Chiral Peptide Nucleic Acid Research Articles

Enhanced recognition of cystic fibrosis W1282X DNA point mutation by chiral peptide nucleic acid probes by a surface plasmon resonance biosensor.

Peptide nucleic acids (PNAs) containing an insert of three chiral monomers based on D-lysine ('chiral box') were synthesized and used as probes in Biospecific Interaction Analysis (BIA) for the recognition of DNA containing the W1282X point mutation of the cystic fibrosis gene. Hybridization experiments carried out in solution showed enhanced mismatch recognition when compared with the analogous achiral PNAs and oligonucleotides. The signal intensity was lower, but the selectivity of the Biacore response was found to be much higher than that observed with achiral PNAs. The newly designed chiral PNA probes were also found to hybridize with a 1:1 mixture of normal (N-W1282X) and mutated (M-W1282X) DNA oligomers immobilized on the biosensor, thus allowing discrimination not only between a normal and a mutated sequence (healthy/homozygous), but also between homo- and heterozygous individuals. These results suggest that 'chiral box' PNAs are potential powerful tools for the analysis of single point mutations of biological/biomedical relevance.

Conformationally Restricted Chiral Peptide Nucleic Acids Derived from Azetidines

The initial experiments towards the chemical synthesis of conformationally rigid peptide nucleic acid analogues with azetidine moieties have been described.

Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex.

Peptide nucleic acids (PNAs) are oligonucleotide analogues in which the sugar-phosphate backbone has been replaced by a pseudopeptide skeleton. They bind DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids more stable than the corresponding nucleic acid complexes. The binding affinity and selectivity of PNAs for nucleic acids can be modified by the introduction of stereogenic centers (such as D-Lys-based units) into the PNA backbone. To investigate the structural features of chiral PNAs, the structure of a PNA decamer containing three D-Lys-based monomers (namely H-GpnTpnApnGpnAdlTdlCdlApnCpnTpn-NH2, in which pn represents a pseudopeptide link and dl represents a D-Lys analogue) hybridized with its complementary antiparallel DNA has been solved at a 1.66-A resolution by means of a single-wavelength anomalous diffraction experiment on a brominated derivative. The D-Lys-based chiral PNA-DNA (LPD) heteroduplex adopts the so-called P-helix conformation. From the substantial similarity between the PNA conformation in LPD and the conformations observed in other PNA structures, it can be concluded that PNAs possess intrinsic conformational preferences for the P-helix, and that their flexibility is rather restricted. The conformational rigidity of PNAs is enhanced by the presence of the chiral centers, limiting the ability of PNA strands to adopt other conformations and, ultimately, increasing the selectivity in molecular recognition.

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.

Synthesis and Hybridization Property of Novel 2′,5′‐isoDNA Mimic Chiral Peptide Nucleic Acids.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Synthesis of the first chiral PNA monomer labelled with a Fischer-type carbene complex

The synthesis, through a cross-metathesis reaction, of the first chiral peptide nucleic acid (PNA) monomer labelled with a Fischer-type carbene complex of chromium is reported. IR analysis of the new bioconjugate shows that the Cr(CO)4 moiety represents a suitable spectroscopic probe for diagnostic purposes.

Fast, Solid‐Phase Synthesis of Chiral Peptide Nucleic Acids with a High Optical Purity by a Submonomeric Strategy

AbstractThe solid‐phase synthesis of chiral peptide nucleic acids (PNAs) usually results in partial epimerization of the products, since the α‐nitrogen atom of the amino acid is involved in an amidic bond. It is also time‐consuming, since all the chiral monomers bearing different nucleobases have to be independently synthesized. In order to prevent racemization and to speed up the synthetic procedure we adopted a submonomeric approach by using a solid‐phase, Boc‐based PNA synthesis in which the chiral backbone orthogonally Nα‐Fmoc‐protected (submonomer) was first linked to the growing chain on the resin, followed by Fmoc‐deprotection and derivatization with the carboxymethylnucleobase. The submonomer bearing the D‐lysine residue was designed by protecting the Nα‐(aminoethyl)amino acid moiety with an Fmoc protecting group, compatible with standard Boc chemistry, and with the use of an MBHA‐PS resin, normally employed for PNA synthesis. Different synthetic pathways towards the desired submonomer were studied by using the amino acid D‐lysine as a chiral synthon, obtaining a fast method leading to a high yield and an excellent enantiomeric excess of the submonomer. The solid‐phase submonomeric reaction conditions were optimized for the synthesis of a thyminyl PNA dimer and then used to synthesize two different chiral PNAs. In this way two advantages were obtained: a lower degree of racemization in the coupling step during the solid‐phase synthesis and the possibility of using the same submonomer for every different nucleobase. All the D‐lysine‐based chiral PNAs were obtained in good yields and, as compared with PNAs synthesized by other coupling methods, showed the highest optical purity reported so far. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Synthesis and hybridization property of novel 2′,5′-isoDNA mimic chiral peptide nucleic acids

2′,5′-isoDNA mimic chiral peptide nucleic acid (isoPNA) monomers derived from d- and l-aspartic acids were synthesized. These novel monomers were incorporated in aminoethylglycine peptide nucleic acid (aegPNA) thymine dodecamers, and the hybridization properties to RNA and DNA were demonstrated by UV thermal denaturation.

