Artificial DNA: PNA & XNA最新文献

{"title":"Artificial DNA and surface plasmon resonance.","authors":"Roberta D'Agata,&nbsp;Giuseppe Spoto","doi":"10.4161/adna.21383","DOIUrl":"https://doi.org/10.4161/adna.21383","url":null,"abstract":"<p><p>The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years.   Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows forbetter exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.21383","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30781569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting pre-miRNA by peptide nucleic acids: a new strategy to interfere in the miRNA maturation.","authors":"Concetta Avitabile,&nbsp;Michele Saviano,&nbsp;Luca D'Andrea,&nbsp;Nicoletta Bianchi,&nbsp;Enrica Fabbri,&nbsp;Eleonora Brognara,&nbsp;Roberto Gambari,&nbsp;Alessandra Romanelli","doi":"10.4161/adna.20911","DOIUrl":"https://doi.org/10.4161/adna.20911","url":null,"abstract":"<p><p>PNAs conjugated to carrier peptides have been employed for the targeting of miRNA precursor, with the aim to develop molecules able to interfere in the pre-miRNA processing. The capability of the molecules to bind pre-miRNA has been tested in vitro by fluorescence assayes on Thiazole Orange labeled molecules and in vivo, in K562 cells, evaluating the amount of miRNA produced after treatment of cells with two amounts of PNAs.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.20911","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30692067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PNA bearing 5-azidomethyluracil: a novel approach for solid and solution phase modification.","authors":"Alex Manicardi, Alessandro Accetta, Tullia Tedeschi, Stefano Sforza, Rosangela Marchelli, Roberto Corradini","doi":"10.4161/adna.20158","DOIUrl":"10.4161/adna.20158","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/91/adna-3-53.PMC3429531.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30745228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Letter from the editors.","authors":"Roberto Corradini,&nbsp;Stefano Sforza","doi":"10.4161/adna.21100","DOIUrl":"https://doi.org/10.4161/adna.21100","url":null,"abstract":"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.","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.21100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30748872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays.","authors":"Stefano Rossi,&nbsp;Alessandro Calabretta,&nbsp;Tullia Tedeschi,&nbsp;Stefano Sforza,&nbsp;Sergio Arcioni,&nbsp;Luciana Baldoni,&nbsp;Roberto Corradini,&nbsp;Rosangela Marchelli","doi":"10.4161/adna.20603","DOIUrl":"https://doi.org/10.4161/adna.20603","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.20603","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30745230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of decoy molecules targeting NF-kappaB transcription factors in Cystic fibrosis IB3-1 cells: recruitment of NF-kappaB to the IL-8 gene promoter and transcription of the IL-8 gene.","authors":"Alessia Finotti,&nbsp;Monica Borgatti,&nbsp;Valentino Bezzerri,&nbsp;Elena Nicolis,&nbsp;Ilaria Lampronti,&nbsp;Maria Dechecchi,&nbsp;Irene Mancini,&nbsp;Giulio Cabrini,&nbsp;Michele Saviano,&nbsp;Concetta Avitabile,&nbsp;Alessandra Romanelli,&nbsp;Roberto Gambari","doi":"10.4161/adna.21061","DOIUrl":"https://doi.org/10.4161/adna.21061","url":null,"abstract":"<p><p>One of the clinical features of cystic fibrosis (CF) is a deep inflammatory process, which is characterized by production and release of cytokines and chemokines, among which interleukin 8 (IL-8) represents one of the most important. Accordingly, there is a growing interest in developing therapies against CF to reduce the excessive inflammatory response in the airways of CF patients. Since transcription factor NF-kappaB plays a critical role in IL-8 expression, the transcription factor decoy (TFD) strategy might be of interest. In order to demonstrate that TFD against NF-kappaB interferes with the NF-kappaB pathway we proved, by chromatin immunoprecipitation (ChIP) that treatment with TFD oligodeoxyribonucleotides of cystic fibrosis IB3-1 cells infected with Pseudomonas aeruginosa leads to a decrease occupancy of the Il-8 gene promoter by NF-kappaB factors. In order to develop more stable therapeutic molecules, peptide