Modified peptide nucleic acids are internalized in mouse macrophages RAW 264.7 and inhibit inducible nitric oxide synthase

Metal-containing peptide nucleic acid conjugates

Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA·DNA hybrid stability, and last but not least as probes for molecular and cell biology.

Preparation, 99mTc-labeling and biodistribution studies of a PNA oligomer containing a new ligand derivative of 2,2'-dipicolylamine

A new azido derivative of 2,2'-dipicolylamine (Dpa), 2-azido-N,N-bis((pyridin-2-yl)methyl)ethanamine, (Dpa-N(3)) was readily prepared from the known 2-(bis(pyridin-2-ylmethyl)amino)ethanol (Dpa-OH). It was demonstrated that Dpa-N(3) could be efficiently labeled with both [Re(CO)(3)(H(2)O)(3)]Br and [(99m)Tc(H(2)O)(3)(CO)(3)](+) to give [Re(CO)(3)(Dpa-N(3))]Br and [(99m)Tc(CO)(3)(Dpa-N(3))](+), respectively. Furthermore, Dpa-N(3) was successfully coupled, on the solid phase, to a Peptide Nucleic Acid (PNA) oligomer (H-4-pentynoic acid-spacer-spacer-tgca-tgca-tgca-Lys-NH(2); spacer= -NH-(CH(2))(2)-O-(CH(2))(2)-O-CH(2)-CO-) using the Cu(I)-catalyzed [2+3] azide/alkyne cycloaddition (Cu-AAC, often referred to as the prototypical "click" reaction) to give the Dpa-PNA oligomer. Subsequent labeling of Dpa-PNA with [(99m)Tc(H(2)O)(3)(CO)(3)](+) afforded [(99m)Tc(CO)(3)(Dpa-PNA)] in radiochemical yields >90%. Partitioning experiments in a 1-octanol/water system were carried out to get more insight on the lipophilicity of [(99m)Tc(CO)(3)(Dpa-N(3))](+) and [(99m)Tc(CO)(3)(Dpa-PNA)]. Both compounds were found rather hydrophilic (log D(o/w) values at pH=7.4 are -0.50: [(99m)Tc(CO)(3)(Dpa-N(3))](+) and -0.85: [(99m)Tc(CO)(3)(Dpa-PNA)]. Biodistribution studies of [(99m)Tc(CO)(3)(Dpa-PNA)] in Wistar rats showed a very fast blood clearance (0.26 ± 0.1 SUV, 1h p.i.) and modest accumulation in the kidneys (5.45 ± 0.45 SUV, 1h p.i.). There was no significant activity in the thyroid and the stomach, demonstrating a high in vivo stability of the (99m)Tc-labeled Dpa-PNA conjugate.

Therapeutically promising PNA complementary to a regulatory sequence for c-myc: pharmacokinetics in an animal model of human Burkitt's lymphoma

In Burkitt's lymphoma (BL) cells c-myc is often translocated in proximity to the Emu enhancer of the Ig gene locus. This translocation causes c-myc hyperexpression and an increase in the cells' proliferative capacity. A peptide nucleic acid (PNA) complementary to enhancer Emu intronic sequence (PNAEmu), linked to a nuclear localization signal (NLS), selectively and specifically blocks the expression of the c-myc oncogene under Emu control in vitro, suggesting potential therapeutic use. To explore this issue further, we have determined the pharmacokinetics of (14)C-labeled PNAEmu in SCID mice where a human tumor is established by inoculation of cells from a BL cell line. The data demonstrate that the compound has a relatively long life in vivo in tissues and, in particular, in BL tumor mass. Furthermore, in this animal model, PNAEmu shows low or no toxicity. All these results are in favor of a successful preclinical application in a BL human tumor animal model of a PNA targeting a regulatory, nontranscribed DNA sequence that can selectively inhibit the hyperexpression of a translocated gene linked to neoplastic cell expansion.

