Contact information:
Scott K. Silverman
Department of Chemistry, Box 57-5
600 South Mathews Avenue
University of Illinois at Urbana-Champaign
Urbana, IL 61801

tel (217) 244-4489
fax (217) 244-8024
email scott@scs.illinois.edu

Research interests:
The Silverman laboratory is 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. Please visit our lab webpage for more information on our research.

http://www.scs.illinois.edu/silverman/

An in vitro translation, selection and amplification system for peptide nucleic acids. Brudno Y, Birnbaum ME, Kleiner RE, Liu DR Nat Chem Biol 2010 Feb 6(2):148-55 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 2 Feb 2010 The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Giuliodori AM, Di Pietro F, …, Gualerzi CO, Pon CL Mol Cell 2010 37:21-33 [full text] Selected by | Scott K Silverman / Hiroji Aiba Evaluated 21 Jan 2010 Site-specific covalent modification of RNA guided by functionality-transfer oligodeoxynucleotides. Onizuka K, Taniguchi Y, Sasaki S Bioconjug Chem 2009 Apr 20(4):799-803 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 4 Dec 2009 In silico selection of RNA aptamers. Chushak Y, Stone MO Nucleic Acids Res 2009 Jul 37(12):e87 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 4 Dec 2009 Site-selective scission of human genome by artificial restriction DNA cutter. Ito K, Katada H, Shigi N, Komiyama M Chem Commun (Camb) 2009 Nov 21 (43):6542-4 [abstract on PubMed] [related articles] [full text] Selected by | Scott K Silverman Evaluated 5 Nov 2009 PCR with an Expanded Genetic Alphabet. Malyshev DA, Seo YJ, Ordoukhanian P, Romesberg FE J Am Chem Soc 2009 Sep 29 [abstract on PubMed] [related articles] [full text] Selected by | Scott K Silverman Evaluated 8 Oct 2009 A DNAzyme with three protein-like functional groups: enhancing catalytic efficiency of M2+-independent RNA cleavage. Hollenstein M, Hipolito CJ, Lam CH, Perrin DM Chembiochem 2009 Aug 17 10(12):1988-92 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 27 Aug 2009 UNA (unlocked nucleic acid): a flexible RNA mimic that allows engineering of nucleic acid duplex stability. Langkjaer N, Pasternak A, Wengel J Bioorg Med Chem 2009 Aug 1 17(15):5420-5 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 6 Aug 2009 One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors. Huang Z, Pei W, …, Shi H, Niu L Nucleic Acids Res 2009 Jul 37(12):4022-32 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 27 Jul 2009 The effect of microwave irradiation on DNA hybridization. Edwards WF, Young DD, Deiters A Org Biomol Chem 2009 Jun 21 7(12):2506-8 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 11 Jun 2009 Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization. Young DD, Lusic H, Lively MO, Deiters A Nucleic Acids Res 2009 May 37(8):e58 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 14 May 2009 A deoxyribozyme, Sero1C, uses light and serotonin to repair diverse pyrimidine dimers in DNA. Thorne RE, Chinnapen DJ, Sekhon GS, Sen D J Mol Biol 2009 Apr 24 388(1):21-9 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 29 Apr 2009 Synthesis and polymerase chain reaction amplification of DNA strands containing an unnatural triazole linkage. El-Sagheer AH, Brown T J Am Chem Soc 2009 Mar 25 131(11):3958-64 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 16 Mar 2009 Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. Pitt JN, Ferré-D'Amaré AR J Am Chem Soc 2009 Mar 18 131(10):3532-40 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Michael Yarus Evaluated 26 Feb 2009 Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics. Gherghe CM, Leonard CW, …, Dokholyan NV, Weeks KM J Am Chem Soc 2009 Feb 4 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 12 Feb 2009 DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides. Schlosser K, Li Y Nucleic Acids Res 2009 Feb 37(2):413-20 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K. Silverman