Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

Nucleic Acids Res. 2013 Mar 1;41(5):3257-73. doi: 10.1093/nar/gkt007. Epub 2013 Jan 23.

Abstract

In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasion into duplex DNA (DSI). We thus report on the development of a clamp type of LNA ON-bisLNA-with capacity to bind and invade into supercoiled double-stranded DNA. The bisLNA links a triplex-forming, Hoogsteen-binding, targeting arm with a strand-invading Watson-Crick binding arm. Optimization was carried out by varying the number and location of LNA nucleotides and the length of the triplex-forming versus strand-invading arms. Single-strand regions in target duplex DNA were mapped using chemical probing. By combining design and increase in LNA content, it was possible to achieve a 100-fold increase in potency with 30% DSI at 450 nM using a bisLNA to plasmid ratio of only 21:1. Although this first conceptual report does not address the utility of bisLNA for the targeting of DNA in a chromosomal context, it shows bisLNA as a promising candidate for interfering also with cellular genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Buffers
  • DNA / chemistry
  • DNA Cleavage
  • DNA Restriction Enzymes / chemistry
  • DNA, Superhelical / chemistry*
  • Hydrogen-Ion Concentration
  • Molecular Sequence Data
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / chemistry*
  • Plasmids / chemistry
  • Transition Temperature

Substances

  • Buffers
  • DNA, Superhelical
  • Oligonucleotides
  • locked nucleic acid
  • triplex DNA
  • DNA
  • DNA Restriction Enzymes