The conformational effect of the interaction between various fusogenic peptides and an 18mer single stranded antisense oligonucleotide (ODN), targeted towards the green fluorescent protein mRNA, has been studied by circular dichroism spectroscopy in water and in the presence of anionic lysolipid micelles. The peptides used were the third helix of Antennapedia homeodomain pAntp-(43-58), the flock house virus FHV-gamma-(364-407) peptide, and its N-terminal gamma(1)-(364-384) and C-terminal gamma(2)-(390-407) fragments. The most significant conformational changes were observed in ODN-pAntp-(43-58) and ODN-FHV-gamma(2) complexes. The pAntp-(43-58) forms a complex with ODN through electrostatic interaction resulting in profound changes in the conformation of both the peptide and the ODN. In the case of FHV-gamma(2) peptide the complex formation takes place without altering the structure of ODN, and the decreased ratio of Deltaepsilon(208)/Deltaepsilon(222) reflects the insertion of the complexed peptide into the micelle. (C) 2003 Elsevier Inc. All rights reserved.