TY - JOUR. T1 - Evaluation of the peptide nucleic acid fluorescence in situ hybridisation technology for yeast identification directly from positive blood cultures. T2 - An Italian experience. AU - Farina, Claudio. AU - Perin, Silvana. AU - Andreoni, Stefano. AU - Conte, Marco. AU - Fazii, Paolo. AU - Lombardi, Gianluigi. AU - Manso, Esther. AU - Morazzoni, Cristina. AU - Sanna, Silvana. AU - Bonetti, Cristina. AU - Carretto, Edoardo. AU - Casella, Pietro. AU - Luzzaro, Francesco. AU - Marone, Piero. AU - Passera, Marco. AU - Rocchetti, Andrea. AU - Vigano, Egidio Franco. PY - 2012/9. Y1 - 2012/9. N2 - Fungaemia is an increasing nosocomial pathology. The gold standard for detection of fungaemia is blood culture, but it is time-consuming and its sensitivity for early detection is low. On the other hand, yeasts present different antifungal sensitivity patterns to be quickly detected to allow an effective treatment. The aim of this study was to evaluate the diagnostic performances of PNA-FISH to ...
TY - JOUR. T1 - Targeting peptide nucleic acid (PNA) oligomers to mitochondria within cells by conjugation to lipophilic cations. T2 - implications for mitochondrial DNA replication, expression and disease. AU - Muratovska, A. AU - Lightowlers, R N. AU - Taylor, R W. AU - Turnbull, D M. AU - Smith, R A. AU - Wilce, J A. AU - Martin, S W. AU - Murphy, M P. PY - 2001/5/1. Y1 - 2001/5/1. N2 - The selective manipulation of mitochondrial DNA (mtDNA) replication and expression within mammalian cells has proven difficult. One promising approach is to use peptide nucleic acid (PNA) oligomers, nucleic acid analogues that bind selectively to complementary DNA or RNA sequences inhibiting replication and translation. However, the potential of PNAs is restricted by the difficulties of delivering them to mitochondria within cells. To overcome this problem we conjugated a PNA 11mer to a lipophilic phosphonium cation. Such cations are taken up by mitochondria through the lipid bilayer driven by the membrane ...
Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI
Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI
Erwinia amylovora is a Gram-negative bacterial plant pathogen in the family Enterobacteriaceae and is the causal agent of fire blight, a devastating disease of apple and pear. Fire blight is traditionally managed by the application of the antibiotic streptomycin during bloom, but this strategy has been challenged by the development and spread of streptomycin resistance. Thus, there is an urgent need for effective, specific, and sustainable control alternatives for fire blight. Antisense antimicrobials are oligomers of nucleic acid homologs with antisense sequence of essential genes in bacteria. The binding of these molecules to the mRNA of essential genes can result in translational repression and antimicrobial effect. Here, we explored the possibility of developing antisense antimicrobials against E. amylovora and using these compounds in fire blight control. We determined that a 10-nucleotide oligomer of peptide nucleic acid (PNA) targeting the start codon region of an essential gene acpP is able to
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. Although these technologies have begun to enable targeted genome modifications, there remains a need for new technologies that are scalable, affordable, and easy to engineer. In this paper, we propose a new tool for genetic engineering, the pseudocomplementary peptide nucleic acid nucleases (pcPNANs), which are composed of a pseudocomplementary PNA (pcPNA) specific for a DNA target sequence, a FokI nuclease cleavage domain and a nuclear localization signal. pcPNANs may induce targeted DNA double-strand breaks that activate DNA damage response pathways and enable custom alterations. Their cleavage-site is determined by simple Watson-Crick rule, and thus pcPNANs for aimed cleavage of genomes can be straightforwardly designed and synthesized without any selection procedure. Accordingly, the cleavage-site and site-specificity
TY - JOUR. T1 - A cyclopentane conformational restraint for a peptide nucleic acid. T2 - Design, asymmetric synthesis, and improved binding affinity to DNA and RNA. AU - Myers, Michael C.. AU - Witschi, Mark A.. AU - Larionova, Nataliya V.. AU - Franck, John M.. AU - Haynes, Russell D.. AU - Hara, Toshiaki. AU - Grajkowski, Andrzej. AU - Appella, Daniel H.. PY - 2003/7/24. Y1 - 2003/7/24. N2 - (Matrix presented) A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of cyclopentane-modified PNA is reported, and its binding properties were determined. The cyclopentane ring leads to a significant improvement in the binding properties of the resulting PNA to DNA and RNA.. AB - (Matrix presented) A strategy to restrict the highly flexible backbone conformation of a peptide nucleic acid (PNA) by incorporation of a cyclopentane ring is proposed. An asymmetric synthesis of ...
