Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA

Biochemistry. 2009 Nov 24;48(46):10882-93. doi: 10.1021/bi901506f.

Abstract

Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding to RNA. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometimes weak when many A-U pairs are present. It is known, however, that replacement of uridine with 2-thiouridine significantly improves binding and selectivity. To test for additional improvement of binding and of the specificity for binding A over G, LNA-2-thiouridine was synthesized for the first time and incorporated into many LNA-2'-O-methyl-RNA/RNA duplexes. UV melting was used to measure the thermodynamic effect of replacing 2'-O-methyluridine with 2'-O-methyl-2-thiouridine or LNA-2-thiouridine. The 2-thiouridine usually enhances binding and selectivity. Selectivity is optimized when a single 2-thiouridine is placed at an internal position in a duplex.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleic Acid Hybridization
  • Nucleotides / chemistry*
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / chemistry*
  • Pyrenes / chemistry
  • RNA / chemical synthesis
  • RNA / chemistry*
  • RNA, Double-Stranded / chemistry*
  • Ribose / analogs & derivatives*
  • Ribose / chemistry
  • Spectrophotometry, Ultraviolet
  • Thermodynamics
  • Thiouridine / analogs & derivatives*
  • Thiouridine / chemical synthesis*
  • Thiouridine / chemistry
  • Transition Temperature
  • Uridine / analogs & derivatives
  • Uridine / chemistry

Substances

  • 2'-O-4'-C-methylene-ribofuranosyl nucleotide
  • 2-thiouridine
  • Nucleotides
  • Oligonucleotides
  • Pyrenes
  • RNA, Double-Stranded
  • Thiouridine
  • RNA
  • Ribose
  • pyrene
  • Uridine