Scott K Silverman

1991 …2017
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Research Output 1991 2017

Article

Adenosine is inherently favored as the branch-site RNA nucleotide in a structural context that resembles natural RNA splicing

Zelin, E., Wang, Y. & Silverman, S. K., Mar 7 2006, In : Biochemistry. 45, 9, p. 2767-2771 5 p.

Research output: Contribution to journalArticle

RNA Splicing
Adenosine
Nucleotides
RNA
Catalytic DNA
Catalytic DNA
RNA
substrate
Nucleotides
Substrates

A deoxyribozyme that synthesizes 2′,5′-branched RNA with any branch-site nucleotide

Pratico, E. D., Wang, Y. & Silverman, S. K., Oct 18 2005, In : Nucleic acids research. 33, 11, p. 3503-3512 10 p.

Research output: Contribution to journalArticle

Catalytic DNA
Nucleotides
RNA
Ligation
Biochemical Phenomena

A DNA enzyme that mimics the first step of RNA splicing

Coppins, R. L. & Silverman, S. K., Mar 1 2004, In : Nature Structural and Molecular Biology. 11, 3, p. 270-274 5 p.

Research output: Contribution to journalArticle

RNA Splicing
DNA
Enzymes
Hydroxyl Radical
Catalytic RNA

A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation

Chu, C. C., Wong, O. Y. I. & Silverman, S. K., Sep 5 2014, In : Chembiochem : a European journal of chemical biology. 15, 13, p. 1905-1910 6 p.

Research output: Contribution to journalArticle

Peptide Nucleic Acids
Peptides
Catalytic DNA
DNA
Nucleic Acids

A general two-step strategy to synthesize lariat RNAs

Wang, Y. & Silverman, S. K., Feb 1 2006, In : RNA. 12, 2, p. 313-321 9 p.

Research output: Contribution to journalArticle

RNA
Catalytic DNA
Ligases

Allosteric control of ribozyme catalysis by using DNA constraints

Zelin, E. & Silverman, S. K., Nov 5 2007, In : ChemBioChem. 8, 16, p. 1907-1911 5 p.

Research output: Contribution to journalArticle

Catalytic RNA
Catalysis
RNA
DNA
hammerhead ribozyme

A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains

Dokukin, V. & Silverman, S. K., Aug 25 2014, In : Chemical Communications. 50, 66, p. 9317-9320 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Protein-Tyrosine Kinases
Catalysts
DNA
Nucleotide Aptamers

An early transition state for folding of the P4-P6 RNA domain

Silverman, S. K. & Cech, T. R., Feb 1 2001, In : RNA. 7, 2, p. 161-166 6 p.

Research output: Contribution to journalArticle

RNA
Thermodynamics
RNA Folding
Ions
Tetrahymena

A regenerative link in the ionic fluxes through the weaver potassium channel underlies the pathophysiology of the mutation

Silverman, S. K., Kofuji, P., Dougherty, D. A., Davidson, N. & Lester, H. A., Dec 24 1996, In : Proceedings of the National Academy of Sciences of the United States of America. 93, 26, p. 15429-15434 6 p.

Research output: Contribution to journalArticle

Potassium Channels
GTP-Binding Proteins
Mutation
Neurologic Mutant Mice
Inwardly Rectifying Potassium Channel

A simple molecular model for thermophilic adaptation of functional nucleic acids

Blose, J. M., Silverman, S. K. & Bevilacqua, P. C., Apr 10 2007, In : Biochemistry. 46, 14, p. 4232-4240 9 p.

Research output: Contribution to journalArticle

Molecular Models
Nucleic Acids
RNA
Free energy
Base Pairing

Assessing histidine tags for recruiting deoxyribozymes to catalyze peptide and protein modification reactions

Chu, C. C. & Silverman, S. K., Jan 1 2016, In : Organic and Biomolecular Chemistry. 14, 20, p. 4697-4703 7 p.

Research output: Contribution to journalArticle

His-His-His-His-His-His
Catalytic DNA
histidine
Histidine
peptides

Asymmetrical contributions of subunit pore regions to ion selectivity in an inward rectifier K+ channel

Silverman, S. K., Lester, H. A. & Dougherty, D. A., Sep 1998, In : Biophysical journal. 75, 3, p. 1330-1339 10 p.

