Phosphonate Analogues of Peptide Nucleic Acids and Related Compounds: Synthesis and Hybridization Properties

Abstract

The synthesis of a set of novel chimeric oligomers representing PNA and phosphono-PNA analogues has been accomplished, and their binding affinity to complementary DNA and RNA strands was evaluated.     

Synthesis and Hybridization Properties of Modified Oligonucleotides with PNA-DNA Dimer Blocks

Abstract

Different modified PNA-DNA dimer-analogous synthons (I and II) were synthesized as phosphoramidites. These dimer units were assembled by a 5′-modified deoxythymidine and a modified PNA monomer. These synthons were used in the routine coupling procedure for oligonucleotides. Therefore no PNA coupling chemistry is necessary to synthesize PNA-DNA chimeric oligonucleotides. Various deoxyoligonucleotides were synthesized introducing the dimer blocks I and II at different positions in the sequences. Melting temperatures of the modified oligonucleotides with their complementary DNA analogues were determined.

Backbone modifications of oligonucleotides are required in the antisense strategy for protection against endonucleolytic cleavage in biological environment. Peptide nucleic acids (PNA fragments) are known to be nuclease resistant analogues, which show stable and discriminating hybridization. For this reason we prepared chimeric PNA-DNA oligomers by incorporation of two different modified PNA-DNA dimer blocks (Scheme A) into oligonucleotides. Melting temperatures of the modified oligonucleotides with their complementary DNA were determined.     

Long Range Electron Transfer in PNA/DNA Duplexes

Abstract

The conductive properties of PNA/DNA is examined. The electron donor is covalently linked to a fixed site in PNA which unambiguously places the acceptor in the hybrid duplex. The study shows that PNA/DNA acts like an insulator.     

PNA∗Synthesis and Diagnostic Application

Abstract

An optimized automated PNA synthesis protocol is reported. Under optimal conditions the product yield of a test 17-mer PNA is approximately 90 %. The average coupling yield is 99.4 %. The synthesis strategy is Boc/Z. The protocol is developed in a 5 pmole scale but is easily scaled up to 10–50 μmole scale syntheses on the automated synthesizer (ABI 433A). DNA capture experiments by PNA was used to develop a method for PNA-mediated purification of genomic Chlamydia DNA from urine. This purification removed efficiently substances that impeded DNA amplification.

     

6-Thioguanine in Peptide Nucleic Acids. Synthesis and Hybridization Properties

Abstract

The synthesis of N-((2-amino-6-benzylthiopurine-9-yl)acetyl)-N-(2-tBoc-aminoethyl)glycine 4 and its incorporation into a peptide nucleic acid (PNA) oligomer are described. Introduction of a single 6-thioguanine residue (6sG) in the PNA of a 10-mer PNA:DNA heteroduplex resulted in a decrease in Tm of 8.5°C. Furthermore, we observed a hypochromic and a bathochromic shift of 6 nm above 346 nm when the 6sG containing PNA was hybridized to its complementary DNA strand.     

Structural Pre-organization of Peptide Nucleic Acids

Abstract

Introduction of constraint via chemical bridging in the aegPNA leads to the five or six membered cyclic structures that may contribute towards maintaining the balance between rigidity and flexibility of the PNA backbone. The significant promise of our approach to use the naturally occurring trans-4-hydroxy-L-proline to arrive at different chirally pure cyclic PNA analogs and their DNA binding properties will be presented.     

Pna Array Technology in Molecular Diagnostics

Abstract

A comparative study using immobilised DNA and PNA oligomers demonstrates the suitability of PNA molecules as sequence specific capture probes in the detection of single point mutations in a DNA analyte and in the analysis of complex analyte mixtures.     

Suppression of Exonucleolytic Degradation of Double-Stranded DNA and Inhibition of Exonuclease III by PNA

Abstract

Degradation of double-stranded DNA by Exonuclease III in the presence of complementary anti-parallel PNA was studied. It was found for the first time that the PNA suppresses the degradation of dsDNA in a sequence-specific manner as well as inhibits the activity of Exonuclease III in a non-specific way.     