Characterization and complementation of a Fus3/Kss1 type MAPK from Tuber borchii, TBMK

Mitogen-activated protein kinases (MAPK) are used by organisms to transduce extra cellular signals from the environment in cellular events such as proliferation and differentiation. In the present study, we have characterized the first MAPK from the ectomycorrhizal fungus Tuber borchii (TBMK) which belongs to the YERK1 (yeast extra cellular regulated kinase) subfamily. TBMK is present as a single copy in the genome and the codified protein was phosphorylated during the interaction with the host plant, Tilia americana. Complementation studies showed that TBMK restores pheromone signaling in Saccharomyces cerevisiae and partially restores invasive growth of Fusarium oxysporum that lack the fmk1 gene. This suggests a protein kinase activity and its involvement in the infection processes. Hence, TBMK could play an important role during the pre-symbiotic phase of T. borchii with its host plant in the modulation of genes necessary for the establishment of symbiosis leading to the synthesis of functional ectomycorrhizae.

Medium-sized peptides as built in carriers for biologically active compounds

A growing number of oligopeptides of natural and/or synthetic origin have been described and considered as targeting structures for delivery bioactive compounds into various cell types. This review will outline the discovery of peptide sequences and the corresponding mid-sized oligopeptides with membrane translocating properties and also summarize de novo designed structures possessing similar features. Conjugates and chimera constructs derived from these sequences with covalently attached bioactive peptide, epitope, oligonucleotide, PNA, drug, reporter molecule will be reviewed. A brief note will refer to the present understanding on the uptake mechanism at the end of each section.

Comparison of novel delivery systems for antisense peptide nucleic acids

Peptide nucleic acids (PNAs) provide a powerful tool to study the mechanism of transcription and translation, an innovative strategy to regulate target gene expression. They have been successfully used in antisense technology, for their ability to specifically bind to messenger RNA (mRNA) targets and to inhibit translation of the target genes. However, unlike most of the DNA and RNA oligonucleotides, PNAs are poorly penetrated through the cell membrane, partially due to their uncharged property. To enhance the efficiency in PNA delivery, many strategies have been explored. We here compare the efficacy of three different delivery strategies for antisense PNA: 1) conjugation to hydrophobic peptides, 2) adsorption onto polymeric microspheres and 3) encapsulation in autologous erythrocytes. To this purpose, we designed and prepared PNA sequences able to inhibit the expression of macrophage enzymes involved in inflammatory process, i.e. nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX-2) and tested their antisense activity in a murine macrophage cellular model. Both delivery through polymeric microspheres and encapsulation into erythrocytes allowed the antisense activity of unmodified PNAs at nanomolar concentration.

Complexation to cationic microspheres of double-stranded peptide nucleic acid-DNA chimeras exhibiting decoy activity

The major aim of this paper was to determine whether cationic microspheres (CM), consisting of the permeable polymer Eudragit RS 100 plus the cationic surfactant dioctadecyl-dimethyl-ammonium bromide (DDAB(18)), could bind to double-stranded peptide nucleic acid PNA-DNA-PNA (PDP) chimeras exhibiting decoy activity against NF-kappaB transcription factors. Microspheres were produced by the 'solvent evaporation method' and centrifugation at 500, 1,000 and 3,000 rpm to obtain different-sized microparticles. Microsphere morphology, size and size distribution were determined by optical and electron microscopy observations. In order to determine their binding activity, double-stranded DNA-based and PDP-based decoy molecules were incubated with different amounts of microparticles in the presence of 100 ng of either (32)P-labeled DNA-DNA or DNA-PDP hybrid molecules or cold PDP-PDP hybrids. The complexes were analyzed by agarose gel electrophoresis. The resistance of (32)P-labeled DNA-DNA and DNA-PDP molecules in the presence of serum or cellular extracts was evaluated after binding to CM by gel electrophoresis analysis. DDAB(18) Eudragit RS 100 microspheres are able to bind to DNA-PDP and PDP-PDP hybrids, to deliver these molecules to target cells and to protect DNA-PDP molecules from enzymatic degradation in simulated biological fluids. In addition, when assayed in ex vivo conditions, DDAB(18) Eudragit RS 100 microspheres exhibited low toxicity. The results presented in this paper demonstrate that CM can be considered suitable formulations for pharmacogenomic therapy employing double-stranded PDP chimeras.

Peptide nucleic acid (PNA) binding-mediated gene regulation

Peptide nucleic acids (PNAs) are synthetic oligonucleotides with chemically modified backbones. PNAs can bind to both DNA and RNA targets in a sequence-specific manner to form PNA/DNA and PNA/RNA duplex structures. When bound to double-stranded DNA (dsDNA) targets, the PNA molecule replaces one DNA strand in the duplex by strand invasion to form a PNA/DNA/PNA [or (PNA)2/DNA] triplex structure and the displaced DNA strand exists as a single-stranded D-loop. PNA has been used in many studies as research tools for gene regulation and gene targeting. The D-loops generated from the PNA binding have also been demonstrated for its potential in initiating transcription and inducing gene expression. PNA provides a powerful tool to study the mechanism of transcription and an innovative strategy to regulate target gene expression. An understanding of the PNA-mediated gene regulation will have important clinical implications in treatment of many human diseases including genetic, cancerous, and age-related diseases.

