publication #66 by Silverman



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]
 

Click here for a pdf file of Publication #65 by Baum & Silverman



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]
 

Click here for a pdf file of Publication #64 by Chandra & Silverman



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]
[Featured as a Research Highlight in the Mar. 2008 issue of Nature Chemical Biology]
 

Click here for a pdf file of Publication #63 by Pradeepkumar, Höbartner, Baum & Silverman



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]
 

Click here for a pdf file of Publication #62 by Patel, Baum & Silverman



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

Click here for a pdf file of Publication #61 by Höbartner & Silverman



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]
 

Click here for a pdf file of Publication #60 by Zelin & Silverman



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]
 

Click here for a pdf file of Publication #59 by Höbartner & Silverman



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]
[Chem. Commun. "Hot Article" feature story]
 

Click here for a pdf file of Publication #58 by Höbartner, Pradeepkumar, & Silverman



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]
 

Click here for a pdf file of Publication #57 by Pratico & Silverman



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]
 

Click here for a pdf file of Publication #56 by Baum & Silverman



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]
 

Click here for a pdf file of Publication #55 by Silverman



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]
 

Click here for a pdf file of Publication #54 by Blose, Silverman & Bevilacqua



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]
 

Click here for a pdf file of Publication #53 by Silverman



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]
 

Click here for a pdf file of Publication #52 by Silverman



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]
 

Click here for a pdf file of Publication #51 by Silverman & Hergenrother



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]
 

Click here for a pdf file of Publication #50 by Wang & Silverman



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, 5774-5777. [pdf] [Supp Info] [PubMed entry]
 

Click here for a pdf file of Publication #49 by Miduturu & Silverman



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]
 

Click here for a pdf file of Publication #48 by Wang & Silverman



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]
 

Click here for a pdf file of Publication #47 by Zelin, Wang & Silverman



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]
 

Click here for a pdf file of Publication #46 by Smalley & Silverman



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]
[RSC Chemistry World highlight]
[UIUC College of LAS News highlight]
 

Click here for a pdf file of Publication #45 by Miduturu & Silverman



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

Click here for a pdf file of Publication #44 by Wang & Silverman



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

Click here for a pdf file of Publication #43 by Silverman



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]
 

Click here for a pdf file of Publication #42 by Höbartner & Silverman



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]
 

Click here for a pdf file of Publication #41 by Purtha et al.



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]
 

Click here for a pdf file of Publication #40 by Coppins & Silverman



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]
[UIUC press release]
[Front-page story in News-Gazette (Champaign, Illinois), Sunday, July 17, 2005: newspaper website link]
[Front-page story in News-Gazette (Champaign, Illinois), Sunday, July 17, 2005: PDF of newspaper story]
[Science Daily highlight]
[Daily Science News highlight]
[EurekAlert! highlight]
[Medical News Today highlight]
[Nanotechnology Now highlight]
[PhysOrg.com highlight]
[medilexicon.com highlight]
[bio.com highlight]
[Bioinfo Online highlight]
[Omniomix highlight]
 

Click here for a pdf file of Publication #39 by Miduturu & Silverman



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]
[Featured as a Research Highlight in the Sept. 2005 issue of Nature Chemical Biology]
 

Click here for a pdf file of Publication #38 by Wang & Silverman



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]
 

Click here for a pdf file of Publication #37 by Pratico, Wang & Silverman



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]
[Chosen as a Biochemistry "Hot Article" for July 2005]
 

Click here for a pdf file of Publication #36 by Hoadley, Purtha et al.



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]
 

Click here for a pdf file of Publication #35 by Jin, Miduturu et al.



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]
 

Click here for a pdf file of Publication #34 by Coppins & Silverman



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]
 

Click here for a pdf file of Publication #33 by Semlow & Silverman



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]
 

Click here for a pdf file of Publication #32 by Wang & Silverman



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]
 

Click here for a pdf file of Publication #31 by Coppins & Silverman



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]
 

Click here for a pdf file of Publication #30 by Silverman



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]
 

Click here for a pdf file of Publication #28 by Silverman



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]
 

Click here for a pdf file of Publication #27 by Prior et al.



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]
 

Click here for a pdf file of Publication #26 by Coppins & Silverman



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]
 

Click here for a pdf file of Publication #24 by Wang & Silverman



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]
 

Click here for a pdf file of Publication #23 by Ricca, Wolf & Silverman



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] [PubMed entry]
[UIUC press release]
[UIUC College of LAS news story]
[Science Daily highlight]
[EurekAlert! highlight]
[Innovations Report highlight]
 

Click here for a pdf file of Publication #22 by Wang & Silverman



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]
 

Click here for a pdf file of Publication #21 by Flynn-Charlebois et al.



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]
 

Click here for a pdf file of Publication #20 by Silverman



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]
 

Click here for a pdf file of Publication #19 by Flynn-Charlebois et al.



