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1.  Letter from the Editors 
Artificial DNA, PNA & XNA  2012;3(2):29-30.
We are happy to publish this special issue dedicated to Prof. Rosangela Marchelli. This issue not only celebrates her long-standing scientific activity on occasion of her significant anniversary, but it is meant to recognize her contribution to Bioorganic Chemistry in the field of Artificial DNA, and in particular of Peptide Nucleic Acids.
doi:10.4161/adna.21100
PMCID: PMC3429528  PMID: 22777061
2.  PNA bearing 5-azidomethyluracil 
Artificial DNA, PNA & XNA  2012;3(2):53-62.
Fmoc- and Boc-protected modified monomers bearing 5-azidomethyluracil nucleobase were synthesized. Four different solid-phase synthetic strategies were tested in order to evaluate the application of this series of monomers for the solid-phase synthesis of modified PNA. The azide was used as masked amine for the introduction of amide-linked functional groups, allowing the production of a library of compounds starting from a single modified monomer. The azide function was also exploited as reactive group for the modification of PNA in solution via azide-alkyne click cycloaddition.
doi:10.4161/adna.20158
PMCID: PMC3429531  PMID: 22772040
modified uracil; peptide nucleic acids; PNA; solid-phase modification; click reaction; orthogonal protection
3.  Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays 
Artificial DNA, PNA & XNA  2012;3(2):63-72.
PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes.
doi:10.4161/adna.20603
PMCID: PMC3429532  PMID: 22772038
PNA; olive oil; hazelnut oil; SNP; cultivar identification; DNA fingerprinting
4.  C(5) modified uracil derivatives showing antiproliferative and erythroid differentiation inducing activities on human chronic myelogenous leukemia K562 cells 
European Journal of Pharmacology  2011;672(1-3):30-37.
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.
doi:10.1016/j.ejphar.2011.09.024
PMCID: PMC3271358  PMID: 21958870
Erythroid differentiation; Tumor growth; Isoorotic acid derivative; Chronic myelogenous leukemia; Beta-thalassemia
5.  Molecular computing by PNA:PNA duplex formation 
Artificial DNA, PNA & XNA  2011;2(1):16-22.
Molecular computing is potentially one of the most powerful tools for the development of massive parallel computing protocols. In the present paper, a first example of the use of PNA:PNA interactions in molecular computing is described. A series of short PNA sequences have been designed with a four base stretch coding for variables and solutions. Hybridization of the components in different combinations was tested both in solution and in a microarray format. A series of PNA representing the solutions were spotted on a microarray surface in order to simulate the hardware. A series of PNA representing the variables, labeled with TAMRA, were used to interrogate the device enabling to solve non-deterministic logic operations. The system was shown to be able to solve a two-variable equation with a high signal to noise ratio. This paper intends to provide a proof of principle that PNA, on account of their stability and specificity of binding, are most suitable for constructing organic-type computers.
doi:10.4161/adna.2.1.15459
PMCID: PMC3116582  PMID: 21686248
molecular computing; SAT problem; PNA:PNA; microarray; fluorescence
6.  A pyrenyl-PNA probe for DNA and RNA recognition 
Artificial DNA, PNA & XNA  2010;1(2):83-89.
The design and the synthesis of a PNA oligomer containing a pyrenyl residue in the backbone were performed. PNA sequence was chosen complementary to a “G rich” target sequence involved in G-quadruplex formation. The pyrenyl unit replaced a nucleobase in the middle of the PNA through covalent linkage to the backbone by a carboxymethyl unit. A systematic study on the binding properties of this probe towards DNA and RNA complementary strands was carried out by UV and fluorescence spectroscopy. UV melting curves indicated that the PNA probe binds more tightly to RNA rather than to DNA. Thermodynamic data obtained by Van't Hoff fitting of the melting curves indicated that, in the case of RNA, a more favorable interaction occurs between the pyrenyl unit and the RNA nucleobases, leading to a very favorable enthalpic contribution.
The fluorescence analysis showed specific quenching of the pyrene emission associated to the formation of the full-match PNA-DNA or PNA-RNA duplexes. Again, this behavior was more evident in the case of RNA, consistently with the stronger interaction of the pyrenyl unit with the complementary strand. In order to study the sequence specificity of the pyrenyl-PNA probe (pyr-PNA), recognition experiments on mismatched DNA and RNA sequences were also performed.
doi:10.4161/adna.1.2.13899
PMCID: PMC3116571  PMID: 21686243
peptide nucleic acid; pyrene; DNA; RNA; fluorescence
7.  Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences 
Nucleic Acids Research  2008;36(5):1464-1471.
Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this ‘double-duplex invasion’, a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the α-nitrogen of N-(2-aminoethyl)-d-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-d-lysine, the invasion successfully occurred even at highly G–C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-d-lysine, their l-isomers hardly invaded, showing crucial importance of the d-chirality. The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.
doi:10.1093/nar/gkm1154
PMCID: PMC2275137  PMID: 18203747
8.  Isolation and Characterization of a New Less-Toxic Derivative of the Fusarium Mycotoxin Diacetoxyscirpenol after Thermal Treatment 
Trichothecenes are an important class of mycotoxins that act as potent protein synthesis inhibitors in eukaryotic organisms. The compound 4,15-diacetoxyscirpenol is highly toxic for plants and animals. Potatoes are especially prone to be contaminated with 4,15-diacetoxyscirpenol after infection with Fusarium sambucinum. In the current study, the reduction of 4,15-diacetoxyscirpenol during thermal treatment in aqueous solution was monitored. A new derivative was detected and named DAS-M1. After isolation, DAS-M1 was characterized with LC–HR-MS and LC–MS/MS and structurally elucidated with 1H, 13C, and 2D NMR. Potatoes were inoculated with F. sambucinum, and the infected potatoes were cooked at 100 or 121 °C, respectively. A reduction of 4,15-diacetoxyscirpenol from about 26% (1 h at 100 °C) to 100% (4 h at 121 °C) was detected by means of LC–MS/MS analysis. The effects of different pH values on the reduction of 4,15-diacetoxyscirpenol were investigated, showing higher conversion rates at more acidic pH values. In addition, the toxicity of 4,15-diacetoxyscirpenol and DAS-M1 was compared in vitro using a wheat germ transcription/translation assay and in vivo on Saccharomyces cerevisiae. The results show that the inhibitory effect of DAS-M1 on yeast growth is about 50 times lower and inhibition of protein synthesis is about 100 times lower than that of 4,15-diacetoxyscirpenol.
doi:10.1021/jf2022176
PMCID: PMC3175691  PMID: 21800832
diacetoxyscirpenol; trichothecene; mycotoxin; detoxification; potatoes; Fusarium
9.  Cellular Uptakes, Biostabilities and Anti-miR-210 Activities of Chiral Arginine-PNAs in Leukaemic K562 Cells 
Chembiochem  2012;13(9):1327-1337.
A series of 18-mer peptide nucleic acids (PNAs) targeted against micro-RNA miR-210 was synthesised and tested in a cellular system. Unmodified PNAs, R8-conjugated PNAs and modified PNAs containing eight arginine residues on the backbone, either as C2-modified (R) or C5-modified (S) monomers, all with the same sequence, were compared. Two different models were used for the modified PNAs: one with alternated chiral and achiral monomers and one with a stretch of chiral monomers at the N terminus. The melting temperatures of these derivatives were found to be extremely high and 5 m urea was used to assess differences between the different structures. FACS analysis and qRT-PCR on K562 chronic myelogenous leukaemic cells indicated that arginine-conjugated and backbone-modified PNAs display good cellular uptake, with best performances for the C2-modified series. Resistance to enzymatic degradation was found to be higher for the backbone-modified PNAs, thus enhancing the advantage of using these derivatives rather than conjugated PNAs in the cells in serum, and this effect is magnified in the presence of peptidases such as trypsin. Inhibition of miR-210 activity led to changes in the erythroid differentiation pathway, which were more evident in mithramycin-treated cells. Interestingly, the anti-miR activities differed with use of different PNAs, thus suggesting a role of the substituents not only in the cellular uptake, but also in the mechanism of miR recognition and inactivation. This is the first report relating to the use of backbone-modified PNAs as anti-miR agents. The results clearly indicate that backbone-modified PNAs are good candidates for the development of very efficient drugs based on anti-miR activity, due to their enhanced bioavailabilities, and that overall anti-miR performance is a combination of cellular uptake and RNA binding.
doi:10.1002/cbic.201100745
PMCID: PMC3401907  PMID: 22639449
cell permeation; cellular differentiation; chiral PNA; microRNA; peptide nucleic acids; RNA

Results 1-9 (9)