Zwitterionic oligonucleotides: a study on binding properties of 2'-O-aminohexyl modifications

Nucleosides Nucleotides Nucleic Acids. 2005;24(8):1167-85. doi: 10.1081/NCN-200067400.

Abstract

2'-O-Aminohexyl side chains provide excellent conditions for zwitterionic interstrand and intrastrand interactions of oligonucleotides. 2'-O-Aminoalkylated phosphoramidites of adenosine and uridine were synthesized and incorporated in increasing number into homo adenosine and homo uridine/thymidine dodecamers, respectively. CD spectra of these dodecamers with complementary sense DNA exhibited a B-DNA type structure. While duplex stability values of all tested oligonucleotides were lower than those of the native oligonucleotides, they were significantly higher than those of 2'-O-heptyl modified oligonucleotides. The destabilization amounted to 0.9, 1.5, and 2.7 degrees C per modification for 2'-O-aminohexyl adenosine, 2'-O-aminohexyl uridine, and 2'-O-heptyl adenosine substitutions. These findings are pointing to a duplex stabilizing effect of the interaction of side chain amino groups with backbone phosphoric acid.

MeSH terms

  • Amines / chemical synthesis
  • Amines / chemistry*
  • Base Pairing*
  • Circular Dichroism
  • Nucleic Acid Hybridization
  • Nucleotides / chemistry*
  • Oligodeoxyribonucleotides / chemical synthesis
  • Oligodeoxyribonucleotides / chemistry*

Substances

  • Amines
  • Nucleotides
  • Oligodeoxyribonucleotides