Peptide nucleic acid-ionic self-complementary peptide conjugates: highly efficient DNA condensers with specific condensing mechanism

Abstract

A new type of conjugated molecule including T′3-(AKAE)2, T′3-(IKIE)2, and A′3-(AKAE)2 was designed by linking short peptide nucleic acid (PNA) segments with short ionic self-complementary peptide (ISCP) sequences. These short conjugates showed high hybridization affinity and specificity for λ-DNA. They can induce efficient DNA condensation at low micromole concentrations via a specific mechanism that involves the base pair recognition between DNA and the PNA segment and the self-aggregation of the bound PNA-ISCP molecules. Atomic force microscopy (AFM) and dynamic light scattering (DLS) measurements indicated that λ-DNA took an elongated conformation while it compacted into globules when interacting with the PNA-ISCP conjugates. The ethidium bromide displacement assay indicated that the PNA-ISCP conjugates induced DNA condensation in a way different from conventional cationic condensers such as polyethyleneimine (PEI) and hexadecyltrimethylammonium bromide (CTAB). The interaction between T′3-(AKAE)2 and a single chain oligonucleotide, d(A)36, was further studied and the results revealed that the PNA-ISCP conjugates bound with DNA mainly via base pairing recognition. The volume ratio of λ-DNA and the λ-DNA/PNA-ISCP globules was calculated based on AFM measurements, which was near 1:1, suggesting that the condensation was an intramolecular folding process for λ-DNA, which was prompted by the self-aggregation of the bound PNA-ISCP molecules.