Delivery of antisense peptide nucleic acids (PNAs) to the cytosol by disulphide conjugation to a lipophilic cation

Peptide nucleic acids (PNAs) are effective antisense reagents that bind specific mRNAs preventing their translation. However, PNAs cannot cross cell membranes, hampering delivery to cells. To overcome this problem we made PNAs membrane-permeant by conjugation to the lipophilic triphenylphosphonium (TPP) cation through a disulphide bond. The TPP cation led to efficient PNA uptake into the cytoplasm where the disulphide bond was reduced, releasing the antisense PNA to block expression of its target gene. This method of directing PNAs into cells is a significant improvement on current procedures and will facilitate in vitro and pharmacological applications of PNAs.

Formulations for natural and peptide nucleic acids based on cationic polymeric submicron particles

This article describes the production and characterization of cationic submicron particles constituted with Eudragit RS 100, plus different cationic surfactants, such as dioctadecyl-dimethyl-ammonium bromide (DDAB18) and diisobutyphenoxyethyl-dimethylbenzyl ammonium chloride (DEBDA), as a transport and delivery system for DNA/DNA and DNA/peptide nucleic acid (PNA) hybrids and PNA-DNA chimeras. Submicron particles could offer advantages over other delivery systems because they maintain unaltered physicochemical properties for long time periods, allowing long-term storage, and are suitable for industrial production. Submicron particles were characterized in terms of size, size distribution, morphology, and zeta potential. Moreover, the in vitro activity and ability of submicron particles to complex different types of nucleic acids were described. Finally, the ability of submicron particles to deliver functional genes to cells cultured in vitro was determined by a luciferase activity assay, demonstrating that submicron particles possess superior transfection efficiency with respect to commercially available, liposome-based transfection kits.

An efficient and versatile synthesis of bisPNA-peptide conjugates based on chemoselective oxime formation

Oligomers with two identical peptide nucleic acid sequences joined by a flexible hairpin linker (bisPNA) can stably bind to specific DNA sequences without altering plasmid supercoiling, thus offering a unique opportunity to attach various functional entities to high molecular weight DNA. Current synthetic approaches, however, severely limit the possibility to link peptides or other chemical moieties (i.e., sugars, oligonucleotides, etc.) to bisPNA. Here we report a novel strategy for the synthesis of bisPNA-peptide conjugates in which chemoselective ligation of bisPNA to peptides was accomplished through oxime formation between an oxy-amine-containing peptide and a bisPNA-methyl ketone (complementary modifications can also be used). The described synthesis is highly efficient, does not require a protection strategy, and is carried out under mild aqueous conditions. Through this methodology long peptide sequences in either C to N or N to C polarity can be linked to bisPNA. In addition, this protocol makes the conjugation of cysteine-containing peptides feasible and allows disulfide bond formation to be controlled. This same approach can be exploited to link oligonucleotides, sugars, or other chemical entities to bisPNA.

Cellular delivery of peptide nucleic acid (PNA)

Peptide nucleic acid (PNA) is a DNA mimic having a pseudopeptide backbone that makes it extremely stable in biological fluids. PNA binds complementary RNA and DNA with high affinity and specificity. These qualities make PNA a leading agent among "third generation" antisense and antigene agents. Unfortunately, fast progress in the exploration of PNA as an experimental and therapeutical regulator of gene expression has been hampered by the poor cellular uptake of PNA. However, a number of transfection protocols for PNA have now been established. These include microinjection, electroporation, co-transfection with DNA, conjugation to lipophilic moieties, conjugation to peptides, etc. Here we give a short introduction to the basic findings on PNA as an antisense and antigene agent in cell-free in vitro systems. This is followed by a comprehensive evaluation of the most interesting literature concerning cellular delivery and the intracellular effect of PNA. Also the current progress as regards using PNA as co-factor in DNA delivery is reviewed.

