Antisense properties of peptide nucleic acid

Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose phosphate backbone has been replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNA-oligomers can be synthesized in relatively large amounts, are highly stable in biological environments, and bind complementary DNA and RNA targets with remarkably high affinity and specificity. Thus PNA possesses many of the properties desired for a good antisense agent. Until recently, limited uptake of PNA into cells has been the major obstacle for applying PNA as an antisense agent in cell cultures and in vivo. Here, the antisense properties of PNA in vitro and in vivo will be reviewed. In particular, we will focus on recent observations indicating that PNA equipped with or without various uptake moieties may function as an efficient and gene-specific inhibitor of translation in Escherichia coli and in certain mammalian cell types.

Inhibition of human telomerase in immortal human cells leads to progressive telomere shortening and cell death

The correlation between telomerase activity and human tumors has led to the hypothesis that tumor growth requires reactivation of telomerase and that telomerase inhibitors represent a class of chemotherapeutic agents. Herein, we examine the effects of inhibition of telomerase inside human cells. Peptide nucleic acid and 2'-O-MeRNA oligomers inhibit telomerase, leading to progressive telomere shortening and causing immortal human breast epithelial cells to undergo apoptosis with increasing frequency until no cells remain. Telomere shortening is reversible: if inhibitor addition is terminated, telomeres regain their initial lengths. Our results validate telomerase as a target for the discovery of anticancer drugs and supply general insights into the properties that successful agents will require regardless of chemical type. Chemically similar oligonucleotides are in clinical trials and have well characterized pharmacokinetics, making the inhibitors we describe practical lead compounds for testing for an antitelomerase chemotherapeutic strategy.

Antisense PNA tridecamers targeted to the coding region of Ha-ras mRNA arrest polypeptide chain elongation

We have previously described the rational design of mutation-selective antisense oligonucleotides targeted to codon 12 of oncogenic Ha-ras mRNA. In order to further improve the biological efficacy of these unmodified oligonucleotides, we have studied three different classes of modifications: peptide nucleic acid backbone (PNA), sugar modification (2'-O-methyl) and phosphoramidate linkage (PN). We show that PNA is unique among the investigated steric blocking agents in its ability to specifically inhibit the translation of Ha-ras mRNA in vitro. The PNA-RNA hybrid (Tm=86 degrees C), which is not dissociated by cellular proteins and resists phenol extraction and urea denaturing conditions, specifically blocks the translation of mutated Ha-ras mRNA. A PNA tridecamer which forms with wild-type Ha-ras mRNA a duplex with a central mismatch had little effect on mRNA translation. Codon 12 is located close to the translation initiation site and hybridization of the PNA at this position may interfere with the assembly of the translation initiation complex. To test whether polypeptide chain elongation can also be blocked, we have targeted PNA tridecamers to codons in the 74, 128 and 149 regions. These PNAs form equally stable duplexes as that formed by the PNA targeted to the codon 12 region (ten G.C base-pairs out of 13). We show that PNA-RNA duplexes block the progression of the 80 S ribosome. Therefore, it is possible to arrest translation with concomitant production of a truncated protein by using duplex-forming PNA oligonucleotides targeted to a G+C-rich sequences. Our data demonstrate for the first time that a non-covalent duplex can arrest the translation machinery and polypeptide chain elongation.

Telomerase inhibition by peptide nucleic acids reverses 'immortality' of transformed human cells

Telomerase activity, the ability to add telomeric repeats to the ends of chromosomes, has been detected in most immortal cell lines including tumor cells, but is low or absent in most diploid, mortal cells such as those of somatic tissues. Peptide nucleic acids (PNAs), analogs of DNA or RNA which bind to complementary nucleic acids with very high affinity, were co-electroporated into immortal human cells along with a selectable plasmid. Introduction of PNAs inverse-complementary to telomerase RNA effectively inhibited telomerase activity in intact cells, shortened telomeres, reduced colony size, and arrested cell proliferation after a lag period of 5-30 cell generations, consistent with suppression of their 'immortality'. Electroporation of selection plasmid alone had no effect, while PNAs of altered sequence were markedly less effective in each assay. This constitutes the first demonstration of cell growth arrest through telomerase inhibition, upon treatment of intact cells with an exogenous compound which can be efficiently delivered in vivo. The phenotype of telomerase-inhibited transformed cells differs from senescence of normal diploid fibroblasts, but rather resembles the crisis state of incompletely transformed cells.

