Scott K Silverman

1991 …2017
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Research Output 1991 2017

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Article

Fluorescence of covalently attached pyrene as a general RNA folding probe

Smalley, M. K. & Silverman, S. K., Jan 1 2006, In : Nucleic acids research. 34, 1, p. 152-166 15 p.

Research output: Contribution to journalArticle

RNA Folding
RNA Probes
Fluorescence
RNA
Nucleotides

Functional compromises among pH tolerance, site specificity, and sequence tolerance for a DNA-hydrolyzing deoxyribozyme

Xiao, Y., Chandra, M. & Silverman, S. K., Nov 9 2010, In : Biochemistry. 49, 44, p. 9630-9637 8 p.

Research output: Contribution to journalArticle

Catalytic DNA
DNA Cleavage
DNA
Substrates
Hydrolysis

General deoxyribozyme-catalyzed synthesis of native 3′-5′ RNA linkages

Purtha, W. E., Coppins, R. L., Smalley, M. K. & Silverman, S. K., Sep 28 2005, In : Journal of the American Chemical Society. 127, 38, p. 13124-13125 2 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
RNA Cleavage
nucleic acid
cleavage

Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes

Walsh, S. M., Konecki, S. N. & Silverman, S. K., Dec 1 2015, In : Journal of Molecular Evolution. 81, 5-6, p. 218-224 7 p.

Research output: Contribution to journalArticle

Catalytic DNA
peptide
Protein-Tyrosine Kinases
tyrosine
phosphotransferases (kinases)

Improved deoxyribozymes for synthesis of covalently branched DNA and RNA

Lee, C. S., Mui, T. P. & Silverman, S. K., Jan 17 2011, In : Nucleic acids research. 39, 1, p. 269-279 11 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
DNA
Nucleic Acids
Ribonucleotides

Improvement of DNA adenylation using T4 DNA ligase with a template strand and a strategically mismatched acceptor strand

Patel, M. P., Baum, D. A. & Silverman, S. K., Apr 1 2008, In : Bioorganic Chemistry. 36, 2, p. 46-56 11 p.

Research output: Contribution to journalArticle

DNA Ligases
DNA
Substrates
Polynucleotide 5'-Hydroxyl-Kinase
Ligases

In vitro evolution of an RNA-cleaving DNA enzyme into an RNA ligase switches the selectivity from 3′-5′ to 2′-5′

Flynn-Charlebois, A., Prior, T. K., Hoadley, K. A. & Silverman, S. K., May 7 2003, In : Journal of the American Chemical Society. 125, 18, p. 5346-5350 5 p.

Research output: Contribution to journalArticle

Catalytic DNA
Catalyst selectivity
Ligases
RNA
DNA

In vivo incorporation of unnatural amino acids into ion channels in Xenopus oocyte expression system

Nowak, M. W., Gallivan, J. P., Silverman, S. K., Labarca, C. G., Dougherty, D. A. & Lester, H. A., Jan 1 1998, In : Methods in enzymology. 293, p. 504-529 26 p.

Research output: Contribution to journalArticle

Xenopus
Ion Channels
Oocytes
Amino Acids
Membranes

Lanthanide ions as required cofactors for DNA catalysts

Dokukin, V. & Silverman, S. K., May 1 2012, In : Chemical Science. 3, 5, p. 1707-1714 8 p.

Research output: Contribution to journalArticle

Lanthanoid Series Elements
Catalytic DNA
Ions
Catalysts
DNA

Merely two mutations switch a DNA-hydrolyzing deoxyribozyme from heterobimetallic (Zn2+/Mn2+) to monometallic (Zn 2+-only) behavior

Xiao, Y., Allen, E. C. & Silverman, S. K., Feb 14 2011, In : Chemical Communications. 47, 6, p. 1749-1751 3 p.

Research output: Contribution to journalArticle

Catalytic DNA
DNA
Switches
Nucleotides
Metal ions
RNA Splicing
Oligonucleotides
Exons
RNA
Phosphates

Modulation of DNA constraints that control macromolecular folding

Miduturu, C. V. & Silverman, S. K., Mar 13 2006, In : Angewandte Chemie - International Edition. 45, 12, p. 1918-1921 4 p.

Research output: Contribution to journalArticle

DNA
Modulation
RNA
Macromolecules
Conformations

Modulation of RNA tertiary folding by incorporation of caged nucleotides

Höbartner, C. & Silverman, S. K., Nov 11 2005, In : Angewandte Chemie - International Edition. 44, 44, p. 7305-7309 5 p.

Research output: Contribution to journalArticle

Nucleotides
RNA
Modulation
Molecules

Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes

Heller, D. A., Jin, H., Martinez, B. M., Patel, D., Miller, B. M., Yeung, T. K., Jena, P. V., Höbartner, C., Ha, T., Silverman, S. K. & Strano, M. S., Feb 2009, In : Nature Nanotechnology. 4, 2, p. 114-120 7 p.

