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DNA-based aptamers are widely employed as bioreceptors, owing to their tuneable affinity and specificity towards their targets. The use of peptide nucleic acids (PNAs) has instead proven challenging for this purpose, due to the absence of selection methods for the independent discovery of suitable receptors and due to the difficult mimicry of established DNA-based ones. Despite that PNAs exceed homologous DNA or RNA in terms of complementary base pairing, they can fail to reproduce alternative modes of binding because of their different structural features. The remarkable stability and charge distribution of PNAs could be beneficial to produce sensing bioreceptors, especially in the development of electronic devices such as field-effect transistor-based (FET) biosensors. We hereby report for the first time a high-affinity PNA aptamer for cardiac Troponin I (cTnI), a biomarker of acute myocardial infarction, able to interact with this specific protein in the picomolar range. The PNA aptamer was immobilized onto a graphene-based FET (gFET) transducer, and its ability in the direct detection of cTnI was compared with that of a DNA-based one of the same sequence. Similar dissociation constants were recorded for both receptors in 0.01 × PBS, as well as comparable detection limits of 6.0 ± 1.0 pg mL-1 (PNA aptamer) and 3.3 ± 0.7 pg mL-1 (DNA aptamer). Apart from the non-trivial demonstration that a PNA can behave as an aptamer, the tested receptor proved to be more consistent upon working in more complex biological matrices. [Display omitted] • First high-affinity PNA aptamer examplified for cardiac Troponin I (cTnI). • Integration of azide-terminated PNA onto graphene based field effect transistor. • PNA test receptor was highly adapted for working in more complex solutions. [ABSTRACT FROM AUTHOR]

We have shown previously that a T10 peptide nucleic acid (PNA) bound to the transcriptional terminator of a Saccharomyces cerevisiae tDNAIle(TAT) gene arrests elongating yeast RNA polymerase (pal) III at a position that precedes by 20 bp the upstream end of the PNA roadblock (Dieci, G., Corradini, R., Sforza, S., Marchelli, R., and Ottonello, S. (2001) J. Biol. Chem. 276, 5720–5725). Here, a PNA-binding cassette was placed at various distances downstream of a functional tDNAIle transcriptional terminator (T6) that is not bound by the T10 PNA, and the effect of the PNA roadblock on RNA 3′-end formation, transcript release, and transcription reinitiation was examined. With a PNA roadblock placed as close as 5 hp downstream of the T6 terminator, pol III could still reach the termination site and complete pre-tRNA synthesis, implying that the catalytic site-to-front edge (C-F) distance of the polymerase can shorten by >10 bp upon recognition of the terminator element. In addition, transcripts synthesized by a PNA-roadblocked terminating pal III were found to be released from transcription complexes. Interestingly, however, the same roadblock dramatically reduced the rate of transcription reinitiation. Also, when placed 5 bp downstream of a mutationally inactivated terminator element (T3GT2), the PNA roadblock restored transcription termination, thus indicating that the inactivated terminator is compromised in its ability to cause pol III pausing, but can still induce C-F distance shortening and transcript release. The latter two activities were found to be further impaired in variants of the inactivated terminator bearing fewer than three consecutive T residues (T2G2T2 and TG2TGT). The data indicate that RNA polymerase pausing, C-F distance shortening, and transcript release are functionally distinguishable features of the termination process and point to the RNA release propensity of pol III as a major determinant of its remarkably high termination efficiency. [ABSTRACT FROM AUTHOR]

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. [Copyright &y& Elsevier]

Abstract: N γ-Carboxyalkyl modified peptide nucleic acids (PNAs), containing the four canonical nucleobases, were prepared via solid-phase oligomerization. The inserted peptoid monomers 1 and 2 were constructed through simple synthetic procedures, utilizing appropriate glycidol and iodoalkyl electrophiles. Thermal denaturation studies, performed with complementary antiparallel DNA strands, demonstrated that the length of the N γ-side chain strongly influences the modified PNAs hybridization properties. Moreover, multiple negative charges on the oligoamide backbone, when present on γ-nitrogen C6 side chains proved to be beneficial for the oligomers’ water solubility and DNA hybridization specificity. [Copyright &y& Elsevier]