Dive into the research topics of Synthesis and DNA-recognition behavior of a novel peptide ribonucleic acid with a serine backbone (oxa-PRNA). Together they form a unique fingerprint. ...
TY - JOUR. T1 - Silencing gene expression by targeting chromosomal DNA with antigene peptide nucleic acids and duplex RNAs. AU - Janowski, Bethany A.. AU - Hu, Jiaxin. AU - Corey, David R.. N1 - Funding Information: ACKNOWLEDGMENTS We thank S. Younger, D. Ly and B. Armitage for comments. This work was supported by the National Institutes of Health (grants NIGMS 60642 and 73042 to D.R.C.), the High-Q Foundation, Applied Biosystems and the Robert A. Welch Foundation (grant I-1244 to D.R.C.).. PY - 2006/6. Y1 - 2006/6. N2 - The value of recognizing cellular RNA sequences by short interfering RNAs (siRNAs) in mammalian cells is widely appreciated, but what might be learned if it were also possible to recognize chromosomal DNA? Recognition of chromosomal DNA would have many applications, such as inhibiting gene expression, activating gene expression, introducing mutations, and probing chromosome structure and function. We have shown that antigene peptide nucleic acids (agPNAs) and antigene duplex ...
Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe-target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb ...
TY - JOUR. T1 - Peptide nucleic acids conjugated to short basic peptides show improved pharmacokinetics and antisense activity in adipose tissue. AU - Wancewicz, Edward V.. AU - Maier, Martin A.. AU - Siwkowski, Andrew M.. AU - Albertshofer, Klaus. AU - Winger, Theodore M.. AU - Berdeja, Andres. AU - Gaus, Hans. AU - Vickers, Timothy A.. AU - Bennett, C. Frank. AU - Monia, Brett P.. AU - Griffey, Richard H.. AU - Nulf, Christopher J.. AU - Hu, Jiaxin. AU - Corey, David R.. AU - Swayze, Eric E.. AU - Kinberger, Garth A.. PY - 2010/5/27. Y1 - 2010/5/27. N2 - A peptide nucleic acid (PNA) targeting a splice junction of the murine PTEN primary transcript was covalently conjugated to various basic peptides. When systemically administered to healthy mice, the conjugates displayed sequence-specific alteration of PTEN mRNA splicing as well as inhibition of full length PTEN protein expression. Correlating activity with drug concentration in various tissues indicated strong tissue-dependence, with highest ...
TY - JOUR. T1 - Quantitative rRNA-targeted solution-based hybridization assay using peptide nucleic acid molecular beacons. AU - Li, Xu. AU - Morgenroth, Eberhard. AU - Raskin, Lutgarde. N1 - Copyright: Copyright 2009 Elsevier B.V., All rights reserved.. PY - 2008/12. Y1 - 2008/12. N2 - The potential of a solution-based hybridization assay using peptide nucleic acid (PNA) molecular beacon (MB) probes to quantify 16S rRNA of specific populations in RNA extracts of environmental samples was evaluated by designing PNA MB probes for the genera Dechloromonas and Dechlorosoma. In a kinetic study with 16S rRNA from pure cultures, the hybridization of PNA MB to target 16S rRNA exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to nontarget 16S rRNAs. A concentration of 10 mM NaCl in the hybridization buffer was found to be optimal for maximizing the difference between final hybridization signals from target and nontarget 16S rRNAs. Hybridization ...
