Synthesis and polymerisation of lipophilic peptide nucleic acids derived from stearic acid and pentacosa-10,12-diynoic acid

The adenine, cytosine and thymine peptide nucleic acid (PNA) monomers and PNA T₁₀ oligomers bearing either a diacetylenic or stearoyl moiety at the N- or C-terminus have been successfully prepared. The resulting thymine monomeric and T₁₀-mer derivatives have been subsequently incorporated into polydiacetylene-containing liposomes.     

Synthesis of hydrazino-peptide nucleic acid monomers and dimers as new PNA backbone building blocks

We describe the synthesis of new hydrazinoPNA (hydPNA) monomers and new hydPNA-containing dimers. For the hydPNA monomers, the primary terminal amino group of the aminoethylglycine unit of classical aegPNA is replaced by a hydrazine moiety. An appropriate choice of two orthogonal protecting groups on the two hydrazine nitrogen atoms makes it possible to drive their coupling with other monomers selectively on one or the other nitrogen atom, thus obtaining two different types of PNA dimers. These dimers represent new building blocks that can be used to generate novel PNA oligomers.     

Synthesis and characterization of cationic PNA bearing 5-ω-aminopropyl-uracil

5-ω-Aminopropyl-uracil bearing PNA monomers are synthesized for solid phase oligomer synthesis using FMOC protection. Several PNA oligomers with differing amounts of aminopropyluracil modification were prepared. These oligomers were found to associate with complementary DNA oligonucleotides.     

Efficient functional molecule incorporation method to functionalized peptide nucleic acid (PNA): use in synthesis of labeled PNA oligomers

A novel efficient synthetic method for a functionalized PNA (peptide nucleic acid) is described, in which a functional molecule is incorporated in place of a nucleobase. Novel ω-AA-^BocPNA-OH (20-24, AA=amino acid) were designed as PNA precursor monomer units into which functional molecules could be incorporated efficiently. Compounds 20-24 reacted quantitatively with OSu (N-hydroxysuccinimidyl) active ester derivatives and isothiocyanate derivatives of commercial functional molecules to give target functionalized PNA monomer units 25-53. Various types of functionalized PNA monomer units could be efficiently incorporated into multiple predetermined positions in a PNA oligomer by SPPS (solid phase peptide synthesis) in the same way as for the four A(Cbz), G(Cbz), C(Cbz), and T PNA monomer units.     

A systematic study of the solid state and solution phase conformational preferences of β-peptides derived from transpentacin

The solid state and solution phase conformational preferences of a homologous series of β-peptides derived from (S,S)-2-aminocyclopentanecarboxylic acid (transpentacin) have been investigated using a variety of spectroscopic and crystallographic techniques. These studies indicate that the hexamer and pentamer persist as a 12-helix in both the solid state and solution phase. Although the conformational traits of a 12-helix are exhibited by oligomers with as few as three residues in the solid state, in solution the trimer exists as an equilibrium of many alternative conformers whilst the tetramer has been shown to predominantly exist in either a 12-helix or a turn-type conformation.     

Synthesis and characterization of (R)-miniPEG-containing chiral γ-peptide nucleic acids using the Fmoc strategy

Diethylene glycol (miniPEG)-containing chiral γPNA is considered to be one of the best PNA derivatives. Its preparation is mainly based on the Boc strategy for solid phase peptide synthesis (SPPS), requiring the repeated use of trifluoroacetic acid TFA, which is not suitable for the in situ synthesis of PNA arrays and some other applications under mild conditions. Herein, Fmoc/Cbz orthogonal protected miniPEG-containing chiral γPNA monomers were synthesized, and a 15mer γPNA was prepared using the Fmoc strategy under mild conditions.     