Abstract: Lys-based ‘chiral box’ Peptide Nucleic Acids (PNAs with three adjacent 2D-Lys-based chiral monomers) have shown unsurpassed specificity in DNA recognition. In this Letter, the binding performances of arginine-based chiral PNAs were evaluated for PNAs containing in the middle part of the strand either a 2D,5L-Arg monomer or three adjacent 2D-; 2D,5L-; 5L-Arg monomers (‘Extended Chiral Box’), a combination never studied before. The binding performances of the PNAs were studied by evaluating the melting temperatures of fullmatch and mismatch PNA–DNA and PNA–RNA hybrids and by studying their structure by circular dichroism (CD). The data indicated that the arginine side chains inserted in the PNA structure are perfectly equivalent to lysine side chains as far as oligonucleotide recognition is concerned. The insertion of an ‘Extended Chiral Box’ into PNA differently influences the binding properties to DNA and RNA: the additional side chains had no observable effect on binding affinity and selectivity toward DNA, whereas, seemed to slightly disturb the binding affinity to RNA but at the same time highly enhancing the recognition selectivity. [ABSTRACT FROM AUTHOR]

Abstract: The synthesis of new chiral PNA analogues based on lysine is reported. In particular, l- and/or d-lysine-based PNA submonomers bearing two lysine side chains exactly spaced as in the dipeptide Lys-Lys were synthesized and incorporated in the middle of decameric PNA strands, obtaining four diastereomeric (LD, DL, LL and DD) lysine-based chiral PNAs. The hybridization with their complementary antiparallel DNA strand was studied by melting temperature determination and compared with the analogue achiral PNA and chiral PNAs bearing one residue with either of the two lysine enantiomers. The binding abilities were shown to be strongly dependent on the configuration of the stereogenic centres. [Copyright &y& Elsevier]

Abstract: The K562 cell line has been proposed as a useful experimental system to identify anti-tumor compounds acting by inducing terminal erythroid differentiation. K562 cells exhibit a low proportion of hemoglobin-synthesizing cells under standard cell growth conditions, but are able to undergo terminal erythroid differentiation when treated with a variety of anti-tumor compounds. In this paper we report a screening study on a set of different modified C(5) uracil derivatives for the evaluation of their antiproliferative effect in connection with erythroid differentiation pathways, and for defining a new class of drug candidates for the treatment of chronic myelogenous leukemia. Activity of the derivatives tested can be classified in two effect: an antiproliferative effect linked to a high level of erythroid differentiation activity and an antiproliferative effect without activation of gamma globin genes The highest antiproliferative effect and erythroid induction was shown by compound 9, a thymine derivative bearing a n-octyl chain on nitrogen N(1), whereas thymine did not show any effect, suggesting the importance of the linear alkyl chain in position N(1). To our knowledge this compound should be considered among the most efficient inducers of erythroid differentiation of K562 cells. This work is the starting point for the quest of more effective and specific drugs for the induction of terminal erythroid differentiation, for leading new insights in the treatment of neoplastic diseases with molecules acting by inducing differentiation rather than by simply exerting cytotoxic effects. [Copyright &y& Elsevier]

Abstract: The identification of all epigenetic modifications (i.e. DNA methylation, histone modifications and expression of noncoding RNAs such as microRNAs) involved in gene regulation is one of the major steps forward for understanding human biology in both normal and pathological conditions and for development of novel drugs. In this context, microRNAs play a pivotal role. This review article focuses on the involvement of microRNAs in the regulation of gene expression, on the possible role of microRNAs in the onset and development of human pathologies, and on the pharmacological alteration of the biological activity of microRNAs. RNA and DNA analogs, which can selectively target microRNAs using Watson–Crick base pairing schemes, provide a rational and efficient way to modulate gene expression. These compounds, termed antago-miR or anti-miR have been described in many examples in the recent literature and have proved to be able to perform regulatory as well as therapeutic functions. Among these, a still not fully exploited class is that of peptide nucleic acids (PNAs), promising tools for the inhibition of miRNA activity, with important applications in gene therapy and in drug development. PNAs targeting miR-122, miR-155 and miR-210 have already been developed and their biological effects studied both in vitro and in vivo. [Copyright &y& Elsevier]

Abstract: A new submonomeric approach for the Fmoc solid phase synthesis of chiral PNAs is reported here. The design and synthesis of a new d-lysine-based Fmoc submonomer obtained by replacing the nucleobase residue with an Alloc group, compatible with Fmoc chemistry, is described starting from d-lysine and Fmoc-aminoacetaldehyde. The desired submonomer was obtained in high yield with no racemization. The conditions for synthesizing a chiral PNA dimer on solid support by a submonomeric approach have been optimized, allowing to obtain the desired PNA with a very high optical purity. [Copyright &y& Elsevier]