Exemplifying and illustrating recent exciting advances in PNA chemistry, the second edition of Peptide Nucleic Acids: Methods and Protocols serves as a vital complement to the first edition of the book. Since the discovery of peptide nucleic acids, many interesting new derivatives and analogues in
Peptide nucleic acids (PNAs) are polyamide oligomers that can strand invade duplex DNA, causing displacement of one DNA strand and formation of a D-loop. Binding of either a T10 PNA or a mixed sequence 15-mer PNA to the transcribed strand of a G-free transcription cassette caused 90 to 100 percent site-specific termination of pol II transcription elongation. When a T10 PNA was bound on the nontranscribed strand, site-specific inhibition never exceeded 50 percent. Binding of PNAs to RNA resulted in site-specific termination of both reverse transcription and in vitro translation, precisely at the position of the PNA.RNA heteroduplex. Nuclear microinjection of cells constitutively expressing SV40 large T antigen (T Ag) with either a 15-mer or 20-mer PNA targeted to the T Ag messenger RNA suppressed T Ag expression. This effect was specific in that there was no reduction in beta-galactosidase expression from a coinjected expression vector and no inhibition of T Ag expression after microinjection of ...
In this report, we show how a convenient on-resin copper-click functionalization of azido-functionalized peptide nucleic acids (PNAs) allows various PNA-based detection strategies. Firstly, a thiazole orange (TO) clicked PNA probe facilitates a binary readout when combined with F/Q labeled DNA, giving increased sensitivity for antisense detection. Secondly, our TO-PNA conjugate ... read more also allows single nucleotide polymorphism detection. Since antisense detection is also possible in the absence of the TO label, our sensing platform based on azido-d-ornithine containing PNA even allows for additional and more advanced functionalization and sensing strategies. show less ...
In this report, we show how a convenient on-resin copper-click functionalization of azido-functionalized peptide nucleic acids (PNAs) allows various PNA-based detection strategies. Firstly, a thiazole orange (TO) clicked PNA probe facilitates a binary readout when combined with F/Q labeled DNA, giving increa
To optimize patient treatment and rational use of antimicrobials, it is important to provide fast information on findings in blood-cultures (BCs). The purpose of this study was to evaluate the impact of using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) on positive BCs containing Gram-positive cocci in clusters to differentiate between Staphylococcus aureus (SA) and coagulase negative staphylococci (CoNS) on the prescribed antimicrobial therapy and on the number of contacts between microbiologist and clinician. All cases of positive BCs in our laboratory with SA or CoNS in the year 2011 were identified and the charts were reviewed retrospectively. The group of patients with BCs tested with PNA-FISH was compared to the group of patients with untested BCs. A total of 200 patients with SA and 725 patients with CoNS were included. The mean number of contacts was 0.82 when PNA-FISH showed CoNS and 1.39 when PNA-FISH was not done (p ...
Peptide nucleic acids (PNAs) are DNA analogs in which the normal phosphodiester backbone is replaced by 2‐aminoethyl glycine linkages
Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful biomolecula …
This volume is unique to the existing literature in the Peptide Nucleic Acid field, in that it focuses on comparing and contrasting PNA with other available oligonucleotide homologues and considers areas in which these biomolecules could be profitably applied to clinical and diagnostic
The synthesis of the thymine derivative (S)-50, was achieved in high enantiomeric purity (98% ee). The (R) enhanced enantiomer was also synthesized with moderate enantiomeric purity (46% ee). This acyclic pyrimidine analog ((S)-50) is a useful building block for the synthesis of a novel class of oligomers, the aromatic peptide nucleic acids (APNA). The APNA tetramer 70 was prepared from the amino acid monomer (S)-50 using classical peptide synthesis. Chemical shift differences between the $\sp1$H NMR of monomer (S)-57 and tetramer 70 were observed which suggested that base stacking interactions in the oligomers may be favorable. ...