Recognition of Double-Stranded Dna by Peptide Nucleic Acid

Abstract

Peptide nucleic acid (PNA) is an oligonucleotide mimic in which the backbone of DNA has been replaced by a pseudopeptide. We here show that there are distinct variations as to how PNA oligomers interact with double-stranded DNA depending on choice of nucleobases. Thymine-rich homopyrimidine PNA oligomers recognise double-stranded polynucleotides by forming PNA₂-DNA triplexes with the DNA purine strand. By contrast, cytosine-rich homopyrimidine PNAs add to double-stranded polynucleotides as Hoogsteen strands, forming PNA-DNA₂ triplexes, while homopurine, or alternating thymine-guanine, PNA oligomers invade DNA to form PNA-DNA duplexes.     

Conformationally Restrained Chiral PNA Conjugates: Synthesis and DNA Complementation Studies

Abstract

In recent times, PNA (I), a structural mimic of DNA in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine (aeg) linkage has emerged as a potential antisense therapeutic agent.¹ A major limitation of PNAs from an application perspective is their poor solubility in aqueous medium and being achiral, they bind to cDNA in both parallel (N-PNA/5′-DNA) and antiparallel (N-PNA/3′-DNA) modes. In this connection, we have designed spermine conjugated and conformationally constrained PNA analogues to generate the 4-aminoprolyl backbone (II).² These were synthesised and evaluated for their DNA binding abilities by using UV and CD spectroscopic studies. It is seen that incorporation of one 4-aminoprolyl unit at the N-terminus of a PNA chain not only enhances the inherent binding of PNA to DNA, but also imparts significant bias in parallel and antiparallel binding with cDNA. Conjugation of spermine at C-terminus enhanced the PNA solubility.     

PNA-DNA Chimeras Containing 5-Alkynyl-pyrimidine PNA Units. Synthesis,Binding Properties,and Enzymatic Stability

Abstract

Three chimeric dimer synthons (oeg_t^NHT, oeg_up^NHT and oeg_uh^NHT) containing thymine (t), 5-(l-propynyl)-uracil (up) and 5-(1-hexyn-1-yl)-uracil (uh) PNA units with N-(2-hydroxyethyl)glycine (oeg) backbone were synthesized in solution and incorporated into T₂₀ oligonucleotide analogues, using standard P-amidite chemistry. Insertion of dimer blocks led to destabilization of duplexes with dA₂₀ target. The smallest T _m drops were found for chimeras containing oeg_up^NHT dimers. Incorporation of the chimeric synthons into the 3′-end of T₂₀ brought about growing resistance to 3′-exonucleolytic (SV PDE) cleavage in the order of oeg_t^NHT < oeg_up^NHT < oeg_uh^NHT. Due to different endonuclease activities of 3′- and 5′-exonucleases applied, placing of five consecutive dimers at the 5′-terminus resulted in a relatively smaller, but also side-chain dependent, stabilization towards the hydrolysis by 5′-exonuclease (BS PDE). Neither exonucleases (SV and BS PDE) nor an endonuclease (Nuclease P₁) could hydrolyse the unnatural phosphodiester bond linking the 3′-OH of thymidine to the terminal OH of N-(2-hydroxyethyl)glycine PNA backbone.     

Liquid Phase Synthesis of Peptide Nucleic Acid (or Polyamide Nucleic Acid) Dimers

Abstract

The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.     

Automated Chemical Synthesis of PNA and PNA-DNA Chimera on a Nucleic Acid Synthesizer

Abstract

Automated chemical synthesis of PNA and PNA-DNA chimera on a DNA synthesizer using the monomethoxytrityl/acyl protecting group strategy is described.     