Acetylenic and diacetylenic liquid-crystalline monomers: towards ordered conjugated polymers

Abstract

Acetylenic and diacetylenic mesomorphic monomers have been prepared in order to obtain long conjugated polymers able to give high non-linear optical hyperpolarizabilities. Here we report the synthesis of such monomers incorporating cholesteryl and methoxybiphenyl groups; their structural and thermal behaviour are described. The occurrence of mesophases in the acetylenic and diacetylenic derivatives is discussed as a function of the spacer length and of the size of the mesogen moiety. The diacetylenic derivatives containing the methoxybiphenyl groups do not exhibit any liquid-crystalline behaviour but are able to polymerize under U.V. radiation.     

Enantiomeric separation of chiral peptide nucleic acid monomers by capillary electrophoresis with charged cyclodextrins

Direct chiral separation of chiral peptide nucleic acid (PNA) monomers has been achieved for the first time by capillary electrophoresis (CE) with charged cyclodextrins as chiral selectors added to the electrophoretic buffer. Selectively modified 6-deoxy-6-N-histamino-beta-cyclodextrin and sulfobutyl ether-beta-CD were successfully used as chiral selectors for the enantiomeric separation of chiral monomers based on different aminoethylamino acids bearing thymine or adenine as nucleobases. Chiral separations were obtained at low selector concentrations (1-3 mM) with good enantioselectivity and resolution factors. Separations were optimized as a function of pH in order to exploit the effect of the electrostatic interactions between the oppositely charged selector and selectand. The method has been applied to the analysis of the enantiomeric excess of chiral monomers used for the solid phase synthesis of chiral PNA oligomers. CE chiral analysis showed that a very high enantiomeric purity was generally achieved in the synthesis of all monomers, except for histidine and aspartic acid based monomers in which ca. 10% of the "wrong" enantiomer was always present.     

Base dependent pyrrolidine ring pucker in aep-PNA monomers: NMR and PSEUROT analysis

The aep-PNA is a chiral and cyclic PNA analogue, which has a stronger and base dependent binding affinity with complementary DNA. To understand the base dependent properties at monomer level, the structural studies of aep-PNA-(T/C/A) monomers have been carried out focussing on the conformational analysis of pyrrolidine ring pucker in aep-PNA by ¹H NMR and the coupling constant data fitted into PSEUROT software. The results indicate that the type of pyrrolidine pucker depends on the electronic nature of substituent, implying the effect of pyrimidine or purine substituents in determining the ring pucker in monomers. This may consequently influence the aep-PNA oligomer conformation. Since pyrrolidine nucleic acids have emerged as an important class of PNA analogues, present results may have importance for their future development.     

Direct enantiomeric separation of N-aminoethylamino acids: determination of the enantiomeric excess of chiral peptide nucleic acids (PNAs) by GC

Direct chiral separation of N-aminoethylamino acids has been performed for the first time by gas chromatographic (GC) analysis with a Chirasil-Val column, after derivatisation with trifluoroacetic anhydride in dichloromethane, which led to the corresponding piperazin-2-one derivatives, as identified by NMR and GC/MS analysis. The method was used for the analysis of the enantiomeric excess of chiral peptide nucleic acid (PNA) monomers and oligomers after hydrolysis with 6N HCl.     

Utilization of the p-nitrobenzyloxycarbonyl (pNZ) amine protecting group and pentafluorophenyl (Pfp) esters for the solid phase synthesis of spiroligomers

Spiroligomers are a class of peptidomimetics that connect interchangeable, stereochemically pure, cyclic monomers through pairs of amide bonds to form diketopiperazines between the monomers. This enables them to adopt predictable and programmable structure due to the rigidity of the final molecule. We present a new method for the solid phase synthesis of highly functionalized spiroligomers that incorporates the use of the p-nitrobenzyloxycarbonyl (pNZ) as a temporary amine protecting group and the pentafluorophenyl ester for monomer activation. This new method allows for the synthesis of spiroligomers with higher purity and increased yields when compared to previous methods. This improved method of synthesis of functionalized spiroligomers will facilitate the development of applications as catalysts, therapeutics and membrane channels.     

