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.     

Towards a Chemical Etiology of Nucleic Acid Structure

To Leslie E. Orgel, arbiter elegantiarum of contemporary origin-of-life science and far-sighted pioneer of non-enzymic molecular replication, on the occasion of his 70th birthday, with cordial congratulations and best wishes.In the sequel of some general remarks on a chemical etiology of nucleic-acid structure, the paper presents a reproduction of the sequence of slides which were shown in the author's lecture Pyranosyl-RNA at the 8. ISSOL Conference in Orléans. Each slide figure is accompanied by a short explanatory comment.     

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.     

PNA-DNA chimeras containing 5-alkynyl-pyrimidine PNA units. Synthesis, binding properties, and enzymatic stability

Three chimeric dimer synthons (oeg_t(NH)T, oeg_up(NH)T and oeg_uh(NH)T) containing thymine (t), 5-(1-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 Tm drops were found for chimeras containing oeg_up(NH)T 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(NH)T < oeg_up(NH)T < oeg_uh(NH)T. 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.     

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.     

New Strategies for the Chemical Synthesis of Biologically Important Nucleic Acid Derivatives

Abstract

This paper describes general methods for the synthesis of N-phosphorylated ribonucleosides and oligonucleotides containing a 2′-O-phosphorylated or 2′-O-thiophosphorylated ribonucleoside. The NMR-based conformational analysis and computational molecular dynamics simulation of the 2′-O-phosphorylated ribonucleoside residue in such modified oligonucleotides suggested that the ribose residue existed preferentially in a C2′-endo conformation. It was also found that simple heating of 2′-O-phosphorylated oligonucleotides resulted in rapid dethiophosphorylation.     

A Polymeric Support for Chemical and Enzymatic Nucleic Acid Synthesis (1)

Abstract

A non-swellable, highly porous support material -CPG 3000 - was used in building up covalently bound nucleic acids by combined chemical and enzymatic methods. Bases are optimal accessible for hybridization and enzymatic reactions because they are not involved in the linking procedure.     

肽核酸与核酸分子杂交的模式及其在基因诊断领域中的应用

在发明肽核酸(peptide nucleic acid,PNA)后的短短十年间,由于PNA分子独特的生物学性能,使之可以与DNA及RNA分子通过不同的机制形成稳定的复合物,导致PNA在基因诊断领域有得天独厚的优势。本文综述了PNA与核酸分子杂交的几种不同模式以及最近几年PNA在基因诊断领域的一些最新进展。     

Synthesis of Peptide Nucleic Acid Monomers

Abstract

The chemical synthesis of peptide nucleic acid (PNA) monomers is described using Fmoc (backbone), anisoyl (cytosine, adenine), 4-tert-butylbenzoyl (cytosine) and isobutyryl/diphenylcarbamoyl (guanine) protecting group combinations. For the guanine monomer the alkylation was realized both in a Mitsunobu [DIAD, triphenylphosphine or (4-dimethylaminophenyl)diphenylphosphine, tert-butyl glycolate] and in a low-temperature, sodium-hydride mediated alkylation (tert-butyl bromoacetate) to give the N⁹ -substituted derivative.     

Oligonucleotide-templated reactions based on Peptide Nucleic Acid (PNA) probes: Concept and biomedical applications

Sensing technologies based on Peptide Nucleic Acids (PNAs) and oligonucleotide-templated chemistry are perfectly suited for biomedical applications (e.g., diagnosis, prognosis and stratification of diseases) and could compete well with more traditional amplification technologies using expensive dual-labelled oligonucleotide probes. PNAs can be easily synthesised and functionalised, are more stable and are more responsive to point-mutations than their DNA counterpart. For these reasons, fluorogenic PNAs represent an interesting alternative to DNA-based molecular beacons for sensing applications in a cell-free environment, where cellular uptake is not required.     

Progress Towards a Submonomer Synthesis of Peptide Nucleic Acid

Abstract

We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the α-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.     

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.     

Localization of Nucleic Acid Synthesis in Root Meristems

Adenine-8-C1¹⁴ was supplied to roots of Vicia faba and Alliumascalonicum and its incorporation into DNA was studied fromautoradiographs of hydrolysed sections. These roots have a quiescentcentre to the meristem where the cells do not synthesize DNAand probably, therefore, play no part in the construction ofthe root. The boundary between the quiescent centre and thecentral cap initials is clearly denned and this suggests thatthere is as little cell interchange between the histogens asthere is in roots with visibly discrete histogens.     

