PNA Monomer Research Articles

A Facile Synthesis of Red-Shifted Bis-Quinoline (BisQ) Surrogate Base.

Forced intercalation peptide nucleic acids (FIT-PNAs) are DNA mimics that act as RNA sensors. The sensing event occurs due to sequence-specific RNA hybridization, leading to a substantial increase in fluorescence. The fluorophore in the FIT-PNA is termed a surrogate base. This molecule typically replaces a purine in the PNA sequence. BisQ is a surrogate base that connects two quinolines via a monomethine bond. BisQ-based FIT-PNAs have excellent biophysical features that include high brightness and red-shifted emission (λem, max = 613 nm). In this report, we detail two chemical approaches that allow for the facile synthesis of the BisQ PNA monomer. In both cases, the key compound used for the synthesis of BisQ-CH2COOH is the tBu-ester-modified quinoline synthon (compound 5). Subsequently, one method uses the Alloc acid-protected PNA backbone, whereas the other uses the tBu ester-protected PNA backbone. In the latter case, the overall yield for BisQ acid (compound 7) and BisQ PNA monomer syntheses was 61% in six synthetic steps. This is a substantial improvement to the published procedures to date (7% total yield). Lastly, we have prepared an 11-mer FIT-PNA with either BisQ or thiazole orange (TO) and studied their photophysical properties. We find superior photophysical properties for the BisQ FIT-PNA in terms of the brightness and selectivity, highlighting the added value of using this surrogate base for RNA sensing.

A facile route to synthesize N-(Boc-Aminoethylglycin)thymine Ethyl Ester, application to the synthesis of PNA-oligonucleotide conjugates

Peptide nucleic acid oligonucleotide conjugates are attracting immense interest currently because of their use in the biomedical and diagnostic field as antigene and molecular sensors. The efficient PNA synthesis methods can reduce their cost and may increase availability for their wider use. Here we described a facile synthesis of the peptide nucleic acid monomer N-(Boc-Aminoethylglycin)thymine Ethyl Ester [Ethyl 2-(N-(2-((tert-butoxycarbonyl)amino)ethyl)-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetate]. The monomer N-(Boc-Aeg)thymine Ethyl Ester has been prepared in a good yield (96%) by highly efficient procedure involving direct coupling of nucleobase thymine with the backbone Ethyl N-(Boc-aminoethyl)-N-(chloroacetyl)glycinate, which was prepared from the reaction of Ethyl N-[(2-Boc-amino)-ethyl]glycinate with chlroacetylchloride. The key intermediate Ethyl N-[(2-Boc-amino)-ethyl]glycinate involved in the synthesis has been prepared via a scalable and cost-effective route with a yield of (98%). The thyminyl PNA monomer was reported to be used in various synthetic applications, and our cost-effective, highly scalable method of synthesis will expand its wider use. A new method for the synthesis of Thymine-based PNA monomer precursor N-(Boc-Aeg)thymine Ethyl Ester in gram scale with high purity is reported here. In this method, the use of expensive coupling reagents is avoided.

Incorporating G-C Pair-Recognizing Guanidinium into PNAs for Sequence and Structure Specific Recognition of dsRNAs over dsDNAs and ssRNAs.

Recognition of RNAs under physiological conditions is important for the development of chemical probes and therapeutic ligands. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) are promising for the recognition of dsRNAs in a sequence and structure specific manner under near-physiological conditions. Guanidinium is often present in proteins and small molecules for the recognition of G bases in nucleic acids, in cell-penetrating carriers, and in bioactive drug molecules, which might be due to the fact that guanidinium is amphiphilic and has unique hydrogen bonding and stacking properties. We hypothesized that a simple guanidinium moiety can be directly incorporated into PNAs to facilitate enhanced molecular recognition of G-C pairs in dsRNAs and improved bioactivity. We grafted a guanidinium moiety directly into a PNA monomer (designated as R) using a two-carbon linker as guided by computational modeling studies. The synthetic scheme of the PNA R monomer is relatively simple compared to that of the previously reported L monomer. We incorporated the R residue into various dbPNAs for binding studies. dbPNAs incorporated with R residues are excellent in sequence specifically recognizing G-C pairs in dsRNAs over dsDNA and ssRNAs. We demonstrated that the R residue is compatible with unmodified T and C and previously developed modified L and Q residues in dbPNAs for targeting model dsRNAs, the influenza A viral panhandle duplex structure, and the HIV-1 frameshift site RNA hairpin. Furthermore, R residues enhance the cellular uptake of PNAs.