Racemization of chiral PNAs during solid-phase synthesis: effect of the coupling conditions on enantiomeric purity

Chiral peptide nucleic acid (PNA) monomers based on the amino acids Ala, Phe and Lys were synthesized, and their enantiomeric purity was checked either by RP-HPLC after reaction with l-ValOMe or by GC–MS using a Chirasil-Val column after hydrolysis and conversion of PNAs to the corresponding piperazin-2-ones. A model coupling reaction of these monomers with ValOMe was carried out under various conditions in order to evaluate the effect of synthetic parameters (coupling agent, base, preactivation time) on epimerization. The enantiomeric purity of the products decreased in the order: DEPBT>TDBTU>HBTU>HATU. The use of sym-collidine (TMP) as a base produced higher racemization than with DIEA. PNAs containing one or three chiral monomers were subsequently synthesized with different coupling protocols, and the results were found to be consistent with those obtained in solution. High enantiomeric purity was obtained using a DIC/HOBt coupling protocol. A rationale for the observed effects is proposed based on NMR studies.

ChemInform Abstract: Synthesis of Achiral and Chiral Peptide Nucleic Acid (PNA) Monomers Using Mitsunobu Reaction.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Peptide-nucleic acids (PNAs): a tool for the development of gene expression modifiers.

Peptide nucleic acids (PNAs) represent nucleic acid analogues with unique biochemical properties and of great interest for the development of therapeutic agents. The firstly designed and tested PNAs are molecules in which the sugar-phosphate backbone of DNA was replaced with a pseudopeptide chain constituted by N-(2-aminoethyl) glycine monomers. Nucleobases can be linked to this backbone through a carboxymethyl moiety, which allows to maintain a two atom spacer between the backbone and the bases. Since the first reports on PNAs based on N-(2-aminoethyl) glycine backbone, other PNA analogues have been synthesized, with the main purpose of improve biological activities as well as stability and efficient delivery to target cells. Of great interest are chiral PNAs, PNA analogues bearing phosphate groups (PHONA), PNA-DNA and PNA-peptide chimeras, PNA linked to non-peptide vectors. PNAs hybridize to DNA and RNA with high efficiency following the Watson-Crick hybridization rules, forming highly stable PNA/DNA and PNA/RNA duplexes. In addition, homopyrimidine PNAs, as well as PNAs containing a high pyrimidine:purine ratio, are able to bind to DNA or RNA forming highly stable (PNA)(2)-DNA triple helices. Accordingly, therapeutic PNA and PNA analogues could act as antigéne as well as antisense molecules. In addition, recent studies provide evidences for the possible use of PNA-based therapeutic molecules as artificial promoters, as decoy or ribozyme facilitator. Among the therapeutic applications of PNA-based molecules, the most pomising include anti-cancer and anti-viral experimental strategies, but activity of PNAs against bacteria and medically important parasitic organisms have been also reported.

SYNTHESIS AND BINDING AFFINITY OF A CHIRAL PNA ANALOGUE

The synthesis of a chiral peptide nucleic acid (PNA), which is composed of N-aminoethyl-cis-4-nucleobase-L-proline units, was described. The chiral PNA monomers containing all four nucleobases (A, T, C and G) were steroselectively prepared. The x-ray diffraction data from a single crystal confirmed the configuration of a key intermediate. Binding activity of the oligomers with their complementary DNA targets was also investigated.

Synthesis of achiral and chiral peptide nucleic acid (PNA) monomers using Mitsunobu reaction

Peptide nucleic acids (PNAs) are intensively studied DNA analogues. We elaborated an efficient procedure for the synthesis of N-, C-protected pseudodipeptides with a reduced peptide bond and then peptide nucleic acid (PNA) monomers, based on the Mitsunobu reaction of N-Boc-β-amino alcohols with N- o-nitrobenzenesulfonyl-protected ( oNBS-protected) amino acid esters. Using the new procedure, we obtained protected PNA monomer backbones with various amino acid side chains. The pseudodipeptide secondary amine groups were then deprotected by thiolysis, and after appropriate work-up, acylated with thymin-1-ylacetic acid to give the protected monomers. The procedure seems to be of general applicability and allows various modifications of PNA structure by using diverse alcohols and amino acid esters.