Cyanuryl peptide nucleic acid: synthesis and DNA complexation properties

The synthesis of cyanuryl PNA monomer (CyaPNA) 6 was achieved by direct N-monoalkylation of cyanuric acid with N-(2-Boc-aminoethyl)-N′-(bromoacetyl)glycyl ethyl ester 4. Compound 6 was incorporated as a T-mimic into PNA oligomers and biophysical studies on their triplexes/duplex complexes with complementary DNA oligomers indicated unusual stabilization of PNA:DNA hybrids when the cyanuryl unit was located in the middle of the PNA oligomer.     

含羟基和咪唑基团新手性肽核酸的设计与合成

以含丝氨酸和组氨酸残基的手性肽核酸单体替换经典肽核酸单体, 采用固相合成方法设计合成了五个新序列含羟基和咪唑基团的10聚体手性肽核酸, 经ESI-MS或MALDI-TOF-MS证实目标物结构正确.     

Electrochemiluminescent monomers for solid support syntheses of Ru(II)-PNA bioconjugates: multimodal biosensing tools with enhanced duplex stability

The feasibility of devising a solid support mediated approach to multimodal Ru(II)-peptide nucleic acid (PNA) oligomers is explored. Three Ru(II)-PNA-like monomers, [Ru(bpy)(2)(Cpp-L-PNA-OH)](2+) (M1), [Ru(phen)(2)(Cpp-L-PNA-OH)](2+) (M2), and [Ru(dppz)(2)(Cpp-L-PNA-OH)](2+) (M3) (bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine, Cpp-L-PNA-OH = [2-(N-9-fluorenylmethoxycarbonyl)aminoethyl]-N-[6-(2-(pyridin-2yl)pyrimidine-4-carboxamido)hexanoyl]-glycine), have been synthesized as building blocks for Ru(II)-PNA oligomers and characterized by IR and (1)H NMR spectroscopy, mass spectrometry, electrochemistry and elemental analysis. As a proof of principle, M1 was incorporated on the solid phase within the PNA sequences H-g-c-a-a-t-a-a-a-a-Lys-NH(2) (PNA1) and H-P-K-K-K-R-K-V-g-c-a-a-t-a-a-a-a-lys-NH(2) (PNA4) to give PNA2 (H-g-c-a-a-t-a-a-a-a-M1-lys-NH(2)) and PNA3 (H-P-K-K-K-R-K-V-g-c-a-a-t-a-a-a-a-M1-lys-NH(2)), respectively. The two Ru(II)-PNA oligomers, PNA2 and PNA3, displayed a metal to ligand charge transfer (MLCT) transition band centered around 445 nm and an emission maximum at about 680 nm following 450 nm excitation in aqueous solutions (10 mM PBS, pH 7.4). The absorption and emission response of the duplexes formed with the cDNA strand (DNA: 5'-T-T-T-T-T-T-T-A-T-T-G-C-T-T-T-3') showed no major variations, suggesting that the electronic properties of the Ru(II) complexes are largely unaffected by hybridization. The thermal stability of the PNA·DNA duplexes, as evaluated from UV melting experiments, is enhanced compared to the corresponding nonmetalated duplexes. The melting temperature (T(m)) was almost 8 °C higher for PNA2·DNA duplex, and 4 °C for PNA3·DNA duplex, with the stabilization attributed to the electrostatic interaction between the cationic residues (Ru(II) unit and positively charged lysine/arginine) and the polyanionic DNA backbone. In presence of tripropylamine (TPA) as co-reactant, PNA2, PNA3, PNA2·DNA and PNA3·DNA displayed strong electrochemiluminescence (ECL) signals even at submicromolar concentrations. Importantly, the combination of spectrochemical, thermal and ECL properties possessed by the Ru(II)-PNA sequences offer an elegant approach for the design of highly sensitive multimodal biosensing tools.     

