Circular DNA and DNA/RNA hybrid molecules as scaffolds for Ricin inhibitor design

Matthew B. Sturm, Setu Roday, Vern L. Schramm

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A 4324, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5′- and 3′-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (kcat/K m) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (feat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (K = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.

Original languageEnglish (US)
Pages (from-to)5544-5550
Number of pages7
JournalJournal of the American Chemical Society
Volume129
Issue number17
DOIs
StatePublished - May 2 2007

Fingerprint

Ricin
Circular DNA
RNA
Scaffolds
DNA
Molecules
Substrates
Oligonucleotides
Catalysis
28S Ribosomal RNA
Ribosomal RNA
Adenosine

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Circular DNA and DNA/RNA hybrid molecules as scaffolds for Ricin inhibitor design. / Sturm, Matthew B.; Roday, Setu; Schramm, Vern L.

In: Journal of the American Chemical Society, Vol. 129, No. 17, 02.05.2007, p. 5544-5550.

Research output: Contribution to journalArticle

@article{6404c57177954a0ba771c1e5378ced99,
title = "Circular DNA and DNA/RNA hybrid molecules as scaffolds for Ricin inhibitor design",
abstract = "Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A 4324, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5′- and 3′-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (kcat/K m) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (feat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (K = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.",
author = "Sturm, {Matthew B.} and Setu Roday and Schramm, {Vern L.}",
year = "2007",
month = "5",
day = "2",
doi = "10.1021/ja068054h",
language = "English (US)",
volume = "129",
pages = "5544--5550",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "17",

}

TY - JOUR

T1 - Circular DNA and DNA/RNA hybrid molecules as scaffolds for Ricin inhibitor design

AU - Sturm, Matthew B.

AU - Roday, Setu

AU - Schramm, Vern L.

PY - 2007/5/2

Y1 - 2007/5/2

N2 - Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A 4324, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5′- and 3′-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (kcat/K m) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (feat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (K = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.

AB - Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A 4324, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5′- and 3′-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (kcat/K m) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (feat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (K = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.

UR - http://www.scopus.com/inward/record.url?scp=34247857453&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34247857453&partnerID=8YFLogxK

U2 - 10.1021/ja068054h

DO - 10.1021/ja068054h

M3 - Article

VL - 129

SP - 5544

EP - 5550

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 17

ER -