SELECTION OF PROTECTIVE GROUPS UPON OPTIMIZING THE SYNTHESIS OF γ-PNA BASED ON L-GLU

This work is devoted to optimization of the synthesis of γ-S-carboxyethyl monomers of PNA based on L-Glu. PNA are promising compounds that hybridize with DNA or RNA, and due to their properties they are used in molecular biology, personalized medicine, and can also be used to create nanomaterials. To increase the yield of the desired monomers, it has been proposed to replace the benzyl protecting group with the carboxy function of the side radical by cyclohexyl one. Two synthetic schemes were proposed. In the first of them, γ-benzyl-N-Boc-glutamic acid, which was reduced to β-amino alcohol, was the starting compound. The hydroxyl group was protected by a dimethyl-tert-butylsilyl group. The benzyl ester in the side radical was cleaved by reduction on a palladium catalyst using ammonium formate. However, the subsequent acylation of cyclohexyl alcohol failed. In the second of the proposed schemes, a known sequence of reactions was used, which led to the formation of a cyclic derivative of Cbz-protected glutamic acid. Then, the resulting compound was acylated with cyclohexyl alcohol to give the desired ester. The subsequent transformation of the protective groups of the ester resulted in the diprotected L-glutamic acid in three stages. Subsequent reduction gave the desired protected β-amino alcohol containing a cyclohexyl protecting group in the side radical. This compound was further used in the Mitsunobu reaction to obtain a completely protected core of the PNA monomer. Subsequent thiolysis reaction resulted in the formation of the target secondary amine, the stability of which substantially exceeded the stability of its analog with benzyl protection, obtained and investigated before. The structure of the new compounds obtained is confirmed by 1H-NMR spectroscopy.

Synthesis and Improved Cross-Linking Properties of C5-Modified Furan Bearing PNAs.

Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the α- or γ-position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, γ-l-lysine and γ-l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis. It was shown that the l-lysine γ-modification had a beneficial effect on crosslink efficiency due to pre-organization of the PNA helix and a favorable electrostatic interaction between the positively-charged lysine and the negatively-charged DNA backbone. Moreover, the crosslink yield could be optimized by carefully choosing the type of furan PNA monomer. This work is the first to describe a selective and biocompatible furan crosslinking strategy for crosslinking of γ-modified PNA sequences towards single-stranded DNA.

ChemInform Abstract: Pyrimidine‐Fused Heterocyclic Frameworks Based on an N4‐Arylcytosine Scaffold: Synthesis, Characterization, and PNA Oligomerization of the Fluorescent Cytosine Analogue 5,6‐BenzopC.

AbstractThe synthesis of the 5,6‐BenzopC analogue (IIa) and the PNA monomer (IIb) is achieved by Ni‐mediated cyclization of the cytosine derivative (I).

Rapid access with diversity to enantiopure flexible PNA monomers following asymmetric orthogonal strategies

Different synthetic procedures are described in the rapid elaboration of flexible PNA monomers based on the 6-amino-8-base-octanoate and 5-amino-7-base-heptanoate scaffolds. Asymmetric Aza-Michael monoaddition is successfully applied to starting materials derived from sebacic/azelaic long-chain diacids and 6-membered oxacyclohexane commercial derivatives. Chain length, orthogonality of the ester functionalities, and Z/E isomerism of these prime substrates yielded high-valuable multifunctional intermediates through this asymmetric conjugate addition. Key features are the diversity toward PNA monomer synthesis, orthogonal chemoselective transformations, and Mitsunobu nucleobase substitution as an exceptional approach to introduce nucleobases in the final step.

Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes

Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2–PNA triplex, without appreciable binding to single-stranded regions to form an RNA–PNA duplex or, via strand invasion, forming an RNA–PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed −1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2–PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA–PNA and DNA–PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson–Crick-like G–L pair. An RNA2–PNA triplex is significantly more stable than a DNA2–PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone–backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.

Development of a convenient route for the preparation of the N2-Cbz-protected guaninyl synthon required for Boc-mediated PNA synthesis

An efficient, high yielding, chemo- and regioselective, five-step synthetic route to N2-Cbz-guanin-9-yl acetic acid has been developed, which avoids the use of triphosgene. After formation of the N2-Boc protected purine from 2-amino-6-chloropurine, two successive base-controlled alkylations allowed an N9-tert-butyl acetate function followed by an N2-Cbz moiety to be installed. The selectivities of these reactions were confirmed through an X-ray crystallographic study of the 6-(2-nitrophenoxy) analogue. Final hydrolytic dechlorination and removal of the Boc and tert-butyl ester protecting groups were accomplished concomitantly under acidic conditions to afford the guanin-9-yl PNA monomer synthon in an overall yield of 53%.

A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates.

