Synthesis and evaluation of a triplex-forming oligonucleotide- pyrrolobenzodiazepine conjugate

Zhanna V. Zhilina, Amy J. Ziemba, John O. Trent, Michael W. Reed, Vladimir Gorn, Qun Zhou, Wenhu Duan, Laurence Hurley, Scot W. Ebbinghaus

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

In most cases, unmodified oligonucleotides designed as antigene molecules are incapable of binding to DNA with sufficient stability to prevent gene expression. To stabilize binding to a polypurine tract in the HER-2/neu promoter, a triplex forming oligonucleotide (TFO) was conjugated to a pyrrolo[1,4]-benzodiazepine (PBD), desmethyltomaymycin, and site-specific DNA binding was evaluated. An activated ester of the PBD moiety was conjugated by an acylation reaction to a free primary amine on a 50-atom aliphatic linker at the 5' end of the TFO. This long aliphatic linker was designed to provide a bridge from the major groove binding site of the TFO to the minor groove binding site of the PBD. Triplex formation by the resulting TFO-PBD conjugate occurred more slowly and with a nearly 30-fold lower affinity compared to an unconjugated TFO. PBD binding to the triplex target was demonstrated by protection from restriction enzyme digestion, and covalent binding to the exocyclic amino group of guanine was inferred by substituting specific guanines with inosines. Although the binding of the TFO was less efficient, this report demonstrates that in principle, TFOs can be used to direct the binding of a PBD to specific location. Further optimization of TFO-PBD conjugate design, likely involving optimization of the linker and perhaps placing a PBD at both ends of the TFO, will be needed to make gene modification robust.

Original languageEnglish (US)
Pages (from-to)1182-1192
Number of pages11
JournalBioconjugate Chemistry
Volume15
Issue number6
DOIs
StatePublished - Nov 2004

Fingerprint

Oligonucleotides
Guanine
Binding sites
DNA
Binding Sites
pyrrolo(2,1-c)(1,4)benzodiazepine
Acylation
Inosine
Gene expression
Amines
Digestion
Esters
Enzymes
Genes
Gene Expression
Atoms
Molecules

ASJC Scopus subject areas

  • Chemistry(all)
  • Organic Chemistry
  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

Cite this

Zhilina, Z. V., Ziemba, A. J., Trent, J. O., Reed, M. W., Gorn, V., Zhou, Q., ... Ebbinghaus, S. W. (2004). Synthesis and evaluation of a triplex-forming oligonucleotide- pyrrolobenzodiazepine conjugate. Bioconjugate Chemistry, 15(6), 1182-1192. https://doi.org/10.1021/bc0498673

Synthesis and evaluation of a triplex-forming oligonucleotide- pyrrolobenzodiazepine conjugate. / Zhilina, Zhanna V.; Ziemba, Amy J.; Trent, John O.; Reed, Michael W.; Gorn, Vladimir; Zhou, Qun; Duan, Wenhu; Hurley, Laurence; Ebbinghaus, Scot W.

In: Bioconjugate Chemistry, Vol. 15, No. 6, 11.2004, p. 1182-1192.

Research output: Contribution to journalArticle

Zhilina, ZV, Ziemba, AJ, Trent, JO, Reed, MW, Gorn, V, Zhou, Q, Duan, W, Hurley, L & Ebbinghaus, SW 2004, 'Synthesis and evaluation of a triplex-forming oligonucleotide- pyrrolobenzodiazepine conjugate', Bioconjugate Chemistry, vol. 15, no. 6, pp. 1182-1192. https://doi.org/10.1021/bc0498673
Zhilina, Zhanna V. ; Ziemba, Amy J. ; Trent, John O. ; Reed, Michael W. ; Gorn, Vladimir ; Zhou, Qun ; Duan, Wenhu ; Hurley, Laurence ; Ebbinghaus, Scot W. / Synthesis and evaluation of a triplex-forming oligonucleotide- pyrrolobenzodiazepine conjugate. In: Bioconjugate Chemistry. 2004 ; Vol. 15, No. 6. pp. 1182-1192.
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