Backbone modifications of aromatic peptide nucleic acid (APNA ) monomers and their hybridization properties with DNA and RNA

J Org Chem. 2001 May 18;66(10):3372-9. doi: 10.1021/jo001650o.

Abstract

Aromatic peptide nucleic acid (APNA) monomers containing N-(2-aminobenzyl)-glycine, N-(2-aminobenzyl)-(R)- or -(S)-alanine, and N-(2-aminobenzyl)-beta-alanine moieties as part of their backbone were synthesized. These novel analogues were incorporated as a single "point mutation" in PNA hexamers, and their physicochemical properties were investigated by UV thermal denaturation and CD experiments. Destabilization in triplex formation between the PNA-APNA chimeras and complementary DNA or RNA oligomers was observed, as compared to the PNA control. The APNA monomer composed of the N-(2-aminobenzyl)-glycine backbone led to the smallest decrease in the thermal stability of the triplexes formed with DNA and RNA, while maintaining selectivity for base-pairing recognition. Since the PNA-APNA chimeras are more lipophilic than the corresponding PNA homopolymers, these oligomers may also exhibit better cell membrane permeability properties.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminobutyrates / chemical synthesis
  • Aminobutyrates / chemistry
  • Aminobutyrates / metabolism
  • Benzylamines / chemical synthesis
  • Benzylamines / chemistry
  • Benzylamines / metabolism
  • Drug Stability
  • Hot Temperature
  • Nucleic Acid Denaturation
  • Nucleic Acid Hybridization*
  • Peptide Nucleic Acids / chemical synthesis*
  • Peptide Nucleic Acids / chemistry
  • Peptide Nucleic Acids / metabolism
  • Poly A / metabolism
  • Polynucleotides / metabolism*
  • Thymine

Substances

  • Aminobutyrates
  • Benzylamines
  • Peptide Nucleic Acids
  • Polynucleotides
  • Poly A
  • poly(dA)
  • 2-amino-4-phenylbutyric acid
  • Thymine