Cyclopropane PNA: observable triplex melting in a PNA constrained with a 3-membered ring

The first peptide nucleic acid (PNA) with a cyclopropane in the backbone has been synthesized, and the effects of the ring on DNA/RNA binding properties of the PNA have been examined. Well-defined triplex to duplex melting transitions of PNA₂ DNA complexes is clearly observed by variable temperature UV absorbance with the cyclopropane-constrained PNA.     

Characterization and electrical behavior of polyaniline–poly-N-isopropylacrylamide-co-acrylic acid/alumina aqueous dispersions in the presence of dodecyl benzenesulfonic acid

Polymer composites containing polyaniline–poly-N-isopropylacrylamide-co-acrylic acid/alumina (PANI–PNA/Al₂O₃) were synthesized by chemical polymerization of aniline in an aqueous solution containing dispersed PNA/Al₂O₃ in the presence of dodecylbenzene sulfonic acid (DBSA) using different wt% of Al₂O₃ (5%, 10%, 20%, and 30%). The structure and morphology of the polymer matrix were identified by scanning electron microscope (SEM) and atomic force microscope (AFM). Thermal stability and an amended crystallinity were reasserted by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and X-ray diffraction (XRD), respectively. Chemical interaction of Al₂O₃ and PANI was characterized by XPS. The enhancement of the electrical conductivity in the temperature range 293–483 K shows a semiconducting behavior with a negative temperature coefficient of resistivity (TCR). In addition, the conductivity data are characterized by three different regions with small changing jerks with increasing temperature.     

Experimental (FT-IR) and theoretical (DFT) studies on the adsorption behavior of p-nitroaniline (PNA) on gold nanoparticales

This paper reports the studies on the adsorption behavior of p-nitroaniline (PNA) on gold nanoparticales by experiment (FT-IR) and theory (DFT). On dried filter paper coated with gold nanoparticles and in gold aqueous colloids, surface-enhanced Raman scattering (SERS) spectra of p-nitroaniline (PNA) are studied by FT-IR excitation. The Raman frequencies of these two models for the p-nitroaniline (PNA) molecules on different substrate using DFT-B3PW91 with lanl2dz are calculated. Here it is demonstrated the calculated Raman frequencies are in good agreement with experimental values. Experimental (FT-IR) and theoretical (DFT) studies indicate that the adsorption behaviors of PNA molecules are different on these two substrates: in gold aqueous colloids, PNA molecules are adsorbed through the nitro group; while on the gold-coated filter paper, they are titled and there is a certain angle between the benzene rings and the surfaces of gold nanoparticles.     

Rapid label-free visual assay for the detection and quantification of viral RNA using peptide nucleic acid (PNA) and gold nanoparticles (AuNPs)

A rapid label-free visual assay for the detection of viral RNA using peptide nucleic acid (PNA) probes and gold nanoparticles (AuNPs) is presented in this study. Diagnosis is a crucial step for the molecular surveillance of diseases, and a rapid visual test with high specificity could play a vital role in the management of viral diseases. In this assay, the specific agglomerative behavior of PNA with gold nanoparticles was manipulated by its complementation with viral RNA. The assay was able to detect 5–10 ng of viral RNA from various biological samples, such as allantoic fluids, cell culture fluids and vaccines, in 100 μl of test solution. The developed assay was more sensitive than a hemagglutination (HA) test, a routine platform test for the detection of Newcastle disease virus (NDV), and the developed assay was able to visually detect NDV with as little as 0.25 HA units of virus. In terms of the specificity, the test could discriminate single nucleotide differences in the target RNA and hence could provide visual viral genotyping/pathotyping. This observation was confirmed by pathotyping different known isolates of NDV. Further, the PNA-induced colorimetric changes in the presence of the target RNA at different RNA to PNA ratios yielded a standard curve with a linear coefficient of R² = 0.990, which was comparable to the value of R² = 0.995 from real-time PCR experiments with the same viral RNA. Therefore, the viral RNA in a given samples could be quantified using a simple visual spectrophotometer available in any clinical laboratory. This assay may find application in diagnostic assays for other RNA viruses, which are well known to undergo mutations, thus presenting challenges for their molecular surveillance, genotyping and quantification.     