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]
 

Click here for a pdf file of Publication #18 by Young & Silverman



17. "An Early Transition State for Folding of the P4-P6 RNA Domain", S. K. Silverman and T. R. Cech, RNA 2001, 7, 161-166. [pdf]

16. "Multiple Folding Pathways for the P4-P6 RNA Domain", S. K. Silverman, M. L. Deras, S. A. Woodson, S. A. Scaringe, and T. R. Cech, Biochemistry 2000, 39, 12465-12475. [pdf]

15. "Quantifying the Energetic Interplay of RNA Tertiary and Secondary Structure Interactions", S. K. Silverman, M. Zheng, M. Wu, I. Tinoco, Jr., and T. R. Cech, RNA 1999, 5, 1665-1674. [pdf]

14. "RNA Tertiary Folding Monitored by Fluorescence of Covalently Attached Pyrene", S. K. Silverman and T. R. Cech, Biochemistry 1999, 38, 14224-14237. [pdf] [Supp Info]

13. "Energetics and Cooperativity of Tertiary Hydrogen Bonds in RNA Structure", S. K. Silverman and T. R. Cech, Biochemistry 1999, 38, 8691-8702. [pdf] [Supp Info]

12. "Asymmetrical Contributions of Subunit Pore Regions to Ion Selectivity in an Inward Rectifier K+ channel", S. K. Silverman, H. A. Lester, and D. A. Dougherty, Biophys. J. 1998, 75, 1330-1339. [pdf]

11. "Flash Decaging of Tyrosine Sidechains in an Ion Channel", J. C. Miller, S. K. Silverman, P. M. England,  D. A. Dougherty, and H. A. Lester, Neuron 1998, 20, 619-624. [pdf]

10. "In Vivo Incorporation of Unnatural Amino Acids into Ion Channels in Xenopus Oocyte Expression System", M. W. Nowak, J. P. Gallivan, S. K. Silverman, C. G. Labarca, D. A. Dougherty, and H. A. Lester, Methods Enzymol. 1998, 233, 504-529. [pdf]

9. "A Regenerative Link in the Ionic Fluxes through the weaver Potassium Channel Underlies the Pathophysiology of the Mutation", S. K. Silverman, P. Kofuji, D. A. Dougherty, N. Davidson, and H. A. Lester, Proc. Natl. Acad. Sci. USA 1996, 93, 15429-15434. [pdf]

8. "Subunit Stoichiometry of a Heteromultimeric GIRK K+ Channel", S. K. Silverman, D. A. Dougherty, and H. A. Lester, J. Biol. Chem. 1996, 371, 30524-30528. [pdf]

7. "Dose-Response Relations for Unnatural Amino Acids at the Agonist Binding Site of the Nicotinic Acetylcholine Receptor: Tests with Novel Side Chains and with Several Agonists", P. C. Kearney, M. W. Nowak, W. Zhong, S. K. Silverman, H. A. Lester, and D. A. Dougherty, Mol. Pharm. 1996, 50, 1401-1412. [pdf]

6. "Do High-Spin Topology Rules Apply To Charged Polyradicals?  Theoretical And Experimental Evaluation Of Pyridiniums As Magnetic Coupling Units", A. P West, Jr., S. K. Silverman, and D. A. Dougherty, J. Am. Chem. Soc. 1996, 118, 1452-1463. [pdf] [Supp Info]

5. "Nicotinic Receptor Binding Site Probed with Unnatural Amino Acid Incorporation in Intact Cells", M. W. Nowak, P. C. Kearney, J. R. Sampson, M. E. Saks, C. G. Labarca, S. K. Silverman, W. Zhong, J. Thorson, J. N. Abelson, N. Davidson, P. G. Schultz, D. A. Dougherty, and H. A. Lester, Science 1995, 268, 439-442. [pdf]

4. "Conformational Effects on High-Spin Organic Molecules", S. K. Silverman and D. A. Dougherty, J. Phys. Chem. 1993, 118, 1452-1463. [pdf]

3. "New Organic Polymers and Molecules with Very High Spin States", M. W. Nowak, D. A. Dougherty, S. J. Jacobs, S. K. Silverman, M. M. Murray, D. A. Shultz, A. P. West, Jr., and J. A. Clites, Mol. Cryst. Liq. Cryst. 1993, 232, 289-304.[pdf]

2. "Reaction of C60 with Dimethyldioxirane—Formation of an Epoxide and a 1,3-Dioxolane Derivative", Y. Elemes, S. K. Silverman, C. Sheu, M. Kao, C. S. Foote, M. M. Alvarez, and R. L. Whetten, Angew. Chemie, Int. Ed. Engl. 1992, 31, 351-353. [pdf]

1. "Singlet Oxygen and Electron-Transfer Mechanisms in the Dicyanoanthracene-Sensitized Photooxidation of 2,3-Diphenyl-1,4-Dioxene", S. K. Silverman and C. S. Foote, J. Am. Chem. Soc. 1991, 113, 7672-7675. [pdf]


Last updated May 22, 2009