2'-O-[2-(methylthio)ethyl]-modified oligonucleotide: an analogue of 2'-O-[2-(methoxy)-ethyl]-modified oligonucleotide with improved protein binding properties and high binding affinity to target RNA

Biochemistry. 2002 Oct 1;41(39):11642-8. doi: 10.1021/bi020264t.

Abstract

A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Nucleic Acid Heteroduplexes / chemistry
  • Nucleosides / chemistry
  • Oligodeoxyribonucleotides / chemistry
  • Oligodeoxyribonucleotides, Antisense / chemistry
  • Organophosphorus Compounds / chemistry
  • Protein Binding
  • RNA / chemistry*
  • Uridine / analogs & derivatives*
  • Uridine / chemistry*

Substances

  • 2'-O-(2-(methylthio)ethyl) RNA
  • 2-O-(4,4'-dimethoxytrityl)ethylsulfonylethan-2'-yl-phosphate
  • Nucleic Acid Heteroduplexes
  • Nucleosides
  • Oligodeoxyribonucleotides
  • Oligodeoxyribonucleotides, Antisense
  • Organophosphorus Compounds
  • 2'-O-methyluridine
  • RNA
  • Uridine

Associated data

  • PDB/1MLX