Evaluated 4 Feb 2009 Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes. Maksimoska J, Feng L, …, Marmorstein R, Meggers E J Am Chem Soc 2008 Oct 31 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 3 Dec 2008 Tetrazine Ligation: Fast Bioconjugation Based on Inverse-Electron-Demand Diels-Alder Reactivity. Blackman ML, Royzen M, Fox JM J Am Chem Soc 2008 Sep 18 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 25 Sep 2008 Improved procedure for direct coupling of carbohydrates to proteins via reductive amination. Gildersleeve JC, Oyelaran O, Simpson JT, Allred B Bioconjug Chem 2008 Jul 19(7):1485-90 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 24 Sep 2008 Thermolytic release of covalently linked DNA oligonucleotides and their conjugates from controlled-pore glass at near neutral pH. Grajkowski A, Cie¿lak J, …, Freedberg DI, Beaucage SL Bioconjug Chem 2008 Aug 19:1696-706 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 23 Sep 2008 Redesigned tetrads with altered hydrogen bonding patterns enable programming of quadruplex topologies. Benz A, Hartig JS Chem Commun (Camb) 2008 Sep 14 (34):4010-4012 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 2 Sep 2008 Site-selective blocking of PCR by a caged nucleotide leading to direct creation of desired sticky ends in the products. Tanaka K, Katada H, …, Kuzuya A, Komiyama M Chembiochem 2008 Sep 1 9(13):2120-6 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman / Michael Pirrung Evaluated 2 Sep 2008 Peptide mass fingerprinting using isotopically encoded photo-crosslinking amino acids. Wilkins BJ, Daggett KA, Cropp TA Mol Biosyst 2008 Sep 4(9):934-6 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 28 Aug 2008 Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Sando S, Narita A, Hayami M, Aoyama Y Chem Commun (Camb) 2008 Sep 7 (33):3858-60 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman / Günter Mayer Evaluated 27 Aug 2008 Single base interrogation by a fluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy. Cekan P, Sigurdsson ST Chem Commun (Camb) 2008 Aug 7 (29):3393-5 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 25 Jul 2008 Addressing the Numbers Problem in Directed Evolution. Reetz MT, Kahakeaw D, Lohmer R Chembiochem 2008 Jun 20 9(11):1797-1804 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 17 Jul 2008 Artificial DNA Made Exclusively of Nonnatural C-Nucleosides with Four Types of Nonnatural Bases. Doi Y, Chiba J, Morikawa T, Inouye M J Am Chem Soc 2008 Jun 11 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 17 Jun 2008 Probing the Active Site of a Diels-Alderase Ribozyme by Photoaffinity Cross-Linking. Wombacher R, Ja¿schke A J Am Chem Soc 2008 Jun 11 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 17 Jun 2008 Novel DNA Catalysts Based on G-Quadruplex Recognition. Tang Z, Gonçalves DP, …, Marx A, Hartig JS Chembiochem 2008 Mar 18 9(7):1061-1064 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 2 May 2008 Efficient Site-Specific Labeling of Proteins via Cysteines. Kim Y, Ho SO, …, Collart FR, Weiss S Bioconjug Chem 2008 Mar 19 19(3):786-791 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 31 Mar 2008 Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Wieland M, Hartig JS Angew Chem Int Ed Engl 2008 47(14):2604-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 31 Mar 2008 Synthesis of polyester by means of genetic code reprogramming. Ohta A, Murakami H, Higashimura E, Suga H Chem Biol 2007 Dec 14(12):1315-22 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 23 Jan 2008 Synthesis and Quantitative Evaluation of Glycero-D-manno-heptose Binding to Concanavalin A by Fluorous-Tag Assistance. Jaipuri FA, Collet BY, Pohl NL Angew Chem Int Ed Engl 2008 Jan 18 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 21 Jan 2008 Random Walks to Synthetic Riboswitches-A High-Throughput