In vitro transcriptional and translational block of the bcl-2 gene operated by peptide nucleic acid

The antisense and antigene activity of peptide nucleic acid (PNA) targeted to the human B-cell lymphoma (bcl)-2 gene was evaluated in vitro. Several PNAs complementary to different sequences of bcl-2, including the start codon and the 5'-untranslated region (5'-UTR), were tested. One PNA directed against the AUG start codon and another recognizing the 5'-UTR were able to specifically reduce Bcl-2 protein synthesis in a cell-free system; however, only partial inhibition (80 and 54%, respectively) was obtained when they were used singularly. Complete translation block was obtained with the simultaneous presence of both PNAs. A triplex-forming bis-PNA was targeted to a homopurine sequence on the coding strand of the bcl-2 cDNA. In an in vitro transcription assay this PNA specifically inhibited the transcription of bcl-2 at concentrations as low as 300 nM, with the concomitant appearance of a truncated 200-base-long product. These results demonstrate the ability of PNA to selectively modulate both translation and transcription of bcl-2 in vitro and suggest its potential use as an antisense and an antigene agent in order to downregulate bcl-2 expression in tumors.

Peptide nucleic acids as therapeutic agents

Peptide nucleic acids (PNAs) have been around for more than seven years and it was hoped, at their introduction, that they would quickly enter the fields of antisense and antigene technology and drug development. Despite their extremely favorable hybridization and stability properties, as well as the encouraging antisense and antigene activity of PNA in cell-free systems, progress has been slow and experiments on cells in culture and in animals have been lacking. Judging from the very promising results published within the past year, however, there is every reason to believe that both PNA antisense and, possibly, PNA antigene research will strongly pick up momentum again. Specifically, it has been demonstrated that certain peptide-PNA conjugates are taken up very efficiently by, at least some, eukaryotic cells and that antisense down regulation of target genes in nerve cells in culture is attainable using such PNA conjugates. Perhaps even more exciting is that antisense-compatible effects have been reported using PNAs injected into the brain of rats. Finally, it has been shown that the bacterium Escherichia coli is susceptible to antisense gene regulation using PNA.

Antisense oligonucleotides for target validation in the CNS

Although antisense oligonucleotides have been used in cell-based antisense experiments for nearly two decades, studies to investigate the function of CNS proteins in living animals were not successfully conducted until recently. Oligonucleotides are not transported across the blood-brain barrier to any appreciable extent. Consequently, these molecules need to be administered directly into the brain. Antisense approaches may be especially suited to investigation of CNS proteins. Due to their specificity, antisense sequences can more easily and selectively distinguish between closely related proteins, such as receptor subtypes, in contrast to the more traditional pharmacological agents such as small molecule ligands. This review discusses some unique technical aspects surrounding oligonucleotide delivery to the brain, and summarizes some of the more noteworthy applications of antisense tools to the study of CNS protein function during the past two years.

