Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1236218 | ENA |
REPOSITORIES: ENA
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Project description:Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
2021-03-19 | GSE155764 | GEO
Project description:Peptide nucleic acid (PNA) is a neutral DNA analog uniquely suited for triple helical recognition of nucleic acids. However, the practical applications of triplex-forming PNAs have been limited by sequence restrictions, as stable base triples are formed only with purines. Hoogsteen recognition of pyrimidines has been a long-standing challenge. Here, a new approach to improve pyrimidine recognition by enhancing nucleobase stacking in the PNA strand is demonstrated by targeting procursor micro RNA (pre-miRNA). Placing 5-triazolyl uridine adjacent to the modified nucleobases designed for Hoogsteen recognition of pyrimidines in double helical RNA increased the binding affinity while maintaining sequence specificity. The increased binding affinity improved the biological activity of triplex-forming PNAs. RNA-seq analysis targeting mature microRNAs showed that a PNA recognizing a mixed sequence of three nucleobases (G, A, and U) had higher specificity than a similar PNA featuring a uniform purine recognition tract. These results demonstrate a novel strategy to address the issue of pyrimidine recognition, which has been the critical bottleneck for triple helical targeting of nucleic acids.
2026-03-05 | GSE307169 | GEO
Project description:Here, we determined the ability of peptide nucleic acid (PNA) oligomers, coupled to different cell-penetrating peptides (CPPs), to interfere in regulatory RNA circuits of human blood-derived leukocytes. Using RNA-seq, FACS and confocal microscopy we identified octaarginin as a CPP enabling PNA delivery and sequence-dependent RNA inhibition in blood-derived myeloid cells at nanomolar concentration. At 200 nM, an R8-PNA targeting immune-regulatory microRNA-155 was delivered into nearly 100 % of human macrophages within 24 hours without apparent cytotoxicity, and globally de-repressed microRNA-155 target-mRNAs. This was not observed when coupling the PNA inhibitor to a K3 instead of the R8 peptide. We suggest that CPP choice is a fundamental success-determining factor for therapeutic RNA-inhibition in human myeloid leukocytes.
2021-03-01 | GSE152740 | GEO