Selection Based on Cell Motility. Topp S, Gallivan JP Chembiochem 2007 Dec 20 9(2):210-213 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 21 Jan 2008 Intercalation Is Not Required for DNA Light-Switch Behavior. Lutterman DA, Chouai A, …, Dunbar KR, Turro C J Am Chem Soc 2008 Jan 8 0 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 21 Jan 2008 Tertiary Interactions Determine the Accuracy of RNA Folding. Chauhan S, Woodson SA J Am Chem Soc 2008 Jan 8 [Epub ahead of print] [abstract on PubMed] [related articles] [full text] Selected by | Thorsten Dieckmann / Scott K. Silverman Evaluated 21 Jan 2008 Isostable DNA. Ahlborn C, Siegmund K, Richert C J Am Chem Soc 2007 Dec 12 129(49):15218-32 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 3 Jan 2008 Pyrene modification leads to increased catalytic activity in minimal hammerhead ribozymes. Looser V, Langenegger SM, Häner R, Hartig JS Chem Commun (Camb) 2007 Nov 14 (42):4357-9 [abstract on PubMed] [related articles] [full text] Selected by | Scott K. Silverman Evaluated 2 Jan 2008 A small molecule microarray platform to select RNA internal loop-ligand interactions. Childs-Disney JL, Wu M, …, Aminova O, Disney MD ACS Chem Biol 2007 Nov 20 2(11):745-54 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman / Janet Morrow Evaluated 27 Nov 2007 Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. Ying BW, Fourmy D, Yoshizawa S RNA 2007 Nov 13(11):2042-50 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 5 Nov 2007 Orientational and Dynamical Heterogeneity of Rhodamine 6G Terminally Attached to a DNA Helix Revealed by NMR and Single-Molecule Fluorescence Spectroscopy. Neubauer H, Gaiko N, …, Griesinger C, Volkmer A J Am Chem Soc 2007 Sep 27 Epub ahead of print [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K. Silverman Evaluated 3 Oct 2007 Development of a small peptide tag for covalent labeling of proteins. Tanaka F, Fuller R, …, Gobuty S, Barbas CF Bioconjug Chem 2007 Jul-Aug 18(4):1318-24 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K. Silverman Evaluated 23 Aug 2007 A general strategy to solve the phase problem in RNA crystallography. Keel AY, Rambo RP, Batey RT, Kieft JS Structure 2007 Jul 15(7):761-72 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Martin Egli Evaluated 23 Jul 2007 New triphosphate conjugates bearing reporter groups: labeling of DNA fragments for microarray analysis. Alexandrova LA, Jasko MV, …, Zasedatelev AS, Kukhanova MK Bioconjug Chem 2007 May-Jun 18(3):886-93 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 12 Jul 2007 Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2'-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate. Shiba Y, Masuda H, …, Ohgi T, Yano J Nucleic Acids Res 2007 35(10):3287-96 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 12 Jun 2007 A nucleoside triphosphate for site-specific labelling of DNA by the Staudinger ligation. Weisbrod SH, Marx A Chem Commun (Camb) 2007 May 14 (18):1828-30 [abstract on PubMed] [related articles] [full text] Selected by | Scott K Silverman Evaluated 9 May 2007 Novel photolabile protecting group for carbonyl compounds. Wang P, Hu H, Wang Y Org Lett 2007 Apr 12 9(8):1533-5 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 26 Mar 2007 Group II intron folding under near-physiological conditions: collapsing to the near-native state. Fedorova O, Waldsich C, Pyle AM J Mol Biol 2007 Mar 2 366(4):1099-114 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 21 Feb 2007 SELEX and dynamic combinatorial chemistry interplay for the selection of conjugated RNA aptamers. Bugaut A, Toulmé JJ, Rayner B Org Biomol Chem 2006 Nov 21 4(22):4082-8 [abstract on PubMed] [related articles] [order article] Selected by | Peter Wipf / Scott K Silverman / Günter Mayer Evaluated 5 Feb 2007 Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes. Amontov S, Jäschke A Nucleic Acids Res 2006 