Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes

Shannon M. Walsh, Stephanie N. Konecki, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

Deoxyribozymes (DNA enzymes) have been developed for a growing variety of chemical reactions, including with peptide substrates. We recently described the first tyrosine kinase deoxyribozymes, which lacked the ability to discriminate among peptide substrates on the basis of the amino acids surrounding the tyrosine residue. Those deoxyribozymes were identified by in vitro selection using a DNA-anchored peptide substrate in which the residues neighboring tyrosine were all alanine. Here, we performed in vitro selection for tyrosine kinase activity using three peptide substrates in which the neighboring residues included a variety of side chains. For one of these three peptides, we found numerous deoxyribozymes that discriminate strongly in favor of phosphorylating tyrosine when the surrounding residues are specifically those used in the selection process. Three different short peptide sequence motifs of 2–4 amino acids were required for catalysis by three unique deoxyribozymes. For a second peptide substrate, the selection process led to one deoxyribozyme which exhibits partial discrimination among peptide sequences. These findings establish the feasibility of identifying DNA enzymes that catalyze sequence-selective tyrosine phosphorylation, which suggests the downstream practical utility of such deoxyribozymes. More broadly, this outcome reinforces the conclusion that nucleic acid catalysts can discriminate among peptide substrates in the context of biochemically relevant reactions.

Original languageEnglish (US)
Pages (from-to)218-224
Number of pages7
JournalJournal of Molecular Evolution
Volume81
Issue number5-6
DOIs
StatePublished - Dec 1 2015

Fingerprint

Catalytic DNA
peptide
Protein-Tyrosine Kinases
tyrosine
phosphotransferases (kinases)
peptides
Peptides
substrate
Tyrosine
DNA
amino acid
enzyme
Amino Acid Motifs
amino acids
catalysis
nucleic acid
Enzymes
chemical reactions
enzymes
Catalysis

Keywords

  • Deoxyribozyme
  • In vitro selection
  • Kinase
  • Peptide
  • Phosphorylation
  • Post-translational modification

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes. / Walsh, Shannon M.; Konecki, Stephanie N.; Silverman, Scott K.

In: Journal of Molecular Evolution, Vol. 81, No. 5-6, 01.12.2015, p. 218-224.

Research output: Contribution to journalArticle

Walsh, Shannon M. ; Konecki, Stephanie N. ; Silverman, Scott K. / Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes. In: Journal of Molecular Evolution. 2015 ; Vol. 81, No. 5-6. pp. 218-224.
@article{d5e362f2a4ac47229e353d97d103da54,
title = "Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes",
abstract = "Deoxyribozymes (DNA enzymes) have been developed for a growing variety of chemical reactions, including with peptide substrates. We recently described the first tyrosine kinase deoxyribozymes, which lacked the ability to discriminate among peptide substrates on the basis of the amino acids surrounding the tyrosine residue. Those deoxyribozymes were identified by in vitro selection using a DNA-anchored peptide substrate in which the residues neighboring tyrosine were all alanine. Here, we performed in vitro selection for tyrosine kinase activity using three peptide substrates in which the neighboring residues included a variety of side chains. For one of these three peptides, we found numerous deoxyribozymes that discriminate strongly in favor of phosphorylating tyrosine when the surrounding residues are specifically those used in the selection process. Three different short peptide sequence motifs of 2–4 amino acids were required for catalysis by three unique deoxyribozymes. For a second peptide substrate, the selection process led to one deoxyribozyme which exhibits partial discrimination among peptide sequences. These findings establish the feasibility of identifying DNA enzymes that catalyze sequence-selective tyrosine phosphorylation, which suggests the downstream practical utility of such deoxyribozymes. More broadly, this outcome reinforces the conclusion that nucleic acid catalysts can discriminate among peptide substrates in the context of biochemically relevant reactions.",
keywords = "Deoxyribozyme, In vitro selection, Kinase, Peptide, Phosphorylation, Post-translational modification",
author = "Walsh, {Shannon M.} and Konecki, {Stephanie N.} and Silverman, {Scott K}",
year = "2015",
month = "12",
day = "1",
doi = "10.1007/s00239-015-9699-3",
language = "English (US)",
volume = "81",
pages = "218--224",
journal = "Journal of Molecular Evolution",
issn = "0022-2844",
publisher = "Springer New York",
number = "5-6",

}

TY - JOUR

T1 - Identification of Sequence-Selective Tyrosine Kinase Deoxyribozymes

AU - Walsh, Shannon M.

AU - Konecki, Stephanie N.

AU - Silverman, Scott K

PY - 2015/12/1

Y1 - 2015/12/1

N2 - Deoxyribozymes (DNA enzymes) have been developed for a growing variety of chemical reactions, including with peptide substrates. We recently described the first tyrosine kinase deoxyribozymes, which lacked the ability to discriminate among peptide substrates on the basis of the amino acids surrounding the tyrosine residue. Those deoxyribozymes were identified by in vitro selection using a DNA-anchored peptide substrate in which the residues neighboring tyrosine were all alanine. Here, we performed in vitro selection for tyrosine kinase activity using three peptide substrates in which the neighboring residues included a variety of side chains. For one of these three peptides, we found numerous deoxyribozymes that discriminate strongly in favor of phosphorylating tyrosine when the surrounding residues are specifically those used in the selection process. Three different short peptide sequence motifs of 2–4 amino acids were required for catalysis by three unique deoxyribozymes. For a second peptide substrate, the selection process led to one deoxyribozyme which exhibits partial discrimination among peptide sequences. These findings establish the feasibility of identifying DNA enzymes that catalyze sequence-selective tyrosine phosphorylation, which suggests the downstream practical utility of such deoxyribozymes. More broadly, this outcome reinforces the conclusion that nucleic acid catalysts can discriminate among peptide substrates in the context of biochemically relevant reactions.

AB - Deoxyribozymes (DNA enzymes) have been developed for a growing variety of chemical reactions, including with peptide substrates. We recently described the first tyrosine kinase deoxyribozymes, which lacked the ability to discriminate among peptide substrates on the basis of the amino acids surrounding the tyrosine residue. Those deoxyribozymes were identified by in vitro selection using a DNA-anchored peptide substrate in which the residues neighboring tyrosine were all alanine. Here, we performed in vitro selection for tyrosine kinase activity using three peptide substrates in which the neighboring residues included a variety of side chains. For one of these three peptides, we found numerous deoxyribozymes that discriminate strongly in favor of phosphorylating tyrosine when the surrounding residues are specifically those used in the selection process. Three different short peptide sequence motifs of 2–4 amino acids were required for catalysis by three unique deoxyribozymes. For a second peptide substrate, the selection process led to one deoxyribozyme which exhibits partial discrimination among peptide sequences. These findings establish the feasibility of identifying DNA enzymes that catalyze sequence-selective tyrosine phosphorylation, which suggests the downstream practical utility of such deoxyribozymes. More broadly, this outcome reinforces the conclusion that nucleic acid catalysts can discriminate among peptide substrates in the context of biochemically relevant reactions.

KW - Deoxyribozyme

KW - In vitro selection

KW - Kinase

KW - Peptide

KW - Phosphorylation

KW - Post-translational modification

UR - http://www.scopus.com/inward/record.url?scp=84948386918&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84948386918&partnerID=8YFLogxK

U2 - 10.1007/s00239-015-9699-3

DO - 10.1007/s00239-015-9699-3

M3 - Article

VL - 81

SP - 218

EP - 224

JO - Journal of Molecular Evolution

JF - Journal of Molecular Evolution

SN - 0022-2844

IS - 5-6

ER -