Research output: Contribution to journalArticle

Inwardly Rectifying Potassium Channel
Tyrosine
Ions
Oocytes
Voltage-Gated Potassium Channels

Catalytic DNA with phosphatase activity

Chandrasekar, J. & Silverman, S. K., Apr 2 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 14, p. 5315-5320 6 p.

Research output: Contribution to journalArticle

Catalytic DNA
Phosphoric Monoester Hydrolases
DNA
Hydrolysis
Phosphoserine

Characterization of Deoxyribozymes That Synthesize Branched RNA

Wang, Y. & Silverman, S. K., Dec 30 2003, In : Biochemistry. 42, 51, p. 15252-15263 12 p.

Research output: Contribution to journalArticle

Catalytic DNA
Ligation
RNA
Substrates
Nucleotides

Conformational effects on high-spin organic molecules

Silverman, S. K. & Dougherty, D. A., Jan 1 1993, In : Journal of physical chemistry. 97, 50, p. 13273-13283 11 p.

Research output: Contribution to journalArticle

twisting
Ground state
Spin polarization
Molecules
Paramagnetic resonance

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2′,3′-cyclic phosphate RNA substrates

Kost, D. M., Gerdt, J. P., Pradeepkumar, P. I. & Silverman, S. K., Nov 24 2008, In : Organic and Biomolecular Chemistry. 6, 23, p. 4391-4398 8 p.

Research output: Contribution to journalArticle

Catalytic DNA
Regioselectivity
linkages
Ligation
phosphates

Convergent and general one-step DNA-catalyzed synthesis of multiply branched DNA

Mui, T. P. & Silverman, S. K., Dec 1 2008, In : Organic Letters. 10, 20, p. 4417-4420 4 p.

Research output: Contribution to journalArticle

deoxyribonucleic acid
Catalytic DNA
DNA
synthesis
Ribonucleotides

Covalent Tagging of Phosphorylated Peptides by Phosphate-Specific Deoxyribozymes

Sachdeva, A., Chandra, M., Chandrasekar, J. & Silverman, S. K., Mar 1 2012, In : ChemBioChem. 13, 5, p. 654-657 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Phosphopeptides
Phosphorylation
Phosphates
Peptides

Deoxyribozyme-catalyzed labeling of RNA

Baum, D. A. & Silverman, S. K., Jun 29 2007, In : Angewandte Chemie - International Edition. 46, 19, p. 3502-3504 3 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Labeling
Energy transfer
Fluorescence

Deoxyribozymes that synthesize branched and lariat RNA

Wang, Y. & Silverman, S. K., Jun 11 2003, In : Journal of the American Chemical Society. 125, 23, p. 6880-6881 2 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Enzymes
enzyme
Introns

Deoxyribozymes with 2′-5′ RNA ligase activity

Flynn-Charlebois, A., Wang, Y., Prior, T. K., Rashid, I., Hoadley, K. A., Coppins, R. L., Wolf, A. C. & Silverman, S. K., Mar 5 2003, In : Journal of the American Chemical Society. 125, 9, p. 2444-2454 11 p.

Research output: Contribution to journalArticle

Catalytic DNA
Ligases
RNA
Ligation
Nucleotides

Directing the outcome of deoxyribozyme selections to favor native 3′-5′ RNA ligation

Wang, Y. & Silverman, S. K., Mar 1 2005, In : Biochemistry. 44, 8, p. 3017-3023 7 p.

Research output: Contribution to journalArticle

Catalytic DNA
Ligation
RNA
Substrates
Hydroxyl Radical

DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation

Chandra, M. & Silverman, S. K., Mar 12 2008, In : Journal of the American Chemical Society. 130, 10, p. 2936-2937 2 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Catalytic RNA
DNA
Carbon

DNA catalysis of a normally disfavored RNA hydrolysis reaction

Parker, D. J., Xiao, Y., Aguilar, J. M. & Silverman, S. K., Jun 12 2013, In : Journal of the American Chemical Society. 135, 23, p. 8472-8475 4 p.

