Synthesis and hybridization analysis of a small library of peptide-oligonucleotide conjugates

A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA, An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino acids lysine, ornithine, histidine and arginine, the hydrophobic amino acid tryptophan, and alanine as a spacer, Melting temperature analysis indicated that T-m depended principally on the number of cationic residues. The free energies of binding for polycationic peptide-oligonucleotides were enhanced compared with the unmodified 8mer, The origin of this stabilizing effect was found to be derived from a more exothermic enthalpic term. Improvement in Delta G(vH) was found to depend on the presence of positive charge and also the exact identity of the cationic amino acid, with the polyarginine peptide giving the most favourable Delta G(vH) value and the most exothermic Delta H-vH. Further exploration suggested that the cationic peptide fragments interacted mainly with single-stranded rather than duplex DNA, A study of pH dependence showed that the polyhistidine conjugate was particularly sensitive to pH changes near neutrality, as indicated by a significant rise in T-m from 19.5 degrees C at pH 8.0 to 28.5 degrees C at pH 6.0.