34(18):5032-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 3 Jan 2007 A comparative study of bioorthogonal reactions with azides. Agard NJ, Baskin JM, …, Lo A, Bertozzi CR ACS Chem Biol 2006 Nov 21 1(10):644-8 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 6 Dec 2006 Dynamic assembly of primers on nucleic acid templates. Leal NA, Sukeda M, Benner SA Nucleic Acids Res 2006 34(17):4702-10 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 10 Nov 2006 Self-assembly of a group I intron from inactive oligonucleotide fragments. Hayden EJ, Lehman N Chem Biol 2006 Aug 13(8):909-18 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 5 Sep 2006 Quadruplex-based molecular beacons as tunable DNA probes. Bourdoncle A, Estévez Torres A, …, Jullien L, Mergny JL J Am Chem Soc 2006 Aug 30 128(34):11094-105 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 5 Sep 2006 The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. Lee JC, Gutell RR, Russell R J Mol Biol 2006 Jul 28 360(5):978-88 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 31 Jul 2006 Aptamer mediated siRNA delivery. Chu TC, Twu KY, Ellington AD, Levy M Nucleic Acids Res 2006 34(10):e73 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 17 Jul 2006 Aptamers selected for higher-affinity binding are not more specific for the target ligand. Carothers JM, Oestreich SC, Szostak JW J Am Chem Soc 2006 Jun 21 128(24):7929-37 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Milan Stojanovic / Niles Lehman Evaluated 6 Jun 2006 A general approach for the identification of site-specific RNA binders by 19F NMR spectroscopy: proof of concept. Kreutz C, Kählig H, Konrat R, Micura R Angew Chem Int Ed Engl 2006 May 19 45(21):3450-3 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 17 May 2006 Deoxyribozymes that recode sequence information. Tabor JJ, Levy M, Ellington AD Nucleic Acids Res 2006 34(8):2166-72 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 8 May 2006 Conversion of a ribozyme to a deoxyribozyme through in vitro evolution. Paul N, Springsteen G, Joyce GF Chem Biol 2006 Mar 13(3):329-38 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 4 May 2006 Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores. Chiuman W, Li Y J Mol Biol 2006 Mar 31 357(3):748-54 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 24 Mar 2006 An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. Baker BR, Lai RY, …, Heeger AJ, Plaxco KW J Am Chem Soc 2006 Mar 15 128(10):3138-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 21 Feb 2006 Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity. Anderson PC, Mecozzi S Nucleic Acids Res 2005 33(22):6992-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 11 Jan 2006 In vitro selection of DNA aptamers binding ethanolamine. Mann D, Reinemann C, Stoltenburg R, Strehlitz B Biochem Biophys Res Commun 2005 Dec 30 338(4):1928-34 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 11 Jan 2006 Site-specific fluorescent and affinity labelling of RNA by using a small engineered twin ribozyme. Vauléon S, Ivanov SA, Gwiazda S, Müller S Chembiochem 2005 Dec 6(12):2158-62 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 14 Dec 2005 Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. Fedorova O, Pyle AM EMBO J 2005 Nov 16 24(22):3906-16 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 8 Nov 2005 Thermal difference spectra: a specific signature for nucleic acid structures. Mergny JL, Li J, …, Amrane S, Chaires JB Nucleic Acids Res 2005 33(16):e138 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 28 Sep 2005 The kinetics of ligand binding by an adenine-sensing riboswitch. Wickiser JK, Cheah MT, Breaker RR, Crothers DM Biochemistry 2005 Oct 11 44(40):13404-14 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Thorsten Dieckmann Evaluated 19 Sep 2005 Facile conversion of aptamers into sensors using a 2'-ribose-linked fluorophore. Merino