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

On Yi Wong, P. I. Pradeepkumar, Scott K Silverman

Research output: Contribution to journalArticle

Abstract

This study focuses on the development of DNA catalysts (deoxyribozymes) that modify side chains of peptide substrates, with the long-term goal of achieving DNA-catalyzed covalent protein modification. We recently described several deoxyribozymes that modify tyrosine (Tyr) or serine (Ser) side chains by catalyzing their reaction with 5'-triphosphorylated RNA, forming nucleopeptide linkages. In each previous case, the side chain was presented in a highly preorganized three-dimensional architecture such that the resulting deoxyribozymes inherently cannot function with free peptides or proteins, which do not maintain the preorganization. Here we describe in vitro selection of deoxyribozymes that catalyze Tyr side chain modification of tethered and free peptide substrates, where the approach can potentially be generalized for catalysis involving large proteins. Several new deoxyribozymes for Tyr modification (and several for Ser modification as well) were identified; progressively better catalytic activity was observed as the selection design was strategically changed. The best new deoxyribozyme, 15MZ36, catalyzes covalent Tyr modification of a free tripeptide substrate with a kobs of 0.50 h-1 (t1/2 of 83 min) and up to 65% yield. These findings represent an important advance by demonstrating, for the first time,DNA catalysis involving free peptide substrates. The new results suggest the feasibility of DNA-catalyzed covalent modification of side chains of large protein substrates and provide key insights into how to achieve this goal.

Original languageEnglish (US)
Pages (from-to)4741-4749
Number of pages9
JournalBiochemistry
Volume50
Issue number21
DOIs
StatePublished - May 31 2011

Fingerprint

Catalytic DNA
Amino Acids
Peptides
Tyrosine
DNA
Substrates
Catalysis
Serine
Proteins
Catalyst activity
RNA
Catalysts

ASJC Scopus subject areas

  • Biochemistry

Cite this

DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates. / Wong, On Yi; Pradeepkumar, P. I.; Silverman, Scott K.

In: Biochemistry, Vol. 50, No. 21, 31.05.2011, p. 4741-4749.

Research output: Contribution to journalArticle

@article{ab1f878ad0d14c238ca805a492be2a60,
title = "DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates",
abstract = "This study focuses on the development of DNA catalysts (deoxyribozymes) that modify side chains of peptide substrates, with the long-term goal of achieving DNA-catalyzed covalent protein modification. We recently described several deoxyribozymes that modify tyrosine (Tyr) or serine (Ser) side chains by catalyzing their reaction with 5'-triphosphorylated RNA, forming nucleopeptide linkages. In each previous case, the side chain was presented in a highly preorganized three-dimensional architecture such that the resulting deoxyribozymes inherently cannot function with free peptides or proteins, which do not maintain the preorganization. Here we describe in vitro selection of deoxyribozymes that catalyze Tyr side chain modification of tethered and free peptide substrates, where the approach can potentially be generalized for catalysis involving large proteins. Several new deoxyribozymes for Tyr modification (and several for Ser modification as well) were identified; progressively better catalytic activity was observed as the selection design was strategically changed. The best new deoxyribozyme, 15MZ36, catalyzes covalent Tyr modification of a free tripeptide substrate with a kobs of 0.50 h-1 (t1/2 of 83 min) and up to 65{\%} yield. These findings represent an important advance by demonstrating, for the first time,DNA catalysis involving free peptide substrates. The new results suggest the feasibility of DNA-catalyzed covalent modification of side chains of large protein substrates and provide key insights into how to achieve this goal.",
author = "Wong, {On Yi} and Pradeepkumar, {P. I.} and Silverman, {Scott K}",
year = "2011",
month = "5",
day = "31",
doi = "10.1021/bi200585n",
language = "English (US)",
volume = "50",
pages = "4741--4749",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "21",

}

TY - JOUR

T1 - DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates

AU - Wong, On Yi

AU - Pradeepkumar, P. I.

AU - Silverman, Scott K

PY - 2011/5/31

Y1 - 2011/5/31

N2 - This study focuses on the development of DNA catalysts (deoxyribozymes) that modify side chains of peptide substrates, with the long-term goal of achieving DNA-catalyzed covalent protein modification. We recently described several deoxyribozymes that modify tyrosine (Tyr) or serine (Ser) side chains by catalyzing their reaction with 5'-triphosphorylated RNA, forming nucleopeptide linkages. In each previous case, the side chain was presented in a highly preorganized three-dimensional architecture such that the resulting deoxyribozymes inherently cannot function with free peptides or proteins, which do not maintain the preorganization. Here we describe in vitro selection of deoxyribozymes that catalyze Tyr side chain modification of tethered and free peptide substrates, where the approach can potentially be generalized for catalysis involving large proteins. Several new deoxyribozymes for Tyr modification (and several for Ser modification as well) were identified; progressively better catalytic activity was observed as the selection design was strategically changed. The best new deoxyribozyme, 15MZ36, catalyzes covalent Tyr modification of a free tripeptide substrate with a kobs of 0.50 h-1 (t1/2 of 83 min) and up to 65% yield. These findings represent an important advance by demonstrating, for the first time,DNA catalysis involving free peptide substrates. The new results suggest the feasibility of DNA-catalyzed covalent modification of side chains of large protein substrates and provide key insights into how to achieve this goal.

AB - This study focuses on the development of DNA catalysts (deoxyribozymes) that modify side chains of peptide substrates, with the long-term goal of achieving DNA-catalyzed covalent protein modification. We recently described several deoxyribozymes that modify tyrosine (Tyr) or serine (Ser) side chains by catalyzing their reaction with 5'-triphosphorylated RNA, forming nucleopeptide linkages. In each previous case, the side chain was presented in a highly preorganized three-dimensional architecture such that the resulting deoxyribozymes inherently cannot function with free peptides or proteins, which do not maintain the preorganization. Here we describe in vitro selection of deoxyribozymes that catalyze Tyr side chain modification of tethered and free peptide substrates, where the approach can potentially be generalized for catalysis involving large proteins. Several new deoxyribozymes for Tyr modification (and several for Ser modification as well) were identified; progressively better catalytic activity was observed as the selection design was strategically changed. The best new deoxyribozyme, 15MZ36, catalyzes covalent Tyr modification of a free tripeptide substrate with a kobs of 0.50 h-1 (t1/2 of 83 min) and up to 65% yield. These findings represent an important advance by demonstrating, for the first time,DNA catalysis involving free peptide substrates. The new results suggest the feasibility of DNA-catalyzed covalent modification of side chains of large protein substrates and provide key insights into how to achieve this goal.

UR - http://www.scopus.com/inward/record.url?scp=79958105696&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79958105696&partnerID=8YFLogxK

U2 - 10.1021/bi200585n

DO - 10.1021/bi200585n

M3 - Article

VL - 50

SP - 4741

EP - 4749

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 21

ER -