Research output: Contribution to journalArticle

catalysis
RNA
Catalysis
hydrolysis
Hydrolysis

DNA catalysts with tyrosine kinase activity

Walsh, S. M., Sachdeva, A. & Silverman, S. K., Oct 21 2013, In : Journal of the American Chemical Society. 135, 40, p. 14928-14931 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Protein-Tyrosine Kinases
Tyrosine
Catalyst activity
DNA

DNA-Catalyzed Amide Hydrolysis

Zhou, C., Avins, J. L., Klauser, P. C., Brandsen, B. M., Lee, Y. & Silverman, S. K., Mar 2 2016, In : Journal of the American Chemical Society. 138, 7, p. 2106-2109 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Amides
hydrolysis
Hydrolysis
DNA

DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates

Wong, O. Y., Pradeepkumar, P. I. & Silverman, S. K., May 31 2011, In : Biochemistry. 50, 21, p. 4741-4749 9 p.

Research output: Contribution to journalArticle

Catalytic DNA
Amino Acids
Peptides
Tyrosine
DNA

DNA-catalyzed DNA cleavage by a radical pathway with well-defined products

Lee, Y., Klauser, P. C., Brandsen, B. M., Zhou, C., Li, X. & Silverman, S. K., Jan 11 2017, In : Journal of the American Chemical Society. 139, 1, p. 255-261 7 p.

Research output: Contribution to journalArticle

Catalytic DNA
DNA Cleavage
cleavage
DNA
Catalysis

DNA-catalyzed formation of nucleopeptide linkages

Pradeepkumar, P. I., Höbartner, C., Baum, D. A. & Silverman, S. K., Feb 15 2008, In : Angewandte Chemie - International Edition. 47, 9, p. 1753-1757 5 p.

Research output: Contribution to journalArticle

RNA
Tyrosine
DNA
Catalytic DNA
Oligonucleotides

DNA-catalyzed glycosylation using aryl glycoside donors

Hesser, A. R., Brandsen, B. M., Walsh, S. M., Wang, P. & Silverman, S. K., Jan 1 2016, In : Chemical Communications. 52, 59, p. 9259-9262 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Glycosylation
Glycosides
DNA
Oligonucleotides

DNA-catalyzed hydrolysis of esters and aromatic amides

Brandsen, B. M., Hesser, A. R., Castner, M. A., Chandra, M. & Silverman, S. K., Oct 30 2013, In : Journal of the American Chemical Society. 135, 43, p. 16014-16017 4 p.

Research output: Contribution to journalArticle

Amides
ester
hydrolysis
Hydrolysis
Esters

DNA-Catalyzed Introduction of Azide at Tyrosine for Peptide Modification

Wang, P. & Silverman, S. K., Jan 1 2016, In : Angewandte Chemie - International Edition. 55, 34, p. 10052-10056 5 p.

Research output: Contribution to journalArticle

Catalytic DNA
Azides
Peptides
Tyrosine
DNA

DNA-catalyzed lysine side chain modification

Brandsen, B. M., Velez, T. E., Sachdeva, A., Ibrahim, N. A. & Silverman, S. K., Aug 18 2014, In : Angewandte Chemie - International Edition. 53, 34, p. 9045-9050 6 p.

Research output: Contribution to journalArticle

Lysine
DNA
Catalysis
Substrates
Proteins
Catalytic DNA
lysine
nucleic acids
linkages
Nucleic Acids

DNA-catalyzed reductive amination

Wong, O. Y., Mulcrone, A. E. & Silverman, S. K., Dec 2 2011, In : Angewandte Chemie - International Edition. 50, 49, p. 11679-11684 6 p.

Research output: Contribution to journalArticle

Amination
DNA
Guanosine
Nucleic acids
Nucleic Acids

DNA-catalyzed sequence-specific hydrolysis of DNA

Chandra, M., Sachdeva, A. & Silverman, S. K., Oct 2009, In : Nature chemical biology. 5, 10, p. 718-720 3 p.