EJ, Weeks KM J Am Chem Soc 2005 Sep 21 127(37):12766-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 30 Aug 2005 Ribose 2'-F labeling: a simple tool for the characterization of RNA secondary structure equilibria by 19F NMR spectroscopy. Kreutz C, Kählig H, Konrat R, Micura R J Am Chem Soc 2005 Aug 24 127(33):11558-9 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 3 Aug 2005 A new RNA synthetic method with a 2'-O-(2-cyanoethoxymethyl) protecting group. Ohgi T, Masutomi Y, …, Shiba Y, Yano J Org Lett 2005 Aug 4 7(16):3477-80 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Michal Lebl Evaluated 8 Jul 2005 Molecular beacons with a homo-DNA stem: improving target selectivity. Crey-Desbiolles C, Ahn DR, Leumann CJ Nucleic Acids Res 2005 33(8):e77 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 8 Jun 2005 Photoinduced transcription by using temporarily mismatched caged oligonucleotides. Kröck L, Heckel A Angew Chem Int Ed Engl 2005 Jan 7 44(3):471-3 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 24 May 2005 Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline. Anderson PC, Mecozzi S J Am Chem Soc 2005 Apr 20 127(15):5290-1 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Burckhard Seelig / Michael Yarus Evaluated 7 Apr 2005 Nucleobase participation in ribozyme catalysis. Zhao ZY, McLeod A, …, Kurihara T, Lilley DM J Am Chem Soc 2005 Apr 13 127(14):5026-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 23 Mar 2005 8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2'-deoxyribosyl-2-aminopurine with improved properties. Ben Gaied N, Glasser N, …, Burger A, Mély Y Nucleic Acids Res 2005 33(3):1031-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 1 Mar 2005 A fluorescent probe designed for studying protein conformational change. Cohen BE, Pralle A, …, Isacoff EY, Jan LY Proc Natl Acad Sci U S A 2005 Jan 25 102(4):965-70 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 25 Jan 2005 Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. Lee JC, Gutell RR J Mol Biol 2004 Dec 10 344(5):1225-49 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Oliver Weichenrieder Evaluated 15 Dec 2004 De novo synthesis and development of an RNA enzyme. Ikawa Y, Tsuda K, Matsumura S, Inoue T Proc Natl Acad Sci U S A 2004 Sep 21 101(38):13750-5 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 18 Oct 2004 Reduced contact order and RNA folding rates. Sosnick TR, Pan T J Mol Biol 2004 Oct 1 342(5):1359-65 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 24 Sep 2004 Crystal structure of a continuous three-dimensional DNA lattice. Paukstelis PJ, Nowakowski J, Birktoft JJ, Seeman NC Chem Biol 2004 Aug 11(8):1119-26 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Eric Westhof Evaluated 24 Aug 2004 Origin of the intrinsic rigidity of DNA. Mills JB, Hagerman PJ Nucleic Acids Res 2004 32(13):4055-9 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman / Jim Maher Evaluated 18 Aug 2004 Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Schlosser K, Li Y Biochemistry 2004 Aug 3 43(30):9695-707 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Niles Lehman Evaluated 3 Aug 2004 Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography. Cheong HK, Hwang E, …, Choi BS, Cheong C Nucleic Acids Res 2004 32(10):e84 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 2 Jul 2004 A general method for rapid and nondenaturing purification of RNAs. Kieft JS, Batey RT RNA 2004 Jun 10(6):988-95 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 27 May 2004 Directed evolution of protein enzymes using nonhomologous random recombination. Bittker JA, Le BV, Liu JM, Liu DR Proc Natl Acad Sci U S A 2004 May 4 101(18):7011-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | James Stivers / Scott K Silverman Evaluated 12 May 2004 Anion binding to nucleic acids. Auffinger P, Bielecki L, Westhof E Structure 2004 Mar 