Comparative kinetic analysis of PNA and γ-miniPEG-PNA hybridization with RNA by surface plasmon resonance

Nucleic acid analogs that bind RNA through sequence-specific base pairing have emerged as important tools for modulating RNA function. Peptide nucleic acids (PNAs), featuring a neutral N-(2-aminoethyl)-glycine backbone, exhibit high affinity, sequence selectivity and enzymatic stability. Their non-phosphodiester backbone prevents RNase H recruitment, favoring steric and recognition-based mechanisms. However, conventional PNAs are limited by poor aqueous solubility, aggregation, non-specific interactions and insufficient pharmacokinetic properties. This limitation can be addressed by incorporating γ-miniPEG (mp) side chains, which improve solubility, reduce aggregation and preorganize the backbone while retaining favorable binding characteristics. Because biological activity depends on target engagement and residence time, understanding PNA/RNA hybridization kinetics is essential, in addition to cellular uptake, localization and target accessibility. A quantitative understanding of hybridization kinetics is therefore critical for candidate selection. Yet, direct comparisons of γ-miniPEG-modified PNAs with RNA remain scarce; to date, such studies have been limited to mp-PNA/DNA duplexes. Here, we systematically compare the hybridization of RNA, PNA and mp-PNA toward complementary RNA using surface plasmon resonance (SPR) spectroscopy, which enables real-time analysis of association and dissociation kinetics at constant temperature. Unlike thermal melting analysis, SPR resolves individual kinetic steps and provides insights into duplex stability under defined conditions. Our results reveal that dissociation kinetics depend strongly on strand length, whereas association is governed primarily by backbone chemistry. Unmodified PNA associates 5-8-fold faster than RNA while maintaining strong affinity. These findings establish a quantitative kinetic framework for understanding how backbone architecture and oligomer length shape PNA/RNA hybridization dynamics, supporting kinetic characterization as a complement to equilibrium measurements in the evaluation of PNA designs.