The synthesis of an azide containing PNA monomer is described. The monomer was incorporated into two PNA sequences for the purpose of synthesizing an intercalating fluorophore-labeled PNA and a metal binding hairpin using a solid phase copper catalyzed azide-alkyne Huisgen cycloaddition (CuAAC). Click chemistry was performed using 2-ethynylfluorene or 1-ethynylpyrene to add a fluorophore to the PNA, which were tested for their ability to recognize an abasic site on a DNA target. A PNA hairpin possessing azide monomers at each termini was synthesized and reacted with 2-ethynylpyridine to form a hairpin that is stabilized by Ni²⁺.

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

Cationic lipids containing protonated cyclen and different hydrophobic groups linked by uracil-PNA monomer: Synthesis and application for gene delivery

In this report, as candidates for non-viral gene vectors, cationic lipids L1, L2 and L3 based on protonated cyclen and different hydrophobic groups (cholesterol, dodecanol or diosgenin) linked by PNA monomer were designed and synthesized. Their liposomes were easily prepared by mixing the synthesized lipids with dioleoylphosphatidyl ethanolamine (DOPE) under appropriate mole ratios. Agarose gel retardation and fluorescent titration by ethidium bromide (EB) showed the strong DNA-binding ability with the K sv values of 1.21 × 10 7, 3.76 × 10 6 and 2.90 × 10 6 M −1 for the liposomes formed from L1– L3, respectively. These liposomes could retard pDNA at an N/ P ratio of 3 and form lipoplexes with sizes around 200–300 nm and zeta-potential values of +20–50 mV at N/ P ratio from 4 to 10. Besides, the cytotoxicity of the three lipoplexes assayed by MTT is quite different. The results from in vitro transfection in HEK 293T and A549 cell lines showed that the transfection efficiency of L3/DOPE/DNA lipoplex at an N/ P ratio of 6 and lipid/DOPE mole ratio of 1:2 is slightly higher than that of Lipofectamine 2000™, indicating that the title PNA monomer-based cationic lipids have great potential to be efficient non-viral gene vector.

Quantum chemical studies of peptide nucleic acid monomers and role of cyclohexyl modification on backbone flexibility

AbstractPeptide nucleic acids (PNA) bind sequence specifically to DNA/RNA and are of major interest for all fields of molecular biology and could form the basis for gene‐targeted drugs. Modifications are introduced in PNA to overcome problems associated with orientational selectivity in binding, to restrict conformational flexibility of backbone, and to discriminate binding for either DNA or RNA. The addition of geometrical isomers (1R,2S and 1S,2R) of cyclohexyl ring in the backbone of PNA could bring rigidification to PNA backbone and may impart specificity toward RNA. Therefore, quantum chemical studies are aimed to explore the conformational space, to find out preferred stable conformations of PNA and modified (1R,2S and 1S,2R) cyclohexyl PNA monomer. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

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.

DabPna: Design, Synthesis, And Dna Binding Studies

In continuing our research efforts for developing new oligodeoxynucleotide (ODN)-like drugs and diagnostics, we designed diaminobutyric peptide nucleic acids (dabPNAs), nucleopeptides characterized by a diaminobutyric-based building block that is an isomer of the aminoethylglycyl PNA (aegPNA) unit and the acyclic modification of the aminoprolyl PNA (ampPNA) monomer. In this work we present the solid phase synthesis of a dabPNA oligomer and of two aegPNAs containing a single dabPNA unit. A study relative to their binding ability towards DNA is also reported even in comparison with the well known aegPNAs.

Synthesis of A Fluorescent PNA Monomer Containing 5-((9 H -Fluoren-2-YL)Ethynyl)Uracil

Pyrimidine nucleobases bearing 5-phenylethynyl substitution represent compact and intrinsically fluorescent nucleobases. Such nucleobases are capable of selective recognition of a complementary base and may fluorimetrically report on hybridization events. Our past work has demonstrated that the fluorescence of 5-phenylethynyluracils is sensitive to substitution on the phenyl ring, however these are relatively weak fluorophores. We currently are pursuing the functionalization of the phenyl group of these modified nucleobases in order to further improve their fluorescence response, increase their aqueous solubility and stabilize hybrids formed with complementary nucleic acids. As an example of this work, we have synthesized the 5-((9 H-fluoren-2-yl)ethynyl)uracil PNA monomer that will be incorporated into oligomers using Fmoc-based chemistry. Initial evaluation of the fluorescence of the 5-((9 H-fluoren-2-yl)ethynyl)uracil derivative shows that the fluorescence intensity is approximately 50 times greater than a similar 5-phenylethynyluracil derivative when under identical conditions.