PNA targeting the PBS and A-loop sequences of HIV-1 genome destabilizes packaged tRNA3(Lys) in the virions and inhibits HIV-1 replication

During assembly of the HIV-1 virions, cellular tRNA(Lys)(3) is packaged into the virion particles and is utilized as a primer for the initiation of reverse transcription. The 3'-terminal 18 nucleotides of the cellular tRNA(Lys)(3) are complementary to nucleotides 183-201 of the viral RNA genome, referred to as the primer binding sequence (PBS). Additional sequences (A-Loop) upstream of the PBS are essential for tRNA primer selection. We report here that a PNA targeted to PBS and A-Loop sequence (PNA(PBS)) exhibits high specificity for its target sequence and prevents tRNA(Lys)(3) priming on the viral genome. We also demonstrate that PNA(PBS) is able to invade the duplex region of the tRNA(Lys)(3)-viral RNA complex and destabilize the priming process, thereby inhibiting the in vitro initiation of reverse transcription. The endogenously packaged tRNA(Lys)(3) bound to the PBS region of the viral RNA genome in the HIV-1 virion is efficiently competed out by PNA(PBS), resulting in near complete inhibition of initiation of endogenous reverse transcription. Examination of the effect of PNA(PBS) on HIV-1 production in CEM cells infected with pseudotyped HIV-1 virions carrying luciferase reporter exhibited dramatic reduction of HIV-1 replication by nearly 99%. Analysis of the mechanism of PNA(PBS)-mediated inhibition indicated that PNA(PBS) interferes at the step of reverse transcription. These findings suggest the antiviral efficacy of PNA(PBS) in blocking the process of HIV-1 replication.

Cationic liposomes as delivery systems for double-stranded PNA-DNA chimeras exhibiting decoy activity against NF-kappaB transcription factors

Peptide nucleic acids (PNAs) have been recently proposed as useful molecules in pharmacogenetic therapy, especially due to the fact that they show a very high stability with respect to DNA and RNA. However, PNAs are not efficient decoy molecules, are characterized by negligible cell internalization and low solubility and are not suitable to be delivered by liposomes. With respect to the biological activity of PNA-based molecules, PDP deserve great consideration, due to the fact that they exhibit high levels of solubility, and are expected to be resistant to proteinases and exonucleases. In this manuscript we determined whether double-stranded molecules based on PNA-DNA chimeras containing NF-kappaB binding sites, exhibit decoy activity against NF-kappaB transcription factors. In addition, we determined whether they can be complexed by cationic liposomes. The results obtained demonstrated that hybrids based on PNA-DNA chimeras are powerful decoy molecules against NF-kappaB p52 transcription factor. In addition, we found that cationic liposomes can be proposed for in vitro delivery to target cells of these decoy molecules. The results presented in this paper are thus of practical importance, since the simplicity and the versatility of the cationic liposome technology have made cationic liposomes useful nonviral gene delivery systems for human gene therapy.

Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs by extension of the cellular tRNA3(Lys) which anneals to the primer-binding site (PBS) on the 5' non-translated region of the viral RNA genome. The A-rich sequence (A-loop) upstream of the PBS interacts with the anticodon loop of tRNA3(Lys) and has been proposed to be essential for conferring specificity to tRNA3(Lys) for priming the initiation of HIV-1 reverse transcription. We observed that polyamide nucleic acid targeted to the A-loop sequence (PNAAL) exhibits high binding specificity for its target sequence. The PNAAL pre-bound to the A-loop sequence prevents tRNA3(Lys) priming on the viral RNA consequently blocking in vitro initiation of reverse transcription. Further, PNAAL can efficiently disrupt the preformed [tRNA3(Lys)--viral RNA] complex thereby rendering it non-functional for reverse transcription. The endogenous reverse transcription in disrupted HIV-1 virions containing packaged tRNA3(Lys) and its replicating enzyme RT was significantly inhibited by PNAAL, thus providing direct evidence of the involvement of the A-loop region of viral RNA genome in tRNA3(Lys) priming process. These findings suggest the potential of the A-loop region as a critical target for blocking HIV-1 replication.