Peptide Nucleic Acids - CHEMICAL BIOLOGY - reflects the multidimensional character of chemical biology, focusing in particular on the fundamental science of biological structures and systems, the use of chemical and biological techniques to elucidate
Global Peptide Nucleic Acids Industry Market Analysis & Forecast 2018-2023 includes market share, market research report, market trade, market prices, market geography trend and market forecast
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Hi Mick, I keep receiving flyers from a company called Perseptive about pnas they sound real interesting....although no time to go to their seminars on this.. I believe Perseptive are in MA....an address for them may be in the biotech registry (http://www.data-transport.com Martin Mick Jones (mjones at rpms.ac.uk) wrote: : Hi netters : I was wondering about the commercial availability of reagents for the chemical : synthesis of PNAs (peptide or protein nucleic acids). These analogues : (apparently) bind more tightly to DNA strands than a complemantary : oligonucleotide. : PNAs are nucleic acid analogues in which the phospho-sugar backbone is replaced by : a peptide linkage maintaining the correct stereo-chemical base spacing as in : natural DNA. : We are consideing synthesizing our own PNA sequences and would be very grateful if : anybody could provide advice, where to buy the reagents and their cost, and how : difficult it is to do, etc. Anything really. : Thanks in advance. : Mick Jones : ...
Literature indicates that point mutations in codon 12 of the Ki-ras2 gene are associated with colon cancer. The detection of a point mutation in the high background of wild-type cells is very difficult, which represents a problem for many research projects focused on processes that take place during cancerogenesis. Therefore, a quick and easy, yet reliable method of detecting single point mutations is preferred. This article shows an application example for Peptide Nucleic Acid (PNA) oligomers in combination with Hybridization Probes on the LightCycler Instrument. Here, PNAs suppress the codon 12 wild-type PCR product, as they bind to nucleic acids with higher stringency, compared to deoxyribonucleotides, and do not serve as primers for Taq polymerase. Due to these properties, PNAs can be used to detect single point mutations in research samples in a high background of wild-type sequences.. ...
Learn how PNA FISH or Peptide Nucleic Acid FISH rapidly identifies bacteria in blood cultures, decreases antibiotic use and improves antibiotic stewardship.
Affibody molecules are small (7 kDa), non-immunoglobulin scaffold proteins with a potential as targeting agents for radionuclide imaging of cancer. However, high renal re-absorption of Affibody molecules prevents their use for radionuclide therapy with residualizing radiometals. We hypothesized that the use of Affibody-based peptide nucleic acid (PNA)-mediated pretargeting would enable higher accumulation of radiometals in tumors than in kidneys. To test this hypothesis, we designed an Affibody-PNA chimera ZHER2:342-SR-HP1 containing a 15-mer HP1 PNA recognition tag and a complementary HP2 hybridization probe permitting labeling with both (125)I and (111)In. (111)In-ZHER2:342-SR-HP1 bound specifically to HER2-expressing BT474 and SKOV-3 cancer cells in vitro, with a KD of 6±2 pM for binding to SKOV-3 cells. Specific high affinity binding of the radiolabeled complementary PNA probe (111)In-/(125)I-HP2 to ZHER2:342-SR-HP1 pre-treated cells was demonstrated. (111)In-ZHER2:342-SR-HP1 demonstrated ...
PNA is a more basic version of the DNA used to build life from. This research shows it is possible to store information in PNA in the same way it is possible in DNA, and that is is possible to move from a PNA storage system to a DNA storage system. This means life could have formed with the simpler PNA structure then moved up to the more complex DNA system later. ...
There are many ways to genotype nucleotide differences or changes in genome [11]. Currently available techniques that require a separation step include restriction fragment length polymorphism analysis, single-nucleotide extension, oligonucleotide ligation, and direct sequencing. Additional methods, including pyrosequencing [12] and mass spectroscopy [13], are technically complex but can be automated for high-throughput analysis. Furthermore, real-time PCR-based assays that use high resolution melting (HRM) and probe-based systems, FRET probes, molecular beacons, or TaqMan probes have been adapted for continuous mutation detection of amplified products in a closed system. However, their capacity to discriminate DNA variants in the single nucleotide indel as well as SNP variant with single probe has not been examined until now. Furthermore, traditional probe systems that have been used in SNP detection use two or more fluorescence channels for one mutation loci. Thus even a wide range of mutation ...
Norepinephrine transporter-derived homing peptides enable rapid endocytosis of drug delivery nanovehicles into neuroblastoma cells. Nucleic acids in inclusion bodies obtained from E. coli cells expressing human interferon-gamma. Fluorescent peptide nanoparticles, in every color of the rainbow...