Electrochemical and photochemical characterization of novel ferrocenyl–azobenzene labeled PNA monomers for DNA detection

Ferrocenyl–azobenzene carboxylic acid was synthesized and used as electrochemically and spectroscopically active marker that was conjugated to thymine PNA monomer. Ferrocenyl–azobenzene labeled PNA monomer of thymine (Fc–Azo–T) shows highly electrochemical and photochemical activity. The detection limit of Fc–Azo–T can reach 10−6M by using differential pulsed voltammogram (DPV), and the UV–vis limit is in the order 10−7M in ethanol. Fc–Azo–T can undergo facile isomerization by photoirradiation. The results give great motivity for synthesizing ferrocenyl–azobenzene labeled PNA oligomers used as an effective electrochemical and photochemical probes.

Electrochemical Leveling Effect on Multi-Aromatic Monomer Films to Prepare Robust Conducting Polymer Nano- and Microfilms by Vapor Deposition Combined with Electropolymerization

Multi-aromatic conducting polymer films, poly(N-phenyl-1-naphthylamine) (PPNA), were prepared by using a combination of vapor deposition and electrochemical polymerization. The PNA monomer film was vapor deposited on an indium−tin oxide (ITO) glass and was then electropolymerized using cyclic voltammetry in a 1 N HClO4 aqueous solution. An electrochemical rubbing effect happened on the monomer film using the above combined process, producing a robust electrode material of PPNA film in the electrochromic device: ITO/PPNA film//PU−LiClO4//PEDOT:PSS/ITO, where poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonate) is PEDOT:PSS, and polyurethane is PU. Short response time (ca. 10 s) was attained from coloring to bleaching processes. After 200 switching, the stable Coulombic efficiency and optical contrast possess the values of 108 and 28%, respectively.

Single nucleotide specific detection of DNA by native chemical ligation of fluorescence labeled PNA-probes

DNA-directed chemical ligations provide the opportunity to diagnose DNA sequences with very high sequence specificity. Fluorescent labels have been attached to reactive probes to enable the homogeneous detection of DNA and RNA. However, it has frequently been found that the attachment of fluorescent labels results in decreases of ligation fidelity. Herein we describe the development of a fluorogenic ligation reaction that provides for 10 2-fold to perfect sequence selectivity. The reaction is based on the isocysteine-mediated native chemical PNA ligation. It is shown that DNA-induced rate accelerations of ∼43.000-fold can be obtained through subtle variations of the ligation conditions. PNA–thioesters and isocysteine–PNA conjugates were labeled with FAM and TMR fluorophores, respectively. For gaining rapid synthetic access, a convenient on-resin labeling approach was developed. A new PNA monomer featuring an Alloc-protected lysine side chain was synthesized and coupled in solid-phase PNA synthesis. In the event of a ligation reaction the two fluorophores are brought into proximity. It is shown that fluorescence resonance energy transfer provides a positive fluorescence signal which is specific for product formation rather than for loss of starting materials. Single base mutations can be detected within minutes and with very high sequence selectivity at optimized conditions.

Evaluation of two chelators for labelling a PNA monomer with the fac-[ 99mTc(CO) 3] + moiety

A PNA monomer containing thymine as nucleobase ( 1) was synthesized, characterized and coupled to the pyrazolyl containing ligand 3,5-Me 2pz(CH 2) 2N((CH 2) 3COOH)(CH 2) 2NHBoc ( 2) and to a modified cysteine S-(carboxymethyl-pentafluorphenyl)- N-[(trifluor)carbonyl]- l-cysteine methyl ester ( 3) yielding the bifunctional chelators 6 and 7, respectively. Reactions of 6 and 7 with the Re(I) tricarbonyl starting material [Re(CO) 3(H 2O) 3]Br afforded the complexes fac-[Re(CO) 3(κ 3- 6)] + ( 8) and fac-[Re(CO) 3(κ 3- 7)] ( 9), respectively. The identity of 8 and 9 has been established based on IR spectroscopy, elemental analysis, ESI-MS spectrometry and HPLC. The multinuclear NMR spectroscopy ( 1H, 13C, g-COSY, g-HSQC) has also been very informative in the case of complex 8, showing the presence of rotamers in solution. For 9 the NMR spectrum was too complex due to the presence of rotamers and diastereoisomers. The radioactive congeners of complexes 8 and 9, fac-[ 99mTc(CO) 3(κ 3- 6)] + ( 8a) and fac-[ 99mTc(CO) 3(κ 3- 7)] ( 9a), have been prepared by reacting the precursor fac-[ 99mTc(CO) 3(H 2O) 3] + with the corresponding ligands being their identity established by comparing their HPLC chromatograms with the HPLC of the rhenium surrogates.