A novel enzyme-labelled voltammetric magnetogenoassay for DNA sensing based on the use of carboxyl-surface coated magnetic microbeads functionalized with PNA probes and subsequent read-out on screen-printed electrode (SPE) substrates was developed. The assay was validated for determination of non-amplified genomic DNA from genetically modified Roundup Ready soy. Outstanding performance with respect to other genoassays requiring preliminary amplification of target DNA via PCR was demonstrated. The analytical performance was also improved compared to previous methods based on the immobilization of the same PNA probes on SPE substrates, since the method was found capable of achieving LOD and LOQ of 415 fM and 995 fM, respectively. The ability of the magnetogenoassay to detect the presence of Roundup Ready soy DNA sequence was tested on genomic DNA extract from European Reference Material soy flours, demonstrating the capability of the method to match the European Union regulation for labelling of food containing a percentage of GM products greater than 0,9%. [Display omitted] • A sandwich electrochemical magnetogenoassay for the determination of DNA from GM soy was developed. • Fitness for application performed on soy flours reaching femtomolar LOD. • Valuable analytical performances for food safety and authenticity assessment. [ABSTRACT FROM AUTHOR]

Since the identification of microRNAs (miRNAs) involved in the regulation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, miRNAs known to down-regulate the expression of the CFTR and associated proteins have been investigated as potential therapeutic targets. Here we show that miR-101-3p, targeting the 3′-UTR sequence of the CFTR mRNA, can be selectively inhibited by a peptide nucleic acid (PNA) carrying a full complementary sequence. With respect to clinical relevance of microRNA targeting, it is expected that reduction in concentration of miRNAs (the anti-miRNA approach) could be associated with increasing amounts of target mRNAs. Consistently to this hypothesis, we report that PNA-mediated inhibition of miR-101-3p was accompanied by CFTR up-regulation. Next Generation Sequencing (NGS) was performed in order to verify the effects of the anti-miR-101-3p PNA on the Calu-3 miRNome. Upon inhibition of miR-101-3p we observed a fold change (FC) expression <2 of the majority of miRNAs (403/479, 84.13%), whereas we identified a list of dysregulated miRNAs, suggesting that specific miRNA inhibition (in our case miR-101-3p) might be accompanied by alteration of expression of other miRNAs, some of them known to be involved in Cystic Fibrosis (CF), such as miR-155-5p and miR-125b-5p. Image 1 • microRNAs are deeply involved in the regulation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. • miR-101-3p targets the 3′-UTR sequence of the CFTR mRNA. • In Calu-3 cells miR-101-3p can be selectively inhibited by a fully complementary peptide nucleic acid (PNA). • PNA-mediated inhibition of miR-101-3p was accompanied by CFTR up-regulation. • The effects of the anti-miR-101-3p PNA on the Calu-3 miRNome are accompanied by alteration of miRNAs involved in Cystic Fibrosis. [ABSTRACT FROM AUTHOR]

RAS mutations in the blood of colorectal cancer (CRC) patients are emerging as biomarkers of acquired resistance to Epidermal Growth Factor Receptor therapy. Unfortunately, reliable assays granting fast, real-time monitoring of treatment response, capable of refining retrospective, tissue-based analysis, are still needed. Recently, several methods for detecting blood RAS mutations have been proposed, generally relying on multi-step and PCR-based, time-consuming and cost-ineffective procedures. By exploiting a liquid biopsy approach, we developed an ultrasensitive nanoparticle-enhanced plasmonic method for detecting ~1 aM RAS single nucleotide variants (SNVs) in the plasma of CRC patients. The assay does not require the extraction of tumor DNA from plasma and detects it in volumes as low as 40 μL of plasma, which is at least an order of magnitude smaller than that required by state of the art liquid biopsy technologies. The most prevalent RAS mutations are detected in DNA from tumor tissue with 100% sensitivity and 83.33% specificity. Spike-in experiments in human plasma further encouraged assay application on clinical specimens. The assay was proven in plasma from CRC patients and healthy donors, and full discrimination between mutated DNA from patients over wild-type DNA from healthy volunteers was obtained thus demonstrating its promising avenue for cancer monitoring based on liquid biopsy. Image 1 • Nanoparticle-enhanced surface plasmon resonance imaging is used to reveal oncogenic DNA with a liquid biopsy approach. • Circulating DNA is detected with a PCR-free approach and simple pre-analytical treatment of the plasma from cancer patients. • Volumes of plasma as low as 40 μL are used, whereas standard technologies require a few hundreds of microliters of plasma. • RAS mutated DNA from tumor tissue is detected with 100% sensitivity and 83.33% specificity. • Full discrimination between mutated DNA from cancer patients over wild-type DNA from healthy volunteers is obtained. [ABSTRACT FROM AUTHOR]