Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers

Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (gamma PNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and gamma PNA. Both PNA and gamma PNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/gamma PNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like gamma PNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.

Automated summary

This study developed synthetic molecules, PNA and gamma PNA, capable of targeting i-motif DNA structures. The biophysical experiments demonstrated the successful invasion of i-motif by PNA and gamma PNA, showing strong binding and high thermal stability. Targeting KRAS transcription using high-affinity oligonucleotide mimics like gamma PNAs may offer a potential anti-cancer strategy.