Scott K Silverman

1991 …2017
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Research Output 1991 2017

2007

Control of macromolecular structure and function using covalently attached double-stranded DNA constraints

Silverman, S. K., Jan 1 2007, In : Molecular BioSystems. 3, 1, p. 24-29 6 p.

Research output: Contribution to journalReview article

DNA
Nanotechnology
Sensors
Macromolecules
Rigidity

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

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

Review: Recent advances in DNA catalysis

Höbartner, C. & Silverman, S. K., Dec 5 2007, In : Biopolymers. 87, 5-6, p. 279-292 14 p.

Research output: Contribution to journalReview article

Catalytic DNA
Catalysis
DNA
RNA
RNA Cleavage

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

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
2006

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

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

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

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

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

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

Nucleic acid switches and sensors

Silverman, S. K., 2006, New, York, N, Y: Springer Science+Business Media.

Research output: Book/ReportBook

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
2005
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

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 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

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

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

In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

Silverman, S. K., Dec 13 2005, In : Nucleic acids research. 33, 19, p. 6151-6163 13 p.

Research output: Contribution to journalReview article

Catalytic DNA
RNA
DNA
Hydroxyl Radical
Enzymes
RNA Splicing
Oligonucleotides
Exons
RNA
Phosphates

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
Catalytic DNA
Ligation
RNA
Phosphates
linkage (genetics)

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

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
2004

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

Breaking Up Is Easy to Do (If You're a DNA Enzyme that Cleaves RNA)

Silverman, S. K., Jan 2004, In : Chemistry and Biology. 11, 1, p. 7-8 2 p.

Research output: Contribution to journalReview article

Catalytic DNA
RNA
DNA
Enzymes
RNA-cleaving DNA 8-17

Deoxyribozymes: DNA catalysts for bioorganic chemistry

Silverman, S. K., Oct 7 2004, In : Organic and Biomolecular Chemistry. 2, 19, p. 2701-2706 6 p.

Research output: Contribution to journalReview article

Catalytic DNA
nucleic acids
deoxyribonucleic acid
chemistry
catalysts

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

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
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
2003

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

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

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

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

Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA

Silverman, S. K., Apr 1 2003, In : RNA. 9, 4, p. 377-383 7 p.

Research output: Contribution to journalShort survey

Catalytic RNA
RNA
Biosensing Techniques
Oligonucleotides
Research Personnel
2002

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
2001

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
2000

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
1999

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

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

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
1998

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

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

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
1996

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