Defining the peptide nucleic acids (PNA) length requirement for PNA binding-induced transcription and gene expression

Induction of gene expression has great potential in the treatment of many human diseases. Peptide nucleic acid (PNA) as a novel DNA-binding reagent provides an ideal system to induce gene-specific expression. In our recent studies, we have demonstrated that PNA bound to double-stranded DNA targets and, therefore, generated single-stranded D-loops and induced transcription of target genes both in vitro and in vivo. Most importantly, we have demonstrated that treatment of cultured human cells with PNAs led to expression of an endogenous target gene. Therefore, the study of the molecular mechanism of PNA binding-induced gene expression will have great implications for the gene therapy of many human diseases. In the current study, we have investigated the PNA length requirement for PNA binding-induced transcription initiation. Using a series of PNAs with different lengths, we have determined that PNAs with lengths of 16 approximately 18 nt induce very high levels of transcription in a HeLa nuclear extract in vitro transcription system. Transfection of the PNA-bound GFP reporter gene plasmid into human normal fibroblast (NF) cells led to a similar result. Gel-mobility shift assays revealed very strong binding affinities of these PNAs. DNA footprinting analysis further demonstrated the specificity of PNAs binding to the targets. These results lead to important understanding of the molecular mechanism of transcription initiation and highly valuable information in PNA design, especially for PNA binding-induced, gene-specific expression.

Delivery systems for DNA-binding drugs as gene expression modulators

Despite the large number of publications describing the synthesis and physicocharacterization of the binding between drugs and DNA, relatively few examine drug delivery systems (DDSs) for these molecules. The aim to find DDSs for DNA-binding drugs (DBDs) was prompted mainly to reduce the toxicity and/or enhance the tumor specificity of systemically administered drugs. With this in mind, we have reviewed the biological effects of some DBDs that are currently used as antitumor drugs and describe a brief selection of DDSs currently in clinical trials or on the market.

PNA oligomers as tools for specific modulation of gene expression

Small synthetic molecules that can specifically inhibit translation and/or transcription have shown great promise as potential antisense/antigene drugs. Peptide nucleic acid (PNA), an oligonucleotide mimic, has a non-charged achiral polyamide backbone to which the nucleobases are attached. PNA oligomers are extremely stable in biological fluids and they specifically hybridise to DNA or RNA in a complementary manner, forming very strong heteroduplexes. Some of the mRNAs have yet undetermined and possibly long half-lives, successful down regulation of gene expression by antisense oligonucleotides (ON) requires that the antisense agent is long lived. PNA fulfils this requirement better than phosphodiester or phosphorothioate ONs. PNA can inhibit transcription and translation of respective genes by tight binding to DNA or mRNA. First in vitro experiments to specifically down regulate protein expression by PNA have been followed by successful antisense and antigene application of PNA oligomers in vivo. This review discusses the principles of the in vitro and in vivo use of PNA oligonucleotides.

Liposomes as carriers for DNA-PNA hybrids

Peptide nucleic acids (PNAs) are DNA mimics composed of N-(2-aminoethyl)glycine units. This structure gives to PNAs (a) resistance to DNases and proteinases, (b) capacity to hybridize with high affinity to complementary sequences of single-stranded RNA and DNA, and (c) capacity to form highly stable (PNA)(2)-RNA triplexes with RNA targets. Furthermore, DNA-PNA hybrid molecules are capable to reversibly interact with DNA-binding proteins, being therefore of interest for studies on regulation of gene expression by the decoy approach. The major conclusion of this paper is that cationic liposomes are able to efficiently complexate DNA-PNA hybrid molecules and mediate their binding to target cells. Our results are of some interest, since, unlike commonly used nucleic acids analogs, PNA oligomers are not taken up spontaneously into the cells. In addition, they are not suitable for an efficient delivery with commonly used liposomal formulations. Transfection of PNA-DNA hybrid molecules to in vitro cultured cells could be of great interest to determine the applications of these new reagents to experimental alteration of gene expression.

Inhibition of telomerase activity by a cell-penetrating peptide nucleic acid construct in human melanoma cells

We investigated the effect of two peptide nucleic acids (PNAs), which are complementary to the RNA component of human telomerase, on the catalytic activity of the enzyme. PNAs induced a dose-dependent reduction of telomerase activity in cell extracts from human melanoma cell lines and surgical specimens. To down-regulate telomerase in intact cells, we generated a chimeric molecule synthesized by coupling the 13-mer PNA to the Antennapedia peptide. The PNA construct induced a dose- and time-dependent inhibition of telomerase activity. However, a 20-day exposure to the PNA construct only caused a slight increase in melanoma cell doubling time and failed to induce any telomere shortening.