Acetylenic and diacetylenic liquid-crystalline monomers: towards ordered conjugated polymers

Acetylenic and diacetylenic mesomorphic monomers have been prepared in order to obtain long conjugated polymers able to give high non-linear optical hyperpolarizabilities. Here we report the synthesis of such monomers incorporating cholesteryl and methoxybiphenyl groups; their structural and thermal behaviour are described. The occurrence of mesophases in the acetylenic and diacetylenic derivatives is discussed as a function of the spacer length and of the size of the mesogen moiety. The diacetylenic derivatives containing the methoxybiphenyl groups do not exhibit any liquid-crystalline behaviour but are able to polymerize under U.V. radiation.     

Chimeric (aeg-pyrrolidine)PNAs: synthesis and stereo-discriminative duplex binding with DNA/RNA

The design and facile conversion of naturally occurring 4-hydroxyproline to all four diastereomers of thymine pyrrolidine PNA monomer, (2R,4S)-adenine, -guanine and -cytosine monomers and their incorporation into duplex forming PNA oligomers is reported. The interesting results of the hybridization studies with complementary DNA/RNA sequences in either parallel or antiparallel orientation reveal the stereochemistry-dependent DNA vs. RNA discriminations and parallel/antiparallel orientation selectivity.     

Synthesis and enzymatic degradation of end-functionalized biodegradable polyesters

End-functionalization of biodegradable polymers/oligomers based on L-lactide and glycolide by cholesteryl moiety was investigated. We established the feasibility of preparing the functionalized polymers/oligomers, Chol-(LG)_m+n, through ring-opening copolymerization initiated by cholesterol bearing a hydroxyl group, without adding any catalyst. The functionalized polymers/oligomers of different molecular weights were obtained by controlling the feed ratio of the initiator cholesterol to the monomers. The chemical structure of end-functionalized polymers/oligomers was confirmed by FTIR and ¹H NMR. Incorporation of cholesteryl moiety into the polymer chains induces liquid crystallinity in the resultant oligomers when the molecular chains are not very long. The enzymatic degradation studies, for all the samples, were carried out using enzyme, proteinase K. Interestingly, the enzymatic degradation of cholesteryl end-functionalized polymers/oligomers resulted in a lamella-like porous structure on the sample surface, which is altogether different from the commonly reported spherical-pore structure formed during the degradation of conventional polyesters.     

Synthesis and evaluation of (1S,2R/1R,2S)-aminocyclohexylglycyl PNAs as conformationally preorganized PNA analogues for DNA/RNA recognition

Conformationally constrained cis-aminocyclohexylglycyl PNAs have been designed on the basis of stereospecific imposition of 1,2-cis-cyclohexyl moieties on the aminoethyl segment of aminoethylglycyl PNA (aegPNA). The introduction of the cis-cyclohexyl ring may allow the restriction of the torsion angle beta in the ethylenediamine segment to 60-70 degrees that is prevalent in PNA(2):DNA and PNA:RNA complexes. The synthesis of the optically pure monomers (10a and 10b) is achieved by stereoselective enzymatic hydrolysis of an intermediate ester 2. The chiral PNA oligomers were synthesized with (1S,2R/1R,2S)-aminocyclohexylglycyl thymine monomers in the center and N-terminus of aegPNA. Differential gel shift retardation with one or more units of modified monomer units was observed as a result of hybridization of PNA sequences with complementary DNA sequences. Hybridization studies with complementary DNA and RNA sequences using UV-T(m) measurements indicate that PNA with (1S,2R)-cyclohexyl stereochemistry enhances selective binding with RNA over DNA as compared to control aegPNA and PNA with the other (1R,2S) isomer.     

Synthesis of organometallic PNA oligomers by click chemistry

The facile side-specific insertion, on the solid phase, of one or two ferrocene moieties into peptide nucleic acid (PNA) oligomers by click chemistry is presented.     

Peptide nucleic acids (PNAs) with a functional backbone

The synthesis of 10 new T-PNA monomers derived from L-amino acids is presented. The monomers were incorporated into decameric PNA oligomers, and the hybridisation with RNA, DNA and PNA complements studied by thermal stability measurements.