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We report the synthesis of a peptide nucleic acid (PNA) monomer containing preQ 1 , a positively charged guanine analogue. The new monomer was incorporated into PNA oligomers using standard Fmoc-chemistry-based solid-phase synthesis. The preQ 1 unit-containing PNA oligomers exhibited improved affinity for their complementary DNA through electrostatic attraction, and their sequence specificity was not compromised. It could be beneficial to incorporate preQ 1 into PNA oligomers instead of guanine when creating antisense/antigene agents or research tools., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

A combination of antibacterial agents should make the emergence of resistance in bacteria less probable. Thus we have analyzed the synergistic effects between antibacterial antisense peptide nucleic acids (PNA) and conventional antibiotics against Escherichia coli AS19 (lipopolysaccharide defective) strain and a derivative of a pathogenic strain E. coli O157:H7. PNAs were designed to target mRNA transcripts encoding the essential acyl carrier protein (gene acpP) and conjugated to the cell-penetrating peptide (KFF) 3 K for cellular uptake. Antibiotics included aminoglycosides, aminopenicillins, polymyxins, rifamycins, sulfonamides and trimethoprim. Synergies were evaluated using the checkerboard technique. Fractional Inhibitory Concentration indices (FICi) were calculated for all combinations based on the minimal inhibitory concentration of each individual agent. The results demonstrate two novel synergistic combinations of antimicrobial agents, namely, (KFF) 3 K-PNA anti-acpP with polymyxin B and (KFF) 3 K-PNA anti-acpP with trimethoprim (both with FICi = 0.38). Polymyxin B's synergy postulates cell wall targeted antibiotics as attractive agents to improve the uptake of PNA while trimethoprim's interaction with PNA my reveal a new inhibitory mechanism., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. In this study, we have synthesized PNAs incorporating 2-amino-6-vinylpurine (AVP) for the covalent targeting of single-stranded DNA and RNA, and evaluated their reactivities for these targets. PNA containing AVP at the N-terminal position showed a high reactivity to uracil in RNA and thymine in DNA at the complementary site with AVP. In addition, the crosslinking reactions to pre-miR122 with PNA containing AVP increased the inhibition effect for the Dicer processing of pre-miR122 in vitro., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Peptide nucleic acid (PNA) monomers with a methyl group at the β-position have been synthesized. The modified monomers were incorporated into PNA oligomers using Fmoc chemistry for solid-phase synthesis. Thermal denaturation and circular dichroism (CD) studies have shown that PNA containing the S-form monomers was well suited to form a hybrid duplex with DNA, whose stability was comparable to that of unmodified PNA-DNA duplex, whereas PNA containing the R-form monomers was not., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

To investigate the antisense effect of a pyrrolidine-based oxy-peptide nucleic acid (POPNA), we carried out the LacZ reporter assay using a 12-mer trans-l-POPNA conjugated with a cell-penetrating peptide (antisense reagent). The antisense effect of the conjugated POPNA (inhibition of LacZ activity) was comparable to that shown by a Nielsen-type peptide nucleic acid. Furthermore, the conjugated POPNA could switch the LacZ activity over a wide range of ambient temperatures., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

A new mRNA targeting contrast agent consisting of three main functional domains, (i) gadolinium based magnetic resonance reporter part, (ii) antisense peptide nucleic acids targeted to mRNA, and (iii) cholesterol as the delivery vector, was developed and synthesized. The new contrast agent showed efficient cellular uptake and significant contrast enhancement at very low labeling concentrations (0.5 microM). However, after uptake into cells the agent was located predominantly in endosomes like a similar cell penetrating peptide conjugated probe. Our results indicate that this newly developed contrast agent could be used for the labeling of cells for optical as well as magnetic resonance imaging., (2010 Elsevier Ltd. All rights reserved.)

Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5'-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.

Continuing our research on the development of nucleopeptides as ODN analogs for biomedical and bioengineering applications, here we report the synthesis and the chemical-physical characterization of a homoadenine hexamer based on a l-diaminobutyric acid (l-DABA) backbone (dabPNA), and its binding studies with a complementary aegPNA. We demonstrated by CD and UV experiments that the l-dabPNA binds the aegPNA forming a complex with good thermal stability, that we identified as a left-handed triplex.

Cyclic PNAs targeting the HIV-1 TAR RNA loop have been synthesized following a convenient solid-phase strategy which allows on-resin cyclisation. UV-monitored thermal denaturation studies demonstrate that these cyclic PNAs are able to strongly interact with their TAR RNA target, very likely through the formation of a six-base pair stable complex, involving the TAR RNA loop.

Guanidine-based peptide nucleic acid (GPNA) monomers and oligomers containing all four natural (adenine (A), cytosine (C), guanine (G), and thymine (T)) and two unnatural (2-thiouracil (sU) and 2,6-diaminopurine (D)) nucleobases have been synthesized. Thermal denaturation study showed that GPNA oligomers containing alternate D-backbone configuration bind sequence-specifically to DNA and, when incubated with mammalian cells, localized specifically to the endoplasmic reticulum (ER).

The solid phase synthesis of PNA oligomers with the internal dipeptide Gly-Phe is presented and the interaction with complementary DNA investigated. UV absorbance melting experiments with different but complementary DNA sequences show that stable PNA x DNA duplexes are only obtained when there is no DNA base opposite the dipeptide unit. Instead, the dipeptide spacer forms a loop-like structure within the duplex. Further functionalization with N-heterocyclic ligands is described. p-Nitro-phenylalanine is introduced in place of Phe during solid phase synthesis and subsequently reduced to p-amino-phenylalanine. Reaction with activated acids provides the ligand conjugates in high yield and purity. This strategy opens a universal route to a large number of internal substitutions in PNA chemistry.

