Structural Insights on Tiny Peptide Nucleic Acid (PNA) Analogues of miRNA-34a: An in silico and Experimental Integrated Approach

Abstract

In the present work, structural features of the interaction between peptide nucleic acid (PNA)-based analogs of the tumor-suppressor microRNA-34a with both its binding sites on MYCN mRNA were investigated. In particular, the region from base 1 to 8 (“seed” region) of miR-34a was reproduced in the form of an 8-mer PNA fragment (tiny PNA), and binding to target 3'UTR MYCN mRNA, was studied by a seldom reported and detailed NMR characterization, providing evidence for the formation of anti-parallel duplexes with a well-organized structural core. The formation of PNA-3'UTR duplexes was also confirmed by Circular Dichroism, and their melting curves were measured by UV spectroscopy. Nevertheless, this study offered a valuable comparison between molecular dynamics predictions and experimental evidence, which showed great correlation. Preliminary uptake assays were carried out in Neuroblastoma Kelly cells, using short peptide conjugates as carriers and FITC fluorescent tag for subcellular localization. Moderate internalization was observed without the use of transfecting agents. The reported results corroborate the interest toward the design and development of chimeric PNA/RNA sequences as effective RNA-targeting agents.

Nanoscale structures and mechanics of peptide nucleic acids

“…7 However, for peptide nucleic acids, we found very little literature surrounding the microscopic structural and mechanical properties of these polymeric molecules. [8][9][10][11][12][13][14] For short PNA strands and duplexes to be effectively used in experiments related to sequence detection, binding to other nucleic acid chains or in more complex biological processes, it is essential that the elastic properties of PNA strands should be studied in detail. As a start, we want to understand the elastic properties of PNA duplexes (dsPNA) and their hybrid duplexes in an aqueous environment and estimate the length scale at which bending occurs in these molecules.…”

Epigenetic Dysregulation in MYCN-Amplified Neuroblastoma

“…Together, they contribute to NCC identity by inhibiting specific growth signaling pathways, eventually regulating key TFs such as MYCN. In the context of MNA NB, let-7, miR-34a, miR-200b, and miR-204 are tumor suppressor miRNAs found to be downregulated, while miR-17-92 and miR-20a are oncogenic miRNAs that are upregulated [29,31,32]. As MYCN levels need to be tightly controlled to ensure proper development, dysregulation in the MYCN-miRNA interplay could thereby impact the balance between cell proliferation and differentiation of NCCs, potentially leading to tumorigenesis.…”

Advances in Nucleic Acid Research: Exploring the Potential of Oligonucleotides for Therapeutic Applications and Biological Studies

“…The PNA/RNA duplexes held very promising features of affinity and stability and in terms of cellular uptake despite the presence of multiple mismatches. Furthermore, an 8-mer PNA sequence, conjugated with a peptide carrier, was found to show moderate internalization in NB Kelly cells without any transfection agents [ 89 ].…”