Peptide Nucleic Acid Derivatives Research Articles

Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications

Abstract Peptide nucleic acid (PNA) is a DNA analog, in which the sugar-phosphate backbone in DNA is replaced by poly[N-(2-aminoethyl)glycine]. Since its discovery in the early 1990s, PNA has been widely employed in chemistry, biochemistry, medicine, nanotechnology, and many other fields. This account surveys recent developments on the design of PNA derivatives and their applications. In the first part, PNAs for sequence-specific recognition of DNA and RNA (single-strands, double-strands, G-quadruplexes, i-motifs, and others) are comprehensively covered. Modifications of nucleobases and of the main chain effectively promote both the strength of binding and the selectivity of recognition. In the second half of this account, practical applications of PNA are presented. Structural restraints, induced by complex formation of PNA with DNA and RNA substrates, lead to selective transformation of target sites to desired structures. Applications to regulation of gene expression, gene editing, construction of sophisticated nanostructures, and others are also described. Advantages and disadvantages of PNAs, compared with other sequence-recognizing molecules hitherto reported, are discussed in terms of various physicochemical and biological features.

Acid-base and lipophilic properties of peptide nucleic acid derivatives

The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pKa) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pKa values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties.

Synthesis and physicochemical properties of 20-mer peptide nucleic acid conjugates with testosterone 17β-carboxylic acid

Although peptide nucleic acids (PNAs) have improved nuclease resistance compared with DNA or RNA, it is difficult to synthesize long PNAs because of poor elongation yield. Herein we synthesized 20-mer PNAs (PNA20), targeting Nnmt mRNA, as well as its conjugate with testosterone 17β-carboxylic acid, in high purity and yield. This synthesis was conducted using Oxyma as a condensation agent and NMP as a solvent for Fmoc-PNA-C(Bhoc)-OH. The resistance of PNA20 to exonuclease was higher than that of RNA. Furthermore, the abilities of PNA20 and its conjugate to bind to complementary DNA were stronger than that of DNA or RNA. These findings lay the basis for the synthesis of long PNA derivatives toward oligonucleotide therapeutics.

Fluorescence and Morphology of Self-Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates.

Studies carried out in recent decades have revealed that the ability to self-assemble is a widespread property among biomolecules. Small nucleic acid moieties or very short peptides are able to generate intricate assemblies endowed with remarkable structural and spectroscopic properties. Herein, the structural/spectroscopic characterization of aggregates formed by nucleobases and peptide nucleic acid (PNA)-peptide conjugates are reported. At high concentration, all studied nucleobases form aggregates characterized by previously unreported fluorescence properties. The conjugation of these bases, as PNA derivatives, to the dipeptide Phe-Phe leads to the formation of novel hybrid assemblies, which are characterized by an amyloid-like association of the monomers. Although these compounds share the same basic cross-β motif, the nature and number of PNA units have an important impact on both the level of structural order and the intrinsic fluorescence of the self-assembled nanostructure.

Targeting duplex DNA with the reversible reactivity of quinone methides.

DNA alkylation and crosslinking remains a common and effective strategy for anticancer chemotherapy despite its infamous lack of specificity. Coupling a reactive group to a sequence-directing component has the potential to enhance target selectivity but may suffer from premature degradation or the need for an external signal for activation. Alternatively, quinone methide conjugates may be employed if they form covalent but reversible adducts with their sequence directing component. The resulting self-adducts transfer their quinone methide to a chosen target without an external signal and avoid off-target reactions by alternative intramolecular self-trapping. Efficient transfer is shown to depend on the nature of the quinone methide and the sequence-directing ligand in applications involving alkylation of duplex DNA through a triplex recognition motif. Success required an electron-rich derivative that enhanced the stability of the transient quinone methide intermediate and a polypyrimidine strand of DNA to associate with its cognate polypurine/polypyrimidine target. Related quinone methide conjugates with peptide nucleic acids were capable of quinone methide transfer from their initial precursor but not from their corresponding self-adduct. The active peptide nucleic acid derivatives were highly selective for their complementary target.

Conformational studies of chiral d-Lys-PNA and achiral PNA system in binding with DNA or RNA through a molecular dynamics approach

The growing interest in peptide nucleic acid (PNA) oligomers has led to the development of a very wide variety of PNA derivatives. Among others, the introduction of charged chiral groups on a PNA oligomer has proven effective in improving DNA binding ability, complexation direction and cellular uptake. In particular, the introduction of three adjacent chiral monomers based on D-Lys in the middle of the PNA sequence (D-Lys-PNA) has produced noteworthy results in modulating the directionality of the binding with the DNA complementary strand and in mismatch detection. Here, through a molecular dynamics approach, a comparative study has been carried out to investigate the structural properties that drive the interaction of the chiral D-Lys-PNA and the corresponding achiral PNA system with DNA as well as RNA complementary strands, starting from the crystal structure of D-Lys-PNA in complex with DNA. The results obtained complement experimental data and indicate that the binding with the RNA molecule, compared to DNA, is differently affected by the addition of three D-Lys groups on the PNA backbone, suggesting that this modification could be taken into account for the development of new PNA-based molecules able to discriminate between DNA and RNA.