Peptide nucleic acid Peptide nucleic acid (PNA) is a chemical similar to DNA or RNA. PNA is not known to occur naturally in existing life on Earth but is
Peptide nucleic acids have emerged over the past two decades as a promising class of nucleic acid mimics because of their strong binding affinity and sequence selectivity toward DNA and RNA, and resistance to enzymatic degradation by proteases and nucleases. While they have been shown to be effective in regulation of gene expression in vitro, and to a small extent in vivo, their full potential for molecular therapy has not yet been fully realized due to poor cellular uptake. Herein, we report the development of cell-permeable, guanidine-based peptide nucleic acids targeting the epidermal growth factor receptor (EGFR) in preclinical models as therapeutic modality for head and neck squamous cell carcinoma (HNSCC) and nonsmall cell lung cancer (NSCLC). A GPNA oligomer, 16 nucleotides in length, designed to bind to EGFR gene transcript elicited potent antisense effects in HNSCC and NSCLC cells in preclinical models. When administered intraperitoneally in mice, EGFRAS-GPNA was taken-up by several tissues
Given the important role in functioning as oncogenes or tumor suppressors, c-myc mRNA has emerged as a potential biomarker for cancer detection. In particular, abnormal expression of mRNAs is commonly observed at early stages of colon cancer development. Therefore, sensitive detection of c-myc mRNA has become a promising approach to achieving early clinical diagnosis of cancer and paves the way for precision medicine. Recently, a China-U.S. collaborative research team reported a label-free colorimetric protocol based on peptide nucleic acid/silver nanoparticles (PNA/AgNPs) for specific detection of c-myc mRNA biomarkers. A correlated research article entitled A label-free colorimetric assay for detection of c-myc mRNA based on peptide nucleic acid and silver nanoparticles was recently published in the journal of Science Bulletin (2016, vol.61, No. 4: 276-281, Springer), written by Dr. Xia Li from Liaocheng University (Shandong, China), Shandong Taishan Scholar Prof. Jifeng Liu (current, ...
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Investigation of novel lipid-functionalized PNA monomers as potential HIV-1 non-nucleoside reverse transcriptase and/or integrase inhibitors.
Peptide nucleic acids (PNA) are synthetic analogs of DNA that hybridize to complementary oligonucleotide sequences with exceptional affinity and target specificity. The stability of PNA in biological fluids together with the unique hybridization characteristics of these structures suggests that PNA may have considerable potential as antisense agents for experimental use in vivo. To test this hypothesis, we attempted to modulate supraspinal δ-opioid receptor function in rats using PNA sequences designed to be complementary to a region of the rat δ-opioid receptor. Repeated i.c.v. administration of PNA over a period of 5 days significantly inhibited the antinociceptive response and locomotor response to selective δ-opioid receptor agonists. PNA attenuated δ-opioid receptor function in a sequence-specific, target-specific, and reversible manner characteristic of the functional inhibition caused by an antisense mechanism. There were no apparent toxicities arising from the PNA treatment based on ...
A novel sequence of peptide nucleic acid (PNA; beta-Ala-(T10)-beta-Ala-NH2) containing ten thymine monomers and beta-alanine amino acid at both (C and N) terminal of main chain was synthesized manually using solid phase tBoc peptide chemistry. Synthesized PNA (beta-Ala-(T10)-beta-Ala-NH2) were analyzed and purified using RP-HPLC and characterized by MALDI-TOF mass spectrometry. The hybridization of beta-Ala-(T10)-beta-Ala-NH2 with its complementary single strand DNA (cDNA; A10) was established in liquid phase through non denaturing gel electrophoresis and UV-thermal denaturation curve at 1 µM concentration. The Tm of hybrid was observed 40.05 °C. The nano-FET devices were designed and fabricated in our group. The PNAs were covalently immobilized on device surface with alkyl-thiol self assembled monolayer. DAPI nucleic acid stain and fluorescine labeling methods were used to prove the binding of PNA with its cDNA on nano FET surface from 10 nM solution, using fluorescent microscopic imaging. beta-Ala-
The applications for synthetic peptides are as varied as their sequences can be. Synthesize peptides to generate antibodies and purify these with affinity columns using the same peptides. Create substrates for a kinase you want to characterize. Study protein/protein interaction with fluorescent labelled peptides. Determine the specific binding site of a receptor using competing peptide sequences. Phosphopeptides are important research tools but expensive to synthesize. Only small amounts are needed due to their high biological activity.. Peptide Nucleic Acids (PNA) or PNA-peptide chimeras are expensive. Biotin is frequently coupled to a peptide to attach it easily to surfaces loaded with streptavidin. Isotopically labelled peptides as well as peptides with other special labels to be used as enzyme substrates are also prime candidates for synthesis by the MultiPep RSi. Our peptide synthesis service will support all these applications by delivering appropriate peptides when you need them.. ...