12(3):379-88 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 14 Apr 2004 Control of gene expression by a natural metabolite-responsive ribozyme. Winkler WC, Nahvi A, …, Collins JA, Breaker RR Nature 2004 Mar 18 428(6980):281-6 [abstract on PubMed] [related articles] [full text] [order article] Selected by | David M.J. Lilley / Richard Maraia / Samuel Butcher / Eric Westhof / Peter Unrau / Scott K Silverman / Fritz Eckstein / Burckhard Seelig / Andrew D Sharrocks / Janet Morrow / Andres Jaschke / John Burke / Reinhard Luehrmann Evaluated 26 Mar 2004 A new algorithm for RNA secondary structure design. Andronescu M, Fejes AP, …, Hoos HH, Condon A J Mol Biol 2004 Feb 20 336(3):607-24 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 4 Mar 2004 Dinucleotide junction cleavage versatility of 8-17 deoxyribozyme. Cruz RP, Withers JB, Li Y Chem Biol 2004 Jan 11(1):57-67 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Niles Lehman Evaluated 10 Feb 2004 Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA. Cavaluzzi MJ, Borer PN Nucleic Acids Res 2004 32(1):e13 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 3 Feb 2004 Efficient, pH-dependent RNA ligation by the VS ribozyme in trans. McLeod AC, Lilley DM Biochemistry 2004 Feb 3 43(4):1118-25 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 2 Feb 2004 The three-dimensional architecture of the class I ligase ribozyme. Bergman NH, Lau NC, …, Westhof E, Bartel DP RNA 2004 Feb 10(2):176-84 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 2 Feb 2004 An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme. Su LJ, Brenowitz M, Pyle AM J Mol Biol 2003 Dec 5 334(4):639-52 [abstract on PubMed] [related articles] [order article] Selected by | Thorsten Dieckmann / Scott K Silverman Evaluated 9 Jan 2004 In vitro evolution of functional DNA using capillary electrophoresis. Mendonsa SD, Bowser MT J Am Chem Soc 2004 Jan 14 126(1):20-1 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 12 Dec 2003 Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Murakami H, Kourouklis D, Suga H Chem Biol 2003 Nov 10(11):1077-84 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 10 Dec 2003 Selection of the simplest RNA that binds isoleucine. Lozupone C, Changayil S, Majerfeld I, Yarus M RNA 2003 Nov 9(11):1315-22 [abstract on PubMed] [related articles] [FREE full text] Selected by | Niles Lehman / Scott K Silverman Evaluated 18 Nov 2003 Solid-phase oligodeoxynucleotide synthesis: a two-step cycle using peroxy anion deprotection. Sierzchala AB, Dellinger DJ, …, Yamada CM, Caruthers MH J Am Chem Soc 2003 Nov 5 125(44):13427-41 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 4 Nov 2003 Toward the development of new photolabile protecting groups that can rapidly release bioactive compounds upon photolysis with visible light. Banerjee A, Grewer C, …, Carpenter BK, Hess GP J Org Chem 2003 Oct 31 68(22):8361-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 31 Oct 2003 Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding. Blount KF, Tor Y Nucleic Acids Res 2003 Oct 1 31(19):5490-500 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 23 Sep 2003 A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. Breaker RR, Emilsson GM, …, Roth A, Sudarsan N RNA 2003 Aug 9(8):949-57 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 12 Aug 2003 Small structural costs for evolution from RNA to RNP-based catalysis. Garcia I, Weeks KM J Mol Biol 2003 Aug 1 331(1):57-73 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 5 Aug 2003 General plasmids for producing RNA in vitro transcripts with homogeneous ends. Walker SC, Avis JM, Conn GL Nucleic Acids Res 2003 Aug 1 31(15):e82 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 5 Aug 2003 Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction. Xiao M, Leibowitz MJ, Zhang Y Nucleic Acids Res 2003 Jul 15 31(14):3901-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 