Synthesis of 3',5'-Dipeptidyl Oligonucleotides

Peptide-DNA hybrids are richly functionalized analogues of biomolecules that may have applications as hybridization probes and antisense agents with tunable binding and targeting properties. So far, synthetic efforts have mainly focused on hybrids bearing a single peptide chain, either at the 5'- or the 3'-terminus. Such singly modified analogues are vulnerable to nuclease attack at the unmodified terminus. Here we report a convenient and high-yielding solid-phase synthesis of 3'- and 5'-modified analogues of DNA with aminoacyl and peptidyl appendages at both termini. Using MALDI-TOF mass spectra of crude products as the criterion, serine, glycolic acid, hydroxylauric acid, and dimethyl hydroxypropionic acid were tested as 3'-linker residues. The latter, together with a direct amide link at the 5'-terminus, gave the highest yields of hybrids. The optimized procedure assembles hybrids on a controlled pore glass support bearing three consecutive omega-hydroxy lauric acid linkers. This support greatly reduces side reactions observed with conventional supports, probably due to its ability to increase steric accessibility during coupling ("swelling") and its rapid hydrolysis during deprotection with ammonium hydroxide. Dihybrids with aromatic, basic, and acidic amino acid residues were prepared, including H-Phe-Gly-TGCGCA-DP-Phe-OH, where DP denotes the dimethyl hydroxypropionic acid linker, whose structure was confirmed via mass spectrometry and one- and two-dimensional NMR. Further, a mixed coupling with seven Fmoc-protected amino acids was shown to produce a combinatorial library of dipeptidyl DNA hybrids.