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

Overexpression of inducible nitric oxide synthase causes the production of high levels of nitric oxide, which, under pathological conditions, leads to immunosuppression and tissue damage. The results recently obtained using peptide nucleic acids, rather than traditional oligonucleotides as antigen and antisense molecules, prompted us to test their efficacy in the regulation of nitric oxide production, thereby overcoming the obstacle of cellular internalization. The cellular permeability of four inducible nitric oxide synthase antisense peptide nucleic acids of different lengths was evaluated. These peptide nucleic acids were covalently linked to a hydrophobic peptide moiety to increase internalization and to a tyrosine to allow selective 125I radiolabelling. Internalization experiments showed a 3-25-fold increase in the membrane permeability of the modified peptide nucleic acids with respect to controls. Inducible nitric oxide synthase inhibition experiments on intact stimulated macrophages RAW 264.7 after passive permeation of the two antisense peptide nucleic acids 3 and 4 demonstrated a significant decrease (43-44%) in protein enzymatic activity with respect to the controls. These data offer a basis for developing a good alternative to conventional drugs directed against inducible nitric oxide synthase overexpression.

2,5-oligoadenylate-peptide nucleic acids (2-5A-PNAs) activate RNase L

To potentiate the 2-5A (2',5'-oligoadenylate)-antisense and peptide nucleic acid (PNA) approaches to regulation of gene expression, composite molecules were generated containing both 2-5A and PNA moieties. 2-5A-PNA adducts were synthesized using solid-phase techniques. Highly cross-linked polystyrene beads were functionalized with glycine tethered through a p-hydroxymethylbenzoic acid linker and the PNA domain of the chimeric oligonucleotide analogue was added by sequential elongation of the amino terminus with the monomethoxytrityl protected N-(2-aminoethyl)-N-(adenin-1-ylacetyl)glycinate. Transition to the 2-5A domain was accomplished by coupling of the PNA chain to dimethoxytrityl protected N-(2-hydroxyethyl)-N-(adenin-1-ylacetyl)glycinate. Finally, (2-cyanoethyl)-N,N-diisopropyl-4-O-(4,4-dimethoxytrityl)butylphosphor amidite and the corresponding (2-cyanoethyl)-N,N-diisopropylphosphoramidite of 5-O-(4,4'-dimethoxytrityl)-3-O-(tert-butyldimethylsilyl)-N6-benzoyladeno sine were the synthons employed to add the 2 butanediol phosphate linkers and the four 2',5'-linked riboadenylates. The 5'-phosphate moiety was introduced with 2-[[2-(4,4'-dimethoxytrityloxy)ethyl]sulfonyl]ethyl-(2-cyanoethyl) -N,N-diisopropylphosphoramidite. Deprotection with methanolic NH3 and tetraethylammonium fluoride afforded the desired products, 2-SA-pnaA4, 2-5A-pnaA8 and 2-5A-pnaA12. When evaluated for their ability to cause the degradation of two different RNA substrates by the 2-5A-dependent RNase L, these new 2-5A-PNA conjugates were found to be potent RNase L activators. The union of 2-5A and PNA presents fresh opportunities to explore the biological and therapeutic implications of these unique approaches to antisense.

[Inhibition of Bcl-2 expression in HL60 cells by incubation with antisense phosphorothioate oligodeoxynucleotides]

OBJECTIVE

To observe whether the expression of Bcl-2 mRNA and protein in HL60 cells could be decreased by incubation with antisense phosphorothioate oligodeoxnucleotides (ASPO) at different concentrations (5micromol/L,10micromol/L,and 20micromol/L).

METHODS

The expressions of Bcl-2 protein and mRNA in HL60 cells were individually determined by immunocytochemistry, flow cytometry and RT-PCR.

RESULTS

In the presence of ASPO, the levels of Bcl-2 mRNA and protein could be decreased. The inhibitory effect appeared in the first 24 hours of incubation and became intense as the concentration increased and the time prolonged,but it abated after 72 hours of incubation. Inhibition was not noted in the presence of sense phosphorothioate oligodeoxynucleotides(SPO).

CONCLUSION

The data suggested that ASPO could inhibit the expression of Bcl-2 mRNA and protein in HL60 cells and the inhibitory effect depended on the specific sequences, the concentration and the time of incubation, but it could not last very long.