γ sulphate PNA (PNA S): Highly Selective DNA Binding Molecule Showing Promising Antigene Activity

Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.

Specific uptake and interactions of peptide nucleic acid derivatives with biomimetic membranes

There is a growing interest in understanding the uptake mechanism of metal-containing peptide nucleic acid (PNA) bioconjugates into living cells. In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) has been used to explore the membrane specific uptake and interactions of PNA/peptide/Ru(II) conjugates. For all lipid compositions, the unmodified PNA oligomer and its Ru(II) conjugate were found to traverse freely across the membrane in a trans-membrane manner, causing no significant changes in the membrane structure. The nuclear localised signal peptide (NLS) conjugated sequences showed membrane specific activities. In model mammalian and bacterial-mimetic membranes, rapid trans-membrane insertion was observed followed by a concentration dependent disruption and irreversible structural changes to the membrane system. The variations in the magnitude of the structural changes and in their tendency to facilitate disruption are ascribed to hydrophobicity, the cationic charge introduced on modification of the original PNA backbone as well as the physical state of the model membrane used.

Photolabile Peptide Nucleic Acid Monomers: Synthesis and Photodeprotection

The photolabile 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC) group has been introduced as an amino protecting group for peptide nucleic acids (PNA) to be used as building blocks in photolithographic solid-phase PNA synthesis. NPPOC-protected PNA derivatives undergo fast light-promoted deprotection with high per step coupling efficiency.

New Strategy to Antiviral Agents from Peptide Nucleic Acid Derivatives.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Synthesis of macrocyclic peptide nucleic acid derivatives via intramolecular chemical ligation

Macrocyclic peptide nucleic acids can be obtained by direct or indirect intramolecular cyclisation of N-terminal cysteine functionalised PNA-thioesters

Synthesis, Properties and Functions of Peptide Nucleic Acids (PNA) and Their Derivatives

AbstractFor Abstract see ChemInform Abstract in Full Text.

New Strategy to Antiviral Agents from Peptide Nucleic Acid Derivatives

New strategy to develop antiviral agents against HIV and herpes virus from the derivatization of peptide nucleic acid monomers has been described.

ペプチド核酸（ＰＮＡ）およびその類縁体からなる機能性人工核酸の合成と性質

In 1991 Nielsen et al. first described peptide nucleic acid (PNA), which is a DNA mimic with a pseudopeptide backbone composed of N-(2-aminoethyl) glycine units with the nucleobases attached to the glycine nitrogen via carbonyl methylene linkers. PNA is a very attractive molecule as a DNA mimic because it shows high biological stability with strong binding-affinity to complementary DNA and RNA. The limitations of PNA include low aqueous solubility, ambiguity in DNA binding orientation and poor membrane permeability. Various PNA derivatives were reported to improve physicochemical and biological properties of PNA. Chirality was introduced into the achiral PNA backbone to influence the selectivity in DNA binding orientation. PNA backbone was rigidified by introduction of ring structure to preorganize PNA for duplex formation. This review focuses on the chemistry and biological activity of PNA, and gives an overview of backbone modifications of PNA.

Control of tRNA function by antisense PNA derivatives.

The interaction of antisense peptide nucleic acid (PNA) with yeast tRNA(Phe) was investigated. A 6-mer PNA complementary to the 3'-terminal sequence including the 73ACCA end hybridized to the tRNA. While the PNA with a single mismatch did not. PNA is a promising candidate for controlling tRNA functions by the sequence-specific hybridization.

Assessment of High-Affinity Hybridization, RNase H Cleavage, and Covalent Linkage in Translation Arrest by Antisense Oligonucleotides

Antisense oligonucleotides (ONs) are designed to hybridize target mRNA in a sequence-specific manner and inhibit gene expression by preventing translation, either by activation of RNase H or steric blockage of the ribosome complex. Second-generation ONs, which possess greater binding affinity for target RNA relative to the isosequential phosphodiester (PO) ONs, have been developed and include, among others, peptide nucleic acids (PNA) and N3' P5' phosphoramidate oligonucleotides (npONs). In the present study, PNA and npON derivatives were targeted to the coding portion of the complementary mRNA of the N protein of the vesicular stomatitis virus (VSV) in order to evaluate their ability to arrest translation in an in vitro rabbit reticulocyte lysate system. High-affinity hybridization of ONs lacking RNase H activity was not sufficient to block translation in this test system. Only antisense ONs acting via an RNase H mechanism or by steric hindrance through covalent attachment (via transplatin modification) to the target mRNA were found to definitively arrest translation in this study.