Research output: Contribution to journalArticle

Single-walled carbon nanotubes (SWCN)
carbon nanotubes
Nanotubes
Molecules
Optical sensors

Multiple folding pathways for the P4-P6 RNA domain

Silverman, S. K., Deras, M. L., Woodson, S. A., Scaringe, S. A. & Cech, T. R., Oct 10 2000, In : Biochemistry. 39, 40, p. 12465-12475 11 p.

Research output: Contribution to journalArticle

RNA
Kinetics
Ionic strength
Osmolar Concentration
Cacodylic Acid

Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine

Brenner, M. D., Scanlan, M. S., Nahas, M. K., Ha, T. & Silverman, S. K., Mar 2 2010, In : Biochemistry. 49, 8, p. 1596-1605 10 p.

Research output: Contribution to journalArticle

Riboswitch
Guanine
Fluorescence
Fluorescence Resonance Energy Transfer
Conformations

New Organic Polymers and Molecules with Very High Spin States

Dougherty, D. A., Jacobs, S. J., Silverman, S. K., Murray, M. M., Shultz, D. A., West, A. P. & Clites, J. A., Aug 1 1993, In : Molecular Crystals and Liquid Crystals Science and Technology. Section A. Molecular Crystals and Liquid Crystals. 232, 1, p. 289-304 16 p.

Research output: Contribution to journalArticle

Organic polymers
Magnetic materials
Ground state
Molecules
polymers

Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells

Nowak, M. W., Kearney, P. C., Sampson, J. R., Saks, M. E., Labarca, C. G., Silverman, S. K., Zhong, W., Thorson, J., Abelson, J. N., Davidson, N., Schultz, P. G., Dougherty, D. A. & Lester, H. A., Jan 1 1995, In : Science. 268, 5209, p. 439-442 4 p.

Research output: Contribution to journalArticle

Nonsense Codon
Nicotinic Receptors
Xenopus
Phenylalanine
Oocytes

Optimization and generality of a small deoxyribozyme that ligates RNA

Ricca, B. L., Wolf, A. C. & Silverman, S. K., Jul 25 2003, In : Journal of Molecular Biology. 330, 5, p. 1015-1025 11 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Ligation
Ligases
Sagittaria
Catalytic DNA
Ligation
RNA
Phosphates
linkage (genetics)

Phosphoserine lyase deoxyribozymes: DNA-catalyzed formation of dehydroalanine residues in peptides

Chandrasekar, J., Wylder, A. C. & Silverman, S. K., Aug 5 2015, In : Journal of the American Chemical Society. 137, 30, p. 9575-9578 4 p.

Research output: Contribution to journalArticle

Catalytic DNA
Phosphoserine
Lyases
peptide
Peptides

Practical and general synthesis of 5′-adenylated RNA (5′-AppRNA)

Silverman, S. K., Apr 1 2004, In : RNA. 10, 4, p. 731-746 16 p.

Research output: Contribution to journalArticle

RNA
Solid-Phase Synthesis Techniques
Ligation
RNA Ligase (ATP)
Polynucleotide 5'-Hydroxyl-Kinase

Pursuing DNA catalysts for protein modification

Silverman, S. K., May 19 2015, In : Accounts of chemical research. 48, 5, p. 1369-1379 11 p.

Research output: Contribution to journalArticle

Catalytic DNA
Catalysts
DNA
Amides
Proteins

Quantifying the energetic interplay of RNA tertiary and secondary structure interactions

Silverman, S. K., Zheng, M., Wu, M., Tinoco, I. & Cech, T. R., Dec 1 1999, In : RNA. 5, 12, p. 1665-1674 10 p.

Research output: Contribution to journalArticle

Small Nuclear RNA
RNA
Point Mutation
Magnetic Resonance Spectroscopy
Introns

Rational modification of a selection strategy leads to deoxyribozymes that create native 3′-5′ RNA linkages

Coppins, R. L. & Silverman, S. K., Dec 22 2004, In : Journal of the American Chemical Society. 126, 50, p. 16426-16432 7 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Ligation
duplex
Hydroxyl Radical

Reaction of C60 with Dimethyldioxirane—Formation of an Epoxide and a 1,3‐Dioxolane Derivative

Elemes, Y., Silverman, S. K., Sheu, C., Kao, M., Foote, C. S., Alvarez, M. M. & Whetten, R. L., Mar 1992, In : Angewandte Chemie International Edition in English. 31, 3, p. 351-353 3 p.

