Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Abstract

Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA’s chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA’s binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA’s binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.

A Single‐Molecule Insight into the Ionic Strength‐dependent, Cationic Peptide Nucleic Acids‐Oligonucleotides Interactions

“…This design allows PNAs to retain the specificity of Watson‐Crick and Hoogsteen bases recognition. PNAs constitute a unique class of polynucleotides binding ligands capable of interacting with their target sites efficiently and in a highly sequence‐specific manner, are less susceptible to biological degradation by nucleases, proteases, and peptidases, do not require high salt concentration for binding due to the absence of Coulombic repulsion interactions manifested between negatively charged DNA strands, and are useful in nucleic acid detection systems and as antisense molecules, and became an extremely useful research tool in many assays and diagnostics [2–8] . PNAs high binding affinity and sequence selectivity toward DNAs, biochemical stability and facile functionalization, made them attractive for oligonucleotide sensing applications [9] …”

“…PNAs constitute a unique class of polynucleotides binding ligands capable of interacting with their target sites efficiently and in a highly sequence-specific manner, are less susceptible to biological degradation by nucleases, proteases, and peptidases, do not require high salt concentration for binding due to the absence of Coulombic repulsion interactions manifested between negatively charged DNA strands, and are useful in nucleic acid detection systems and as antisense molecules, and became an extremely useful research tool in many assays and diagnostics. [2][3][4][5][6][7][8] PNAs high binding affinity and sequence selectivity toward DNAs, biochemical stability and facile functionalization, made them attractive for oligonucleotide sensing applications. [9] Despite the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNAs or RNAs, the ionic conditions proved relevant for PNA-dsDNA interactions, [10] and in a landmark paper, authors have presented compelling evidence that high concentrations of salt (> 1 M) led to a lowering of the PNA-DNA duplexes melting temperature and hence augmented structural destabilization.…”

Nicked Invader probes: multistranded and sequence-unrestricted recognition of double-stranded DNA

“…Considerable attention has been devoted to the development of molecules that recognize specific sequences of double-stranded DNA (dsDNA) due to the prospect for tools that enable regulation of gene expression at the transcriptional level, detection of diagnostically important sequences, and gene editing. Long before the advent of CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) endonucleases, 1,2 oligomeric probes recognizing nucleobase-specific features accessible from the duplex grooves, such as triplex forming oligonucleotides (TFOs) 3,4 and peptide nucleic acids (PNAs), 5–7 or pyrrole-imidazole polyamides, 8,9 were extensively studied. However, these dsDNA-targeting probes have a limited target scope.…”

Fluorobenzene Nucleobase Analogues for Triplex‐Forming Peptide Nucleic Acids

“…In addition, novel Janus‐wedge triplets [15] and other innovative heterocycles [16] have been investigated for molecular recognitions of complex folded RNA and DNA [17] . However, further development of novel heterocyclic nucleobases, especially for recognition of Hoogsteen faces of pyrimidine nucleosides, is required to expand the applications of PNA‐dsRNA triplexes in biological systems [18] …”

“…[17] However, further development of novel heterocyclic nucleobases, especially for recognition of Hoogsteen faces of pyrimidine nucleosides, is required to expand the applications of PNA-dsRNA triplexes in biological systems. [18] In the present study, we tested five fluorinated PNA nucleobases in comparison to unsubstituted benzene. We found that F2, and the closely related F3, as nucleobase surrogates in triplex forming PNA preferred binding the Hoogsteen face of UÀ A base pair, though with relatively modest affinity and selectivity over other base pairs.…”