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.     

Label‐Free Bioelectronic Detection of Point Mutation by Using Peptide Nucleic Acid Probes

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probes with a label‐free protocol is described. The detection of PNA‐DNA and DNA‐DNA hybridizations were accomplished based on the oxidation signal of guanine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). It was observed that the oxidation signals of guanine obtained from the PNA and DNA probe modified CPEs were higher than those obtained from the PNA‐DNA and DNA‐DNA hybrid modified CPEs due to the accessible unbound guanine bases. The detection of hybridization between PNA probe and point mutation containing DNA target sequences was clearly observed due to the difference of the oxidation signals of guanine bases, because the point mutation was guanine nearly at the middle of the sequence. The effect of the DNA target concentration on the hybridization signal was also observed. The PNA probe was also challenged with excessive and equal amount of noncomplementary DNA and also mixtures of point mutation and target DNA.     

PNA encoding (PNA=peptide nucleic acid): from solution-based libraries to organized microarrays

Microarray-based technologies have attracted attention in chemical biology by virtue of their miniaturized format, which is well suited to probe ligand-protein interactions or investigate enzymatic activity in complex biological mixtures. A number of research groups have reported the preparation of surfaces on microarrays with specific functional groups to chemoselectively attach small molecules from libraries. We have developed an alternative method whereby libraries are encoded with peptide nucleic acid (PNA), such that libraries which exist as mixtures in solution self-assemble into an organized microarray through hybridization to produce readily available DNA arrays. This allows libraries synthesized by split and mix methods to be decoded in a single step. An asset of this method compared to direct spotting is that libraries can be used in solution for bioassays prior to self-assembly into the microarray format.     

Backbone extended pyrrolidine PNA (bepPNA): a chiral PNA for selective RNA recognition

Synthesis of cationic, chiral PNA analogues with an extra atom in the backbone (bepPNA) is reported. The (2S,4S) geometry of the pyrrolidine ring, and an additional carbon atom in the backbone of homopyrimidine-bepPNAs resulted in the optimization of the inter-nucleobase distance, such that selective binding to complementary RNA over DNA was observed in the triplex mode. It was evident from circular dichroism studies that oligomers with mixed aminoethylglycyl-bep (aeg-bep) repeating units, and also bepPNA with homogeneous backbone attained structures quite different from those of aegPNA₂:RNA/DNA complexes. The bepPNA, when incorporated in a duplex forming mixed purine-pyrimidine sequence, also showed a preference for binding complementary RNA over DNA.     

Dde-protected PNA monomers, orthogonal to Fmoc, for the synthesis of PNA-peptide conjugates

Peptide nucleic acids have become, arguably, one of the most interesting of DNA mimics. Herein the efficient solution phase synthesis of four novel 1-(4,4-dimethyl-2,6-dioxacyclohexylidene)ethyl/4-methoxytrityl (Dde/Mmt) protected PNA monomers is reported which were then used to synthesise PNA-peptide conjugates through a mild Dde deprotection strategy, which was fully orthogonal to Fmoc chemistry, allowing at will Fmoc peptide and Dde-PNA synthesis.     

Synthesis and oligodeoxynucleotide binding properties of pyrrolidinyl peptide nucleic acids bearing prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones

A series of novel conformationally rigid pyrrolidinyl peptide nucleic acids (PNA) based on d-prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones has been synthesized. Investigation of the binding properties of four stereoisomeric PNAs possessing different stereochemistry at the ACPC part with DNA revealed that a precise stereochemistry of the backbone is very important in determining the binding properties. Only the PNA containing (1S,2S)-ACPC can form a very stable 1:1 complex with the complementary DNA in a sequence-specific manner.