Research output: Contribution to journalArticle

Fullerenes
Epoxy Compounds
Acetone
Derivatives
Temperature

RNA tertiary folding monitored by fluorescence of covalently attached pyrene

Silverman, S. K. & Cech, T. R., Oct 26 1999, In : Biochemistry. 38, 43, p. 14224-14237 14 p.

Research output: Contribution to journalArticle

RNA Folding
Fluorescence
RNA
Chromophores
Nucleotides

Selective Aptamers for Detection of Estradiol and Ethynylestradiol in Natural Waters

Akki, S. U., Werth, C. J. & Silverman, S. K., Jul 16 2015, In : Environmental Science and Technology. 49, 16, p. 9905-9913 9 p.

Research output: Contribution to journalArticle

Nucleotide Aptamers
Estradiol
DNA
Water
fold

Selective stabilization of natively folded RNA structure by DNA constraints

Gerdt, J. P., Miduturu, C. V. & Silverman, S. K., Nov 12 2008, In : Journal of the American Chemical Society. 130, 45, p. 14920-14921 2 p.

Research output: Contribution to journalArticle

RNA
stabilization
DNA
Stabilization
Nucleic Acid Conformation
Singlet Oxygen
Photooxidation
photooxidation
Epoxy Compounds
Electrons

Site-selective depurination by a periodate-dependent deoxyribozyme

Höbartner, C., Pradeepkumar, P. I. & Silverman, S. K., Jun 6 2007, In : Chemical Communications. 22, p. 2255-2257 3 p.

Research output: Contribution to journalArticle

Catalytic DNA
Guanosine
Nucleotides
metaperiodate
Labeling
RNA
Oligonucleotides
Nucleotides
RNA Folding

Structure-function correlations derived from faster variants of a RNA ligase deoxyribozyme

Prior, T. K., Semlow, D. R., Flynn-Charlebois, A., Rashid, I. & Silverman, S. K., Jul 14 2004, In : Nucleic acids research. 32, 3, p. 1075-1082 8 p.

Research output: Contribution to journalArticle

Catalytic DNA
Ligases
RNA
DNA
Enzymes

Subunit stoichiometry of a heteromultimeric G protein-coupled inward- rectifier K+ channel

Silverman, S. K., Lester, H. A. & Dougherty, D. A., Dec 14 1996, In : Journal of Biological Chemistry. 271, 48, p. 30524-30528 5 p.

Research output: Contribution to journalArticle

Inwardly Rectifying Potassium Channel
Xenopus
GTP-Binding Proteins
Stoichiometry
Oocytes

Synthesis and application of a 5′-aldehyde phosphoramidite for covalent attachment of DNA to biomolecules

Miduturu, C. V. & Silverman, S. K., Jul 21 2006, In : Journal of Organic Chemistry. 71, 15, p. 5774-5777 4 p.

Research output: Contribution to journalArticle

Biomolecules
Aldehydes
Amination
DNA
RNA

Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA

Jin, S., Miduturu, C. V., McKinney, D. C. & Silverman, S. K., May 27 2005, In : Journal of Organic Chemistry. 70, 11, p. 4284-4299 16 p.

Research output: Contribution to journalArticle

Nucleosides
Sulfhydryl Compounds
Amines
RNA
Substitution reactions

Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length

Velez, T. E., Singh, J., Xiao, Y., Allen, E. C., Wong, O. Y., Chandra, M., Kwon, S. C. & Silverman, S. K., Dec 10 2012, In : ACS Combinatorial Science. 14, 12, p. 680-687 8 p.

Research output: Contribution to journalArticle

Catalytic DNA
Catalysis
DNA
Nucleotide Aptamers
RNA

The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain

Young, B. T. & Silverman, S. K., Oct 15 2002, In : Biochemistry. 41, 41, p. 12271-12276 6 p.

Research output: Contribution to journalArticle

Thermodynamics
RNA Folding
RNA
Kinetics
Nucleotides

Ty1 reverse transcriptase does not read through the proposed 2′,5′-branched retrotransposition intermediate in vitro

Pratico, E. D. & Silverman, S. K., Sep 1 2007, In : RNA. 13, 9, p. 1528-1536 9 p.

Research output: Contribution to journalArticle

RNA-Directed DNA Polymerase
Complementary DNA
RNA
Ribonuclease H
Catalytic DNA

Use of deoxyribozymes in RNA research.

Silverman, S. K. & Baum, D. A., 2009, In : Methods in enzymology. 469, p. 95-117 23 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Research
Ligation
RNA Cleavage

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

Hoadley, K. A., Purtha, W. E., Wolf, A. C., Flynn-Charlebois, A. & Silverman, S. K., Jun 28 2005, In : Biochemistry. 44, 25, p. 9217-9231 15 p.

Research output: Contribution to journalArticle

Catalytic DNA
RNA
Phosphates
Substrates
Hydroxyl Radical