Applications of peptide nucleic acids

Several exciting new developments in the applications of the DNA mimic peptide nucleic acid (PNA) have been published recently. A possible breakthrough may have come in efforts to develop PNA into gene therapeutic drugs. In eukaryotic systems, antisense activity of PNAs (as peptide conjugates) has been reported in nerve cells and even in rats upon injection into the brain, and antisense activity has also been demonstrated in Escherichia coli. PNA hybridization technology has developed rapidly within in situ hybridization, and exciting new methods based on MALDI-TOF detection have also been presented.

Synthesis of a new class of HIV-1 inhibitors

A new family of molecules potentially inhibitors of the HIV-1 Tat-TAR complex was prepared. These compounds are constituted by dinucleotide analogs (PNA dimer) bound, through a linker, to an arginine residue. In this series, several molecules inhibit viral development in cell culture with a micromolar IC50 and without cellular toxicity until 200 microM concentration.

Inhibition of a DNA-helicase by peptide nucleic acids

Bis-peptide nucleic acid (bis-PNA) binding results in D-loop formation by strand displacement at complementary homopurine stretches in DNA duplexes. Transcription and replication in intact cells is mediated by multienzymatic complexes involving several proteins other than polymerases. The behaviour of the highly stable clamp structure formed by bis-PNAs has thus far been studied with respect to their capacity to arrest RNA polymerases. Little attention has been given to their recognition and processing by DNA helicases. In this report we have investigated the inhibitory effect of a bis-PNA on the DNA-helicase activity of the well characterized herpes simplex type I UL9 protein. Unwinding by UL9 of a synthetic substrate is significantly inhibited by a bis-PNA and the addition of the ICP8 protein, which increases UL9 processivity, does not relieve this inhibition.

Modified (PNA, 2'-O-methyl and phosphoramidate) anti-TAR antisense oligonucleotides as strong and specific inhibitors of in vitro HIV-1 reverse transcription

Natural beta-phosphodiester 16mer and 15mer antisense oligonucleotides targeted against the HIV-1 and HIV-2 TAR RNAs respectively were previously described as sequence-specific inhibitors of in vitro retroviral reverse transcription. In this work, we tested chemically modified oligonucleotide analogues: alpha-phosphodiester, phosphorothioate, methylphosphonate, peptide nucleic acid or PNA, 2'- o -methyl and (N3'-P5') phosphoramidate versions of the 16mer anti-TAR oligonucleotide. PNA, 2'- O -methyl and (N3'-P5') phosphoramidate oligomers showed a strong inhibitory effect compared with the unmodified 16mer, with reverse transcription inhibition (IC50) values in the nanomolar range. The inhibition was sequence-specific, as scrambled and mismatched control oligonucleotides were not able to inhibit cDNA synthesis. No direct binding of the 2'- O -methyl, PNA or (N3'-P5') phosphoramidate anti-TAR oligonucleotides to the HIV-1 reverse transcriptase was observed. The higher T m obtained with 2'- O -methyl, (N3'-P5') phosphoramidate and PNA molecules concerning the annealing with the stem-loop structure of the TAR RNA, in comparison with the beta-phosphodiester oligonucleotides, is correlated with their high inhibitory effect on reverse transcription.

[PNA--peptide nuclei acids. Used as gene-therapeutic drugs]

The principles of gene therapeutic "antigen" and "antisense" drugs are briefly presented. The target of such drugs is the genetic material of the cell--either the DNA itself, or its messenger molecules, mRNA. By exploiting base-complementary principles, "antigen" and especially "antisense" drugs can easily be designed to target specific genes, the activity of which it is medically advantageous to inhibit. These could be virus- or oncogenes. In particular, the prospects of using peptide nucleic acids (PNA) as gene therapeutic drugs are discussed. PNA is a synthetic structural DNA mimic, which chemically is more closely related to peptides and proteins and which has so far shown very promising chemical and (molecular) biological properties in terms of its development into gene therapeutic drugs as well as diagnostic tools.