Mitotic Inhibition and Nucleic Acid Synthesis in Amoeba Nuclei

SEVERAL strains of large mononucleate amoebae contain specific proteins which inhibit mitosis and eventually kill amoebae of strains other than their own^1,2. We now describe experiments to show that this lethal antimitotic factor (AF) inhibits RNA synthesis when injected into susceptible cells.     

蛋白核酸合成抑制剂和蛋白磷酸化对基因表达的调节

环己酰亚胺和放线菌素D明显降低小麦幼苗中BADH基因的表达,表明BADH基因表达在转录和转译水平上受到调控。氯霉素则有增加表达的效应。线粒体可能形成阻遏蛋白参与调节。H7和甘露糖降低BADH基因表达,相应地冈田酸(Okadaic acid)明显增加表达,说明蛋白磷酸化积极参与小麦幼苗中BADH基因表达的调节。     

Nucleic Acid Synthesis in the Chloroplasts of Acetabularia mediterranea

Radioautographic and radiochemical techniques were used to establish the presence of replicating DNA in the chloroplasts of Acetabularia mediterranea. These techniques also demonstrated that these chloroplasts synthesize RNA. It was found that label from thymine was also incorporated into DNA and RNA in these chloroplasts.

With the establishment of protein and nucleic acid synthesis in Acetabularia chloroplasts, it is clear that these chloroplasts carry out those metabolic processes which are most characteristic of autonomous cells.

     

Design of a New Type of Compact Chemical Heater for Isothermal Nucleic Acid Amplification

Previous chemical heater designs for isothermal nucleic acid amplification have been based on solid-liquid phase transition, but using this approach, developers have identified design challenges en route to developing a low-cost, disposable device. Here, we demonstrate the feasibility of a new heater configuration suitable for isothermal amplification in which one reactant of an exothermic reaction is a liquid-gas phase-change material, thereby eliminating the need for a separate phase-change compartment. This design offers potentially enhanced performance and energy density compared to other chemical and electric heaters.     

Inhibitors acting on Nucleic Acid Synthesis in an Oncogenic RNA Virus

IN infection with an oncogenic RNA virus, synthesis of viral RNA seems to be catalysed by an RNA dependent DNA polymerase in the host cell^1–4. Several specific inhibitors of viral DNA polymerases have been found^5–7 and Spiegelman⁸ has shown that the activity of viral enzymes depends strongly on the chemical composition of the template. We report here first a new highly specific poison of the Rauscher murine leukaemia virus (RMLV) DNA polymerases; second, several inactivators of the RNA and DNA template involved in the RMLV enzyme systems; and third, the action of actinomycin D on viral DNA polymerases and on host DNA/RNA polymerase. The results are discussed with respect to the influence of actinomycin D on virus multiplication.     

Synthesis and Cytotoxic Profile of a Diphtheria Toxin-Neurotrophin-4 Chimera

Abstract: A diphtheria toxin-neurotrophin-4/5 (NT-4/5) chimera (DAB₃₈₉-NT4), in which the native receptor binding domain of diphtheria toxin was replaced with a synthetic gene encoding rat NT-4/5, was expressed, refolded, and purified. This fusion toxin has a deduced molecular mass of 60,163 and is formed by joining the first 389 amino acids of diphtheria toxin to amino acids 1–130 of mature rat NT-4/5, using an NH₂-terminal bridge of 33 additional amino acids including six consecutive histidines. Neural cell types expressing only p75^LNGFR or p75^LNGFR and full-length or truncated TrkB were used to evaluate the cytotoxic efficacy of DAB₃₈₉-NT4. The fusion toxin produced a concentration-dependent killing of all cell populations, with LC₅₀ values that largely reflected the known NT-4/5 binding affinities for these receptor proteins. Mean LC₅₀ values ranged from 2,960 p M in p75^LNGFR-expressing neuro-2a neuroblastoma cells to 1,075 and 70 p M , respectively, in hippocampal astrocytes (p75^LNGFR+/truncated TrkB⁺) and cerebellar granule cells (p75^LNGFR+/TrkB⁺). The LC₅₀ for DAB₃₈₉-NT4 in receptor-negative 3T3 fibroblasts was 20 n M . NT-4/5 and brain-derived neurotrophic factor but not ciliary neurotrophic factor added in excess neutralized DAB₃₈₉-NT4 cytotoxicity. NT-4/5, however, did not reduce the cytotoxicity of intact diphtheria toxin.