21 Jul 2003 Site-directed alteration of RNA sequence mediated by an engineered twin ribozyme. Welz R, Bossmann K, …, Fritz HJ, Müller S Angew Chem Int Ed Engl 2003 May 30 42(21):2424-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Kevin J Luebke / Scott K Silverman Evaluated 10 Jun 2003 Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. Bartley LE, Zhuang X, …, Chu S, Herschlag D J Mol Biol 2003 May 16 328(5):1011-26 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 13 May 2003 A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability. Adamidi C, Fedorova O, Pyle AM Biochemistry 2003 Apr 1 42(12):3409-18 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 27 Mar 2003 Nanometer distance measurements on RNA using PELDOR. Schiemann O, Weber A, …, Prisner TF, Sigurdsson ST J Am Chem Soc 2003 Mar 26 125(12):3434-5 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 24 Mar 2003 Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Nakano S, Cerrone AL, Bevilacqua PC Biochemistry 2003 Mar 18 42(10):2982-94 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman / Janet Morrow Evaluated 17 Mar 2003 Hybridization kinetics and thermodynamics of molecular beacons. Tsourkas A, Behlke MA, Rose SD, Bao G Nucleic Acids Res 2003 Feb 15 31(4):1319-30 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 19 Feb 2003 Automated design of specificity in molecular recognition. Havranek JJ, Harbury PB Nat Struct Biol 2003 Jan 10(1):45-52 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Scott K Silverman Evaluated 13 Jan 2003 Energetics of hydrogen bond networks in RNA: hydrogen bonds surrounding G+1 and U42 are the major determinants for the tertiary structure stability of the hairpin ribozyme. Klostermeier D, Millar DP Biochemistry 2002 Dec 3 41(48):14095-102 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 13 Jan 2003 Binding to an RNA aptamer changes the charge distribution and conformation of malachite green. Nguyen DH, DeFina SC, Fink WH, Dieckmann T J Am Chem Soc 2002 Dec 18 124(50):15081-4 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 13 Dec 2002 A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation. Ueyama H, Takagi M, Takenaka S J Am Chem Soc 2002 Dec 4 124(48):14286-7 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 3 Dec 2002 Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups. Chamberlin SI, Merino EJ, Weeks KM Proc Natl Acad Sci U S A 2002 Nov 12 99(23):14688-93 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 21 Nov 2002 Wavelength-controlled orthogonal photolysis of protecting groups. Blanc A, Bochet CG J Org Chem 2002 Aug 9 67(16):5567-77 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 21 Oct 2002 Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. Proctor DJ, Schaak JE, …, Falzone CJ, Bevilacqua PC Biochemistry 2002 Oct 8 41(40):12062-75 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 21 Oct 2002 Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing. Childs JL, Disney MD, Turner DH Proc Natl Acad Sci U S A 2002 Aug 20 99(17):11091-6 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 19 Sep 2002 Specificity of RNA-RNA helix recognition. Battle DJ, Doudna JA Proc Natl Acad Sci U S A 2002 Sep 3 99(18):11676-81 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman / Thorsten Dieckmann / Peter Qin / Douglas Turner Evaluated 10 Sep 2002 Modular engineering of a Group I intron ribozyme. Ohuchi SJ, Ikawa Y, Shiraishi H, Inoue T Nucleic Acids Res 2002 Aug 1 30(15):3473-80 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 9 Aug 2002 The affinity of magnesium binding sites in the Bacillus subtilis RNase P x pre-tRNA complex is enhanced by the protein subunit. Kurz JC, Fierke CA Biochemistry 2002 Jul 30 41(30):9545-58 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 25 Jul 2002 Aminoacyl-tRNA synthesis by a resin-immobilized ribozyme. Murakami