Research output: Contribution to journalArticle

Hydrolysis
Catalytic DNA
DNA
RNA Cleavage
Deoxyribonucleases

DNA-catalyzed serine side chain reactivity and selectivity

Sachdeva, A. & Silverman, S. K., Mar 25 2010, In : Chemical Communications. 46, 13, p. 2215-2217 3 p.

Research output: Contribution to journalArticle

Serine
DNA
Catalytic DNA
Tyrosine

DNA constraints allow rational control of macromolecular conformation

Miduturu, C. V. & Silverman, S. K., Jul 27 2005, In : Journal of the American Chemical Society. 127, 29, p. 10144-10145 2 p.

Research output: Contribution to journalArticle

Conformations
DNA
RNA
nanotechnology
Nanotechnology

DNA Oligonucleotide 3′-Phosphorylation by a DNA Enzyme

Camden, A. J., Walsh, S. M., Suk, S. H. & Silverman, S. K., May 10 2016, In : Biochemistry. 55, 18, p. 2671-2676 6 p.

Research output: Contribution to journalArticle

Phosphorylation
Oligonucleotides
DNA
Enzymes
Catalytic DNA
Magnetic couplings
Pyridine
topology
Topology
rationalization

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

Kearney, P. C., Nowak, M. W., Zhong, W., Silverman, S. K., Lester, H. A. & Dougherty, D. A., Nov 1 1996, In : Molecular Pharmacology. 50, 5, p. 1401-1412 12 p.

Research output: Contribution to journalArticle

Nicotinic Receptors
Binding Sites
Amino Acids
Tyrosine
Cholinergic Agonists

Efficient control of group I intron ribozyme catalysis by DNA constraints

Zelin, E. & Silverman, S. K., Mar 30 2009, In : Chemical Communications. 7, p. 767-769 3 p.

Research output: Contribution to journalArticle

Catalytic RNA
Introns
Catalysis
DNA

Efficient one-step synthesis of biologically related lariat RNAs by a deoxyribozyme

Wang, Y. & Silverman, S. K., Sep 4 2005, In : Angewandte Chemie - International Edition. 44, 36, p. 5863-5866 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Substrates

Efficient RNA 5′-adenylation by T4 DNA ligase to facilitate practical applications

Wang, Y. & Silverman, S. K., Jun 1 2006, In : RNA. 12, 6, p. 1142-1146 5 p.

Research output: Contribution to journalArticle

DNA Ligases
Ligases
Nucleic Acids
Nucleotides
Complementary DNA

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

Silverman, S. K. & Cech, T. R., Jul 6 1999, In : Biochemistry. 38, 27, p. 8691-8702 12 p.

Research output: Contribution to journalArticle

Ribose
Hydrogen
Hydrogen bonds
RNA
Fasteners

Engineering a selective small-molecule substrate binding site into a deoxyribozyme

Höbartner, C. & Silverman, S. K., Oct 16 2007, In : Angewandte Chemie - International Edition. 46, 39, p. 7420-7424 5 p.

Research output: Contribution to journalArticle

Catalytic DNA
Binding sites
Binding Sites
Molecules
Substrates

Establishing broad generality of DNA catalysts for site-specific hydrolysis of single-stranded DNA

Xiao, Y., Wehrmann, R. J., Ibrahim, N. A. & Silverman, S. K., Feb 1 2012, In : Nucleic acids research. 40, 4, p. 1778-1786 9 p.

Research output: Contribution to journalArticle

Single-Stranded DNA
Hydrolysis
Catalytic DNA
DNA
Nucleotides

Experimental tests of two proofreading mechanisms for 5'-splice site selection.

Wang, Y. & Silverman, S. K., Jun 20 2006, In : ACS chemical biology. 1, 5, p. 316-324 9 p.

Research output: Contribution to journalArticle

Site selection
RNA Splice Sites
Introns
RNA
Spliceosomes

Flash decaging of tyrosine sidechains in an ion channel

Miller, J. C., Silverman, S. K., England, P. M., Dougherty, D. A. & Lester, H. A., Apr 1998, In : Neuron. 20, 4, p. 619-624 6 p.

Research output: Contribution to journalArticle

Ion Channels
Tyrosine
Nonsense Codon
Nicotinic Receptors
Cholinergic Receptors