Impact of Cu(II) and Ni(II) on a structure of chiral peptide nucleic acids having four, six and eight thymines in a peptide side chain.

The studies on binding ability of longer chiral peptide nucleic acids (having four, six and eight thymines in a peptide side chain) have shown that the interactions between the nucleic base rings within a ligand molecule have a critical impact on the complex stability. Thymines inserted in the peptide side chain interact with each other as well as with peptide back-bone increasing the structural organization of the cPNA molecule. The metal ion coordination to cPNA, on the other hand, induces a very specific ligand structure, which may have a basic impact on the cPNA self-recognition processes.

Synthesis and properties of chiral peptide nucleic acids with a N-Aminoethyl- d-proline backbone

A synthon of d-proline substituted at the 4-position by thymine and at N by a flexible aminoethyl linker, has been used to prepare a novel chiral peptide nucleic acid (cPNA) with (2 R,4 R) stereochemistry using solid phase methodology. The homothymine decamer cPNA binds to complementary polyadenylic acid to form a 2:1 hybrid with high affinity and specificity according to UV and CD studies, whereas no binding to the corresponding polydeoxyadenylic acid was observed.

DNA Binding of AD-Lysine-Based Chiral PNA: Direction Control and Mismatch Recognition

Peptide nucleic acids (PNAs) are oligonucleotide analogues with a skeleton made up of N-(2-aminoethyl)glycine units; they bind to complementary DNA and RNA with high stability and specificity. In order to improve the binding specificity, solubility and uptake into cells, many modifications have been introduced, some concerning the introduction of stereogenic centres. With the aim of achieving a selective antiparallel binding with DNA, we report in this paper the synthesis and binding abilities of a chiral PNA decamer (H-GTAGATCACT-NH2) bearing three D-Lys-based monomers (a “chiral box”) in the middle of the strand. Indeed, the antiparallel PNA-DNA duplex showed a melting point of 43 °C (determined both by CD and UV spectroscopy), whereas the parallel PNA-DNA duplex failed to form, as shown by the absence of temperature dependence in the UV and CD spectra. Moreover, hybridization experiments carried out with antiparallel DNA strands bearing single mismatches showed that this PNA was excellent in discriminating between mismatched and matched targets. These results indicate that a high chiral constraint in the middle of a PNA sequence strongly affects the direction selectivity, i.e. the antiparallel/parallel preference in the DNA complexation. In particular, a “D-chiral box” favours a highly specific antiparallel DNA binding, thus allowing possible diagnostic applications for the screening of single-point mutations.

Chiral peptide nucleic acids having thymine and adenine in their side chain as specific ligands for NiII and CuII †

Potentiometric and spectroscopic data, including NMR, CD and EPR results, as well as theoretical calculations showed that the insertion of a nucleic base into a peptide chain results in formation of very effective ligands (chiral peptide nucleic acids, C-PNAs) for CuII and NiII. The most effective ligand was that containing thymine base. The thymine moiety interacts with metal ion in the apical position via the O6 oxygen and forms a set of effective hydrogen bonds with the N-terminal amino group. In the case of adenine C-PNA, two nucleic bases may form stacking interactions, which also increases the complex stability. These interactions of nucleic bases mean that metal ion binding to peptide backbone nitrogens of PNAs leads to formation of complexes which are several orders of magnitude stronger than those obtained with oligoglycine. Metal ion binding to C-PNAs, on the other hand, induces specific conformations of the side chain groups, which would affect critically the self-recognition interactions between the C-PNA strands.

Synthesis and characterization of new chiral peptide nucleic acid (PNA) monomers.

PNAs are DNA analogues in which the nucleic acid's backbone is replaced by a chiral or achiral pseudopeptide backbone and nucleobases are attached to the backbone by methylene carbonyl linkers. The easy to modify PNA structure gives the possibility to obtain monomers, and subsequently oligomers, with improved properties. We have synthesised several new PNA monomers, starting from a series of 2'-substituted methyl N-(2-Boc-aminoethyl)glycinates. The pseudodipeptides were obtained using modified Kosynkina's method, based on the reductive amination of N-Boc-protected alpha-amino aldehydes [glycinal, isoleucinal, valinal, tryptophanal, serinal(Bzl), prolinal] with methyl glycinate. The compounds were then acylated with nucleic acid base derivatives by simplified procedure, and the purification was limited to the last step of the synthesis. The applied procedure is useful in synthesis of various chiral PNA monomers.

ChemInform Abstract: Synthesis of New Chiral Peptide Nucleic Acid (PNA) Monomers by a Simplified Reductive Amination Method.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

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.