Peptide nucleic acids (PNAs) C- or N-modified with dioxime ligands were prepared by solid-phase synthesis using iron(II)-clathrochelates as protected dioxime building blocks. These PNA bind complementary DNA sequence specifically, though with much reduced affinity in comparison with nonmodified PNA. The dioxime-PNA conjugates bind Cu2+ and Ni2+ at microM concentration.

PNAs with terminal modifications of varying structure and charge were synthesized and their binding to DNA was studied. A variation in thermal stability of 19. 8 degrees C has been observed between the least and the most stable PNA-DNA duplexes. The most stable duplex melts 7.7 degrees C higher than the duplex of the corresponding non-modified PNA and complementary DNA. It has been shown that sequence fidelity of the PNA conjugate having the highest DNA affinity is significantly better than that of non-modified PNA. The results obtained can be used for the design of PNA probes, whose binding to DNA is sequence independent.

Conjugates of peptide nucleic acids (PNA) and metal binding ligands were prepared using solid-phase synthesis. Stability of duplexes of bis-picolylamine-PNA conjugates and DNA was found to be modulated by equimolar concentrations of bioavailable metal ions: Ni(2+), Zn(2+)>Cu(2+). Sequence specificity of PNA was not compromised in the presence of these metal ions.

The preparation of t-butoxycarbonyl (Boc)-protected O(4)-(o-nitrophenyl) thymine peptide nucleic acid (PNA) monomer is described. This PNA monomer was incorporated into PNA oligomer sequences. The post-synthetic modification of the oligomers to yield fluorescently-labelled PNA oligomers was studied before and after the removal of the protecting groups. In both cases, the desired fluorescently-labelled PNA oligomer was obtained in good yields.

New constrained PNA monomers containing a substituted thiazolidine or a thiazane ring were synthesized and incorporated in the center of a 9-mer homothymine PNA. The PNA/DNA hybrids stability was studied by UV-melting experiments which showed that the presence of the modified unit destabilizes the PNA/DNA triplexes.

A unique conformationally-restricted peptide library was constructed using a loop structure as a structural scaffold. This library was used for the screening of the amino acid sequences that control the interaction between nucleobase triplets. The peptides have PNAs at the C-terminus as the recognition site and the random amino acid sequence at the N-terminus as the effector for the interaction between PNA and its complementary DNA triplets. From the peptide libraries constructed by the positional scanning method, the sequences that affect the interaction between PNA and complementary DNA were selected. The difference in the characteristic results by using A-T and G-C pairs was presented. This study would also give us some useful information about interaction between peptides and nucleic acids, such as relevances between these biomolecules in a prebiotic era.

Chimeric molecules consisting of peptide nucleic acid (PNA) and lactose have been synthesized to test the hypothesis that lactose moieties can promote cell-specific uptake of PNAs. We find that lactose modified PNAs rapidly enter liver-derived HepG2 cells while unmodified PNAs do not and that lactose modified PNAs can inhibit cellular telomerase.

A synthon of D-proline substituted at the 4-position by thymine and at N by a flexible aminoethyl linker, has been used to prepare a novel chiral peptide nucleic acid (cPNA) with (2R,4R) stereochemistry using solid phase methodology. The homothymine decamer cPNA binds to complementary polyadenylic acid to form a 2:1 hybrid with high affinity and specificity according to UV and CD studies, whereas no binding to the corresponding polydeoxyadenylic acid was observed.

2-5A was conjugated to N-(2-aminoethyl)-glycyl PNA by periodate oxidization, followed by coupling with amino-derivatized PNA and final cyanoborohydride reduction. An adduct of 2-5A pentamer with tetrameric thymine PNA activated RNase L with the same potency as earlier versions of 2-5A-PNA or 2-5A-DNA.

Peptides containing peptide nucleic acid (PNA) have been designed and synthesized to construct molecules recognizing a bulge or a loop structure of RNA. Such peptides were here designed from the HIV Rev protein that can bind the stem-loop IIB of the Rev responsive element (RRE) RNA. Variations of PNA modulated the binding affinities of the peptides to RRE IIB RNA.

Homopentamers of PNA consisting of L- and D-lysine were synthesized. It was found that the intramolecular hydrogen bonding has no significant influence on intermolecular interaction. These pentamers show a tendency to form complex with polyA in tris(pH 8.0) solution. The L-conformer has more potential than D-isomer.

A novel approach to monomeric PNA building blocks by a solution phase Ugi multi component reaction (MCR) is described. The reaction is easily performed in 96 well plates. The products precipitate from the reaction solution and are thus obtained in high yields and purity. Those products are not amenable by another multi step synthesis in such a diversity.

The synthesis of PNA-monomers with variations in the substitution pattern using the Ugi-Reaction is described. The one-pot procedure leads to new totally protected PNA-monomers which can be selectively cleaved to N-protected monomeric building blocks for PNA synthesis.

Problems were encountered during attempts to prepare N-terminal cysteine-substituted peptide nucleic acids (PNAs) from commercially available, Fmoc-protected monomers. These problems have been surmounted by the use of an S-t-butylmercapto protecting group on the cysteine moiety. The solid-phase syntheses are carried out via a simplified procedure which should be generally useful for manual PNA synthesis.