nucleic acids (PNAs) based agents were considered. In this respect PNA-DNA-PNA (PDP) chimeras are molecules of great interest from several points of view: (1) they can be complexed with liposomes and microspheres; (2) they are resistant to DNases, serum and cytoplasmic extracts; (3) they are potent decoy molecules. By using electrophoretic mobility shift assay and RT-PCR analysis we have demonstrated that (1) the effects of PDP/PDP NF-kappaB decoy chimera on accumulation of pro-inflammatory mRNAs in P.aeruginosa infected IB3-1 cells reproduce that of decoy oligonucleotides; in particular (2) the PDP/PDP chimera is a strong inhibitor of IL-8 gene expression; (3) the effect of PDP/PDP chimeras, unlike those of ODN-based decoys, are observed even in the absence of protection with lipofectamine. These informations are of great impact, in our opinion, for the development of stable molecules to be used in non-viral gene therapy of cystic fibrosis.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.21061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30745285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introduction of multiphosphonate ligand to peptide nucleic acid for metal ion conjugation.","authors":"Yuichiro Aiba,&nbsp;Yuta Honda,&nbsp;Yue Han,&nbsp;Makoto Komiyama","doi":"10.4161/adna.20727","DOIUrl":"https://doi.org/10.4161/adna.20727","url":null,"abstract":"<p><p>Peptide nucleic acid (PNA) is one of the most widely used synthetic DNA analogs. Conjugation of functional molecules to PNA is very effective to further widen its potential applications. For this purpose, here we report the synthesis of several ligand monomers and introduced them to PNA. These ligand-modified PNAs attract cerium ion and are useful for site-selective DNA hydrolysis. It should be noted that these ligands on PNA are also effective even under the conditions of invasion complex.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.20727","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30745288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzymatic synthesis of DNA strands containing α-L-LNA (α-L-configured locked nucleic acid) thymine nucleotides.","authors":"Torben Højland,&nbsp;Rakesh N Veedu,&nbsp;Birte Vester,&nbsp;Jesper Wengel","doi":"10.4161/adna.19272","DOIUrl":"https://doi.org/10.4161/adna.19272","url":null,"abstract":"We describe the first enzymatic incorporation of an α-L-LNA nucleotide into an oligonucleotide. It was found that the 5′-triphosphate of α-L-LNA is a substrate for the DNA polymerases KOD, 9°Nm, Phusion and HIV RT. Three dispersed α-L-LNA thymine nucleotides can be incorporated into DNA strands by all four polymerases, but they were unable to perform consecutive incorporations of α-L-LNA nucleotides. In addition it was found that primer extension can be achieved using templates containing one α-L-LNA nucleotide.","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.19272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30677914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"\"Artifactual\" arsenate DNA.","authors":"Peter E Nielsen","doi":"10.4161/adna.19672","DOIUrl":"https://doi.org/10.4161/adna.19672","url":null,"abstract":"<p><p>The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA(1) arose much skepticism, primarily due to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present evidence that the identification of arsenate DNA was artifactual.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.19672","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30677447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A DNA nanocapsule with aptamer-controlled open-closure function for targeted delivery.","authors":"Thomas Bentin","doi":"10.4161/adna.19843","DOIUrl":"https://doi.org/10.4161/adna.19843","url":null,"abstract":"<p><p>A DNA capsule fitted with aptamer controlled target sensing has been \"woven\" using a 7308-base single-stranded DNA \"thread\" and 196 staple oligonucleotides. The capsule enables logic-gated molecular cargo delivery to targeted cell surfaces.</p>","PeriodicalId":8444,"journal":{"name":"Artificial DNA: PNA & XNA","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/adna.19843","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30677448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}