Novel antisense oligonucleotides containing hydroxamate linkages: Targeted iron-triggered chemical nucleases

Marvin J. Miller, Hui Li, Catherine Foss

Research output: Contribution to journalArticle

Abstract

Antisense oligonucleotides with iron binding hydroxamate linkages are designed to act as sequence-selective cleaving agents of complementary nucleic acids through Fenton chemistry. Oligothymidylate analogs with hydroxamate linkages were efficiently synthesized from coupling of nucleoside intermediates, activated as p-nitrophenyl carbonates, with hydroxylamine derivatized nucleosides. Iron binding studies showed that hydroxamate linked oligonucleotides are effective iron chelators when there are three nonadjacent internucleosidic hydroxamate linkages available in the same oligonucleotide molecule. However, analysis of the CD spectra of an oligothymidylate 16mer, which contained complete substitution of all phosphates with hydroxamates, indicated that the hydroxamate linkage was too rigid to allow the analog to base pair with the complementary DNA d(A16). Syntheses of mix-linked thymidine oligomers with up to three hydroxamate linkages incorporated in the center of the sequence are also reported. Iron binding of the thymidine oligomer with hydroxamate linkages was confirmed by matrix assisted laser desorption mass spectrometry analysis. Nuclease stability assays showed that the modified oligonucleotides have enhanced resistance toward nuclease S1 (endonuclease) compared to natural oligonucleotides. A thymidine 16mer with three hydroxamate linkages incorporated in the center of the sequence was shown to be able to bind with both iron and its complementary polyA strand. A small destablizing effect was observed when the phosphodiester linkage was changed to the hydroxamate linkage. Under Fenton chemistry conditions, this novel iron binding oligothymidylate analog cleaved the complementary DNA strand sequence-selectively.

Original languageEnglish (US)
Pages (from-to)491-510
Number of pages20
JournalBioMetals
Volume22
Issue number3
DOIs
StatePublished - Jun 2009
Externally publishedYes

Fingerprint

nucleases
Antisense Oligonucleotides
Oligonucleotides
oligonucleotides
linkage (genetics)
Iron
iron
Thymidine
Nucleosides
thymidine
Oligomers
Complementary DNA
complementary DNA
nucleosides
Hydroxylamine
Carbonates
Chelating Agents
Base Pairing
DNA sequences
Nucleic acids

Keywords

  • Antisense oligonucleotides
  • Chemical nucleases
  • Fenton chemistry
  • Hydroxamic acid
  • Iron binding

ASJC Scopus subject areas

  • Biomaterials
  • Metals and Alloys
  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Novel antisense oligonucleotides containing hydroxamate linkages : Targeted iron-triggered chemical nucleases. / Miller, Marvin J.; Li, Hui; Foss, Catherine.

In: BioMetals, Vol. 22, No. 3, 06.2009, p. 491-510.

Research output: Contribution to journalArticle

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