Synthesis of new peptide nucleic acid monomer with glycylglycine backbone

New thymine peptide nucleic acid (PNA) monomer with glycylglycine backbone was prepared. This involved a key step of the coupling between iodinated serine ( 3 ) and 3‐benzoylthymine.     

Synthesis of a ferrocenyl uracil PNA monomer for insertion into PNA sequences

The deprotection of the tert-butyl group of a ferrocenyl uracil Peptide Nucleic Acid (PNA) monomer, Fmoc-aeg(R)-O^tBu (1) was achieved using a two step synthesis involving hydrolysis in basic conditions to give first the zwitterion of ⁺NH₃-aeg(R)-O⁻ (7). Compound 7 was reacted in situ with N-(9-fluorenylmethoxycarbonyloxy)succinimide to obtain the expected compound Fmoc-aeg(R)-OH (2) (Abbreviations: Aeg = (2-aminoethyl)-glycine; Fmoc = 9-fluorenylmethoxycarbonyl; O^tBu = tert-butyl; R = 5-(N-ferroce-nylmethylbenzamido)uracyl).     

New synthesis of a spin-labeled peptide nucleic acid and its interactions with nucleic acids

A new combined solid-liquid phase synthesis method for a spin labeled peptide nucleic acid (PNA) is developed. The methodology involved initial preparation of a protected PNA on solid phase, followed by efficient solution phase coupling to a spin label containing a reactive carboxylic group. This strategy allows to maintain the integrity of the nitroxide moiety during the various steps of chemical synthesis assuring in the same time the fidelity of the hybridization assay. This compound can be used as a reporter molecule to investigate the binding of peptide nucleic acids to oligonucleotide sequences (DNA or RNA) by EPR spectroscopy.     

Morphological characterization of self-assembled peptide nucleic acid amphiphiles

Peptide nucleic acid amphiphiles (PNAA) are a promising set of materials for sequence-specific separation of nucleic acids from complex mixtures. To implement PNAA in micellar separations, the morphology and size of PNAA micelles in the presence and absence of a sodium dodecyl sulfate (SDS) cosurfactant have been studied by small-angle X-ray scattering and dynamic light scattering. We find that a 6-mer PNAA with a 12-carbon n-alkane tail forms ellipsoidal micelles (a = 5.15 nm; b = 3.20 nm) above its critical micelle concentration (CMC) of 110.9 microM. On addition of a stoichiometric amount of complementary DNA, PNAA hybridizes to DNA, suppressing the formation of PNAA micelles. At a ratio of 19:1 SDS/PNAA (total concentration = 20 mM), spherical micelles are formed with outer radius Rs = 2.67 nm, slightly larger than spherical micelles of pure SDS. Capillary electrophoresis studies show that PNAA/DNA duplexes do not comicellize with SDS micelles. No such effects are observed using noncomplementary DNA. The shape and size of the PNAA micelles is also verified by dynamic light scattering (DLS) studies. These results provide an interesting case study with competing electrostatic, hydrophobic, and hydrogen-bonding interactions in micellar systems and make possible the use of PNAA in micellar separations of DNA oligomers.     

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.     

Design of a new oligotriazole peptide nucleic acid analogue (oT-PNA)

We describe in this Letter the synthesis of an original thymine azido-heterotrimer generated by Click Chemistry. This trimer has been obtained from an azido-thymidine and a new chloroethyl-propargylated PNA monomer analogue, after two azidation/click-reaction cycles. Conformational preferences of a rotameric intermediate have also been studied     

Synthesis and characterization of new ferrocenyl bishydrazones

New ferrocenyl bishydrazones (2a–2d) have been efficiently obtained from 1,1′-ferrocenedicarboxaldehyde by a straightforward synthesis. The four new compounds have been fully characterized by NMR (¹H, ¹³C), high-resolution mass spectroscopy, and the molecular structure of compounds (2a–2d) has been elucidated by X-ray diffraction on single crystals.     

Azidopeptide nucleic acid. An alternative strategy for solid-phase peptide nucleic acid (PNA) synthesis

[reaction: see text] A practical and efficient method for PNA synthesis using an azide group to mask the N-terminus is reported. The deprotection was carried out in 5 min, while couplings were complete within 60 min. The near neutral conditions of the phosphine deprotection combined with the base-free coupling using hydroxybenzotriazole-activated monomers make this approach very mild.     

Two-step synthesis of ferrocenyl esters of vanillic acid

Successive reactions of vanillin with aromatic aldehydes at the phenol group and ferroceneboronic acid at the carbonyl group catalyzed with various N-heterocyclic carbenes afforded the corresponding ferrocenyl esters. In these reactions copper(II) sulfate, cinnamic aldehyde, and air oxygen act as oxidants. The resulting ferrocenyl esters of vanillic acid were tested for cytotoxicity.     

The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition

A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.     

