Protection of oligodeoxynucleotides against nuclease degradation through association with self-assembling peptides

Aggregates of the self-assembling peptide EAK16II or EAK16IV and oligodeoxynucleotides (ODNs) were prepared, and their stability upon diluting the solution was investigated by UV–vis spectroscopy. The aggregates prepared at pH 4 and pH 7 did not dissociate after the solution was diluted 5- and 10-fold. The resistance against Escherichia coli exonuclease I of the ODN located in the EAK–ODN aggregates was studied by fluorescence resonance energy transfer (FRET) after the ODN had aggregated with EAK16II or EAK16IV at pH 4 or pH 7. The effect that the peptide sequence, peptide concentration, pH, and centrifugation had on protecting the aggregated ODN against nuclease degradation was investigated. Significant nuclease resistance was obtained after the EAK–ODN aggregates had been prepared at pH 4, with an EAK16IV concentration greater than a threshold value, and ensuring that the solution was not centrifuged immediately after sample preparation. Centrifuging the EAK16IV–ODN solution immediately after sample preparation resulted in the loss of this nuclease protection. However, if the solution of EAK–ODN aggregates was centrifuged 24 h after sample preparation, the nuclease protection afforded by the EAK16IV–ODN aggregates to the ODN was maintained even after being subject to a 10-fold dilution and up to 4 rounds of centrifugation over 4 days.