Triplex Formation Between DNA and Mixed Purine-Pyrimidine PNA Analog with Lysines in Backbone

Abstract

Melting UV experiments and mixing curves indicated slow triplex formation between lysine comprising PNA and DNA complement in 100mM Na⁺ solution.     

APPLICATION OF MITSUNOBU REACTION TO SOLID-PHASE PEPTIDE NUCLEIC ACID (PNA) MONOMER SYNTHESIS

ABSTRACT

PNA type I monomer backbone with a reduced peptide bond was synthesized on a Merrifield resin in Mitsunobu reaction of Boc-amino ethanol with resin-bound o-nitrobenzenesulfonylglycine. The pseudo dipeptide secondary amine group was deprotected by thiolysis and acylated with thymin-1-ylacetic acid. The monomer was released as a methyl ester. The procedure seems to be of general applicability and allows various modifications of PNA structure by using diverse alcohols and amino acid esters.     

Synthesis of New Chiral Peptide Nucleic Acid (PNA) Monomers by a Simplified Reductive Animation Method

Abstract

The aim of this work was the preparation of four new peptide nucleic acid (PNA) monomer backbone by reductive animation of N^α-Boc-protected chiral amino aldehydes, derived from Leu, Phe, Tyr(Bzl), and Thr(Bzl), with methyl glycinate. To the crude 2-substituted methyl N-(2-Boc-aminoethyl)glycinates obtained, thymin-1-ylacetic acid was coupled using TBTU procedure in a one-pot reaction. PNA monomers were isolated and characterized.     

In Vitro Membrane Penetration of Modified Peptide Nucleic Acid (PNA)

Abstract

Efficient cellular uptake is crucial for the success of any drug directed towards targets inside cells. Peptide nucleic acid (PNA), a DNA analog with a promising potential as a gene-directed drug, has been shown to display slow membrane penetration in cell cultures. We here used liposomes as an in vitro model of cell membranes to investigate the effect on penetration of a PNA molecule colvalently modified with a lipophilic group, an adamantyl moiety. The adamantyl attachment was found to increase the membrane-penetration rate of PNA three-fold, as compared to corresponding unmodified PNA. From the penetration behaviour of a number of small and large molecules we could conclude that passive diffusion is the mechanism for liposome-membrane passage. Flow linear dichroism (LD) of the modified PNA in presence of rod-shaped micelles, together with octanol-water distribution experiments, showed that the adamantyl-modified PNA is amphiphilic; the driving force behind the observed increased membrane-penetration rate appears to be an accumulation of the PNA in the lipid double layer.     

Alterations in PNA binding of keratinocytes in oral keratosis

Abstract

Changes in the expression of peanut lectin (PNA) were examined in keratinocytes of oral keratosis showing a mixture of hyperortho- and hyperparakeratinized epithelium. In the hyperorthokeratinized epithelium, which was reacted with anti-filaggrin antibody in both granular and cornified cells, PNA bound to the surface of keratinocytes from the spinous layer to the granular layer. Neither anti-filaggrin nor PNA reactions were detected in keratinocytes of the hyperparakeratinized epithelium. After neuraminidase pretreatment, however, PNA staining appeared in all cells, except cornified cells, of both hyperortho- and hyperparakeratinized epithelia. These findings suggest that PNA-binding epitopes in keratinocytes were modified by sialic acid during the hyperparakeratotic process of oral keratosis.     

Covalent Coupling of a PIM-1 Oncogene Targeted PNA with an Antennapedia Derived Peptide

Abstract

Peptide nucleic acids (PNA) are promising antisense molecule for blocking gene expression in cell culture or in vivo. Nevertheless because they are poor efficient to pass the cellular membrane, it is necessary to use a vectorisation agent to observe an inhibitory effect. We describe the coupling of the rhodamine labeled 17-mer antisense PNA to a fusogenic peptide from antenapedia via S-S linkage, the studies of the penetration of this complex into fibroblast cells and its inhibitory effect on piml targeted protononcogene.