H, Bonzagni NJ, Suga H J Am Chem Soc 2002 Jun 19 124(24):6834-5 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 9 Jul 2002 The rate-limiting step in the folding of a large ribozyme without kinetic traps. Fang XW, Thiyagarajan P, Sosnick TR, Pan T Proc Natl Acad Sci U S A 2002 Jun 25 99(13):8518-23 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 28 Jun 2002 Design, construction, and analysis of a novel class of self-folding RNA. Ikawa Y, Fukada K, …, Shiraishi H, Inoue T Structure 2002 Apr 10(4):527-34 [abstract on PubMed] [related articles] [order article] Selected by | Peter Qin / Scott K Silverman Evaluated 19 Jun 2002 Allosteric hammerhead ribozyme TRAPs. Burke DH, Ozerova ND, Nilsen-Hamilton M Biochemistry 2002 May 28 41(21):6588-94 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 24 May 2002 Rapid compaction during RNA folding. Russell R, Millett IS, …, Herschlag D, Pollack L Proc Natl Acad Sci U S A 2002 Apr 2 99(7):4266-71 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman / Niles Lehman Evaluated 9 Apr 2002 Structural insights into group II intron catalysis and branch-site selection. Zhang L, Doudna JA Science 2002 Mar 15 295(5562):2084-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Samuel Butcher / Scott K Silverman / Peter Qin / Oliver Weichenrieder Evaluated 21 Mar 2002 Synthesis and application of a chain-terminating dinucleotide mRNA cap analog. Peng ZH, Sharma V, Singleton SF, Gershon PD Org Lett 2002 Jan 24 4(2):161-4 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 25 Feb 2002 5'-sulfhydryl-modified RNA: initiator synthesis, in vitro transcription, and enzymatic incorporation. Zhang L, Sun L, …, Gottlieb RL, Zhang B Bioconjug Chem 2001 Nov-Dec 12(6):939-48 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 18 Feb 2002 Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. Du Q, Carrasco N, …, Egli M, Huang Z J Am Chem Soc 2002 Jan 9 124(1):24-5 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 24 Jan 2002 An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini. Jones FD, Ryder SP, Strobel SA Nucleic Acids Res 2001 Dec 15 29(24):5115-20 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman Evaluated 18 Jan 2002 A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase. Stage-Zimmermann TK, Uhlenbeck OC Nat Struct Biol 2001 Oct 8(10):863-7 [abstract on PubMed] [related articles] [full text] [order article] Selected by | Dipankar Sen / Scott K Silverman Evaluated 10 Jan 2002 X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A). Deng J, Xiong Y, Sundaralingam M Proc Natl Acad Sci U S A 2001 Nov 20 98(24):13665-70 [abstract on PubMed] [related articles] [FREE full text] Selected by | P Shing Ho / Scott K Silverman Evaluated 20 Dec 2001 Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. Sherlin LD, Bullock TL, …, Uhlenbeck OC, Scaringe SA RNA 2001 Nov 7(11):1671-8 [abstract on PubMed] [related articles] [FREE full text] Selected by | Scott K Silverman / Stephen Holbrook Evaluated 20 Dec 2001 Diels--Alder bioconjugation of diene-modified oligonucleotides. Hill KW, Taunton-Rigby J, …, Anziano DJ, Sebesta DP J Org Chem 2001 Aug 10 66(16):5352-8 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 21 Sep 2001 Biological relevance of metal binding before protein folding. Pozdnyakova I, Wittung-Stafshede P J Am Chem Soc 2001 Oct 17 123(41):10135-6 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 4 Nov 2001 Synthesis of 5'-deoxy-5'-thioguanosine-5'-monophosphorothioate and its incorporation into RNA 5'-termini. Zhang B, Cui Z, Sun L Org Lett 2001 Jan 25 3(2):275-8 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 20 Sep 2001 Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides. Lenox HJ, McCoy CP, Sheppard TL Org Lett 2001 Jul 26 3(15):2415-8 [abstract on PubMed] [related articles] [order article] Selected by | Scott K Silverman Evaluated 4 Sep 2001

^Top  Back to Faculty Members