Fluorinated olefinic peptide nucleic acid: synthesis and pairing properties with complementary DNA

The fluorinated olefinic peptide nucleic acid (F-OPA) system was designed as a peptide nucleic acid (PNA) analogue in which the base carrying amide moiety was replaced by an isostructural and isoelectrostatic fluorinated C-C double bond, locking the nucleobases in one of the two possible rotameric forms. By comparison of the base-pairing properties of this analogue with its nonfluorinated analogue OPA and PNA, we aimed at a closer understanding of the role of this amide function in complementary DNA recognition. Here we present the synthesis of the F-OPA monomer building blocks containing the nucleobases A, T, and G according to the MMTr/Acyl protecting group scheme. Key steps are a selective desymmetrization of the double bond in the monomer precursor via lactonization as well as a highly regioselective Mitsunobu reaction for the introduction of the bases. PNA decamers containing single F-OPA mutations and fully modified F-OPA decamers and pentadecamers containing the bases A and T were synthesized by solid-phase peptide chemistry, and their hybridization properties with complementary parallel and antiparallel DNA were assessed by UV melting curves and CD spectroscopic methods. The stability of the duplexes formed by the decamers containing single (Z)-F-OPA modifications with parallel and antiparallel DNA was found to be strongly dependent on their position in the sequence with T(m) values ranging from +2.4 to -8.1 degrees C/modification as compared to PNA. Fully modified F-OPA decamers and pentadecamers were found to form parallel duplexes with complementary DNA with reduced stability compared to PNA or OPA. An asymmetric F-OPA pentadecamer was found to form a stable self-complex (T(m) approximately 65 degrees C) of unknown structure. The generally reduced affinity to DNA may therefore be due to an increased propensity for self-aggregation.     

白花丹酸的简易合成法

设计了以邻苯二酚为起始原料的新合成路线, 在不同保护基的条件下用二条合成路线合成了白花丹酸, 方法的特点是以杂原子诱导的芳基锂化反应实现了区域专一性芳酰化; 用KH为碱顺利实现了羰基α位的羧甲基化; 采用环己酮保护酚羟基后, 后处理方便, 收率提高。     

Carbon-rich organometallics: synthesis and characterization of new ferrocenyl end-capped bis(butadiynyl) fluorene derivatives

A new series of ferrocenyl end-capped bis(butadiynyl) fluorene complexes [(η⁵-C₅H₅)Fe(η⁵-C₅H₄)CCCCRCCCC(η⁵-C₅H₄)Fe(η⁵-C₅H₅)] (R = fluoren-9-one-2,7-diyl, 1; 9,9-dihexylfluorene-2,7-diyl, 2; 9-ferrocenylmethylenefluorene-2,7-diyl, 3; 9-ferrocenylphenylmethylenefluorene-2,7-diyl, 4) have been synthesized in moderate yields by the oxidative coupling reactions of ethynylferrocene with half equivalents of the appropriate diethynylfluorene derivatives. All the new complexes have been characterized by FTIR, NMR and UV-vis spectroscopies and fast atom bombardment mass spectrometry. The molecular structures of selected molecules have been determined by X-ray crystallographic techniques. The electronic absorption and redox properties of these carbon-rich molecules were investigated and the data were compared with those for the corresponding 2,7-bis(ferrocenylethynyl)fluorene counterparts. Cyclic voltammetry indicates that the half-wave potential of the terminal ferrocenyl moieties becomes more anodic when the number of ethynyl units increases and when the 9-substituent of the central fluorene ring changes from an electron-donating group to an electron-deficient group.     

Synthesis and anti-hepatitis B virus activity of new pyrimidine peptide nucleic acid analogs

A series of 4-methylsulfanylpyrimidin-2(1H)-one peptide nucleic acid analogs were synthesized and tested for their antiviral activity against hepatitis B virus. Plaque reduction infectivity assay was used to determine the virus count reduction as a result of treatment with tested compounds.     

Modular nucleic acid surrogates. Solid phase synthesis of alpha-helical peptide nucleic acids (alpha PNAs)

[formula: see text] The synthesis and characterization of prototype alpha-helical peptide nucleic acid (alpha PNA) modules 1-3 as well as disulfide dimers 4 and 5 are reported. These molecules combine an alpha-helical peptidyl scaffold with well-defined nucleobase molecular recognition patterns and could serve as a basis for novel antisense and/or antigene agents. Structure assignments for these alpha PNAs were supported by MALDI-TOF mass spectrometry, and the alpha-helical nature of 4 in water was confirmed by circular dichroism (CD) spectroscopy.     

Regioselective alkylation of guanine derivatives in the synthesis of peptide nucleic acid monomers

A method for the synthesis of 6-O-benzyl- and 6-O-benzyl-2-N-benzyloxycarbonyl-protected guanine derivatives starting from 2-amino-6-chloropurin is described. A regioselective alkylation of these N(9)-protected guanine derivatives gave the corresponding α-monomers of chiral peptide nucleic acids, the L-glutamic acid derivatives. It was shown that these compound do not inhibit (in the concentrations <20 µmol L^–1) the topoisomerase I activity.     

Peptide nucleic acid and amino acid modified peptide nucleic acid analysis by capillary zone electrophoresis

A rapid, high resolution, and low sample consumption CZE method is developed for peptide nucleic acid (PNA) analysis for the first time. 30% v/v acetonitrile in PNA sample and 20% v/v acetonitrile in 50 mM borax‐boric acid (pH 8.7) as BGE were employed after optimization. The calibration curves were linear for PNA concentration ranging from 1 to 50 μmol/L. LOD and LOQ of PNA were 0.2 and 1.0 μmol/L, respectively. Since the commercially available reagent gives rise to huge PNA peak and an apparent impurity peak, the purity of PNA was evaluated to be about 81.4% by CZE method, obviously lower than the supplier's purity value of 99.9% evaluated by RP–HPLC, and also lower than 94.8% determined with RP–HPLC by our research group. The CZE method takes only 5 min, needs only 90 nL PNA, much less than 20 min and 20 μL PNA in RP–HPLC method. Moreover, the CZE method is applicable for the analysis of glutamic acid modified and lysine modified PNAs, they show different migration time with their corresponding complementary PNAs. Our results show CZE provides a new choice for PNA and modified PNA analysis, also their purity or quality evaluation.