Biophysical and cellular-uptake properties of mixed-sequence pyrrolidine-amide oligonucleotide mimics

Previously we introduced the positively charged pyrrolidine-amide oligonucleotide mimics (POM), which possess a pyrrolidine ring and amide linkage in place of the sugar-phosphodiester backbone of natural nucleic acids. Short POM homo-oligomers have shown promising DNA and RNA recognition properties. However, to better understand the properties of POM and to assess their potential for use as modulators of gene expression and bioanalytical or diagnostic tools, more biologically relevant, longer, mixed-sequence oligomers need to be studied. In light of this, several mixed-sequence POM oligomers were synthesised, along with fluorescently labelled POM oligomers and a POM-peptide conjugate. UV thermal denaturation showed that mixed-sequence POMs hybridise to DNA and RNA with high affinity but slow rates of association and dissociation. The sequence specificity, influence of terminal amino acids, and the effect of pH and ionic strength on the DNA and RNA hybridisation properties of POM were extensively investigated. In addition, isothermal titration calorimetry (ITC) was used to investigate the thermodynamic parameters of the binding of a POM-peptide conjugate to DNA. Cellular uptake experiments have also shown that a fluorescently labelled POM oligomer is taken up into HeLa cells. These findings demonstrate that POM has the potential for use in a variety of applications, alongside other modified nucleic acids developed to date, such as peptide nucleic acids (PNA) and phosphoramidate morpholino oligomers (PMO).