Comparing the dsDNA-Targeting Characteristics of Invader and acpcPNA Probes
Faculty Mentor Information
Dr. Patrick Hrdlicka, University of Idaho
Presentation Date
7-16-2026
Abstract
Recognition of specific double-stranded DNA (dsDNA) regions by exogenous modalities remains an important challenge in chemical biology, as this would enable applications in diagnostics, gene regulation, and therapeutic development. Invader probes are energetically activated, artificial nucleic acid duplexes capable of efficient sequence-unrestricted recognition of genomic dsDNA targets. More recently, acpcPNA (Pyrrolidinyl peptide nucleic acid) probes have emerged as a potential alternative approach for dsDNA targeting. However, comparative studies with Invader probes have not been performed. In this study, single-stranded acpcPNA probes were directly compared with Invader probes using a TA-rich model target. Thermal denaturation experiments were performed to evaluate the thermodynamic driving forces associated with probe-target recognition, while gel mobility shift assays were used to assess dsDNA invasion efficiency across multiple probe concentrations. Thermal denaturation studies verified that acpcPNA probes display favorable thermodynamic driving forces for dsDNA recognition. However, while Invader probes achieved complete recognition of the model dsDNA target at a 5-fold molar excess, acpcPNA probes required markedly higher concentrations to achieve comparable recognition efficiencies. These findings indicate that Invader probes – at least in this sequence context – are one of the most promising classes of dsDNA-targeting probes.
Comparing the dsDNA-Targeting Characteristics of Invader and acpcPNA Probes
Recognition of specific double-stranded DNA (dsDNA) regions by exogenous modalities remains an important challenge in chemical biology, as this would enable applications in diagnostics, gene regulation, and therapeutic development. Invader probes are energetically activated, artificial nucleic acid duplexes capable of efficient sequence-unrestricted recognition of genomic dsDNA targets. More recently, acpcPNA (Pyrrolidinyl peptide nucleic acid) probes have emerged as a potential alternative approach for dsDNA targeting. However, comparative studies with Invader probes have not been performed. In this study, single-stranded acpcPNA probes were directly compared with Invader probes using a TA-rich model target. Thermal denaturation experiments were performed to evaluate the thermodynamic driving forces associated with probe-target recognition, while gel mobility shift assays were used to assess dsDNA invasion efficiency across multiple probe concentrations. Thermal denaturation studies verified that acpcPNA probes display favorable thermodynamic driving forces for dsDNA recognition. However, while Invader probes achieved complete recognition of the model dsDNA target at a 5-fold molar excess, acpcPNA probes required markedly higher concentrations to achieve comparable recognition efficiencies. These findings indicate that Invader probes – at least in this sequence context – are one of the most promising classes of dsDNA-targeting probes.