Built on work of Nielsen, Egholm, Berg, and Buchardt, in the development of peptide nucleic acid (PNA), first reported in 1991 (Science 1991, 254, 1497), the chemistry team at Carnegie Mellon University has tweaked the chemical structure of PNA by installing a stereocenter at the gamma backbone-hence the name γPNA. This backbone stereochemical modification transforms PNA oligomer from a random-fold into a right-handed (RH) or left-handed (LH) helical motif depending on the stereochemistry, and enables the conformationally-matched RH-γPNA to hybridize to DNA or RNA strand with high affinity and sequence specificity and invade double helical B-form DNA (B-DNA) without sequence restriction. Further improvements in water solubility and biocompatibility were made by incorporating diethylene glycol moiety in the sidechain, and in cell permeability by conjugating the guanidinium group. γPNA is synthetically versatile, in that its chemical structure can be readily modified and its physical and ...
1NR8: Insights into peptide nucleic acid (PNA) structural features: The crystal structure of a D-lysine-based chiral PNA-DNA duplex
The development of gold disk electrodes modified with single-stranded PNA (peptide nucleic acid) for the determination of important DNA sequences is described. The performance of anionic and cationic redox indicators for the generation of current signal is compared. It is shown that the use of cationic redox marker, namely hexaaminoruthenium(III) chloride results in a significantly better analytical parameters, as compared to measurements with other tested markers. The optimized sensor distinguishes itself with high selectivity toward complementary DNA sequences, with almost no electrochemical response toward DNA with one base mismatch. Developed PNA-based sensor was successfully used for detection of DNA sequence responsible for sickle cell anemia.
Spacer 9 is a triethylene glycol chain that is 9 atoms long (6 carbons + 3 oxygens), and is used to incorporate a spacer arm into an oligonucleotide. Spacer 9 can be incorporated in consecutive additions whenever a longer spacer is required. Spacer 9 has been used to form non-nucleotide bridges in hairpin loops in oligonucleotides (1), for linking oligonucleotides to epitopes for drug development (2), and for solid-phase immobilization of hybridization probes (3). Multiple incorporation of Spacer 9 has been used to form long, flexible linker arms between the two domains (double-helix forming and triple-helix forming, respectively) of a bifunctional DNA oligonucleotide, in order to maximize the binding flexibility of the two domains for their respective targets (4). This oligo was used to form a peptide nucleic acid (PNA)-DNA conjugate for use in site-directed recombination applications.. References ...
Affinity Capture and Immobilization Reagents. The high affinity of γPNA allows capture, isolation and immobilization of specific DNA and RNA targets as well as their complexes with proteins. The unprecedented ability of γPNA to invade double-stranded DNA without sequence restrictions means that γPNA can be used to capture even the most elusive targets. We offer γPNA affinity reagents labeled with terminal mono- or bis-biotin groups for capture on streptavidin columns or beads.. A challenge of using a high-affinity reagent such as γPNA is to release the captured target after nonspecific components of a complex mixture have been washed away. PNA Innovations γPNA capture reagents are designed to allow release under mild conditions simply by adding a competitor strand that displaces the captured target from the original γPNA probe.. γPNAs can also be synthesized with terminal amine or thiol groups to allow immobilization on a variety of surfaces for a diverse range of applications, ...
The conditions that led to the formation of the first organisms and the ways that life originates from a lifeless chemical soup are poorly understood. The recent hypothesis of RNA-peptide coevolution suggests that the current close relationship between amino acids and nucleobases may well have extended to the origin of life. We now show how the interplay between these compound classes can give rise to new self-replicating molecules using a dynamic combinatorial approach. We report two strategies for the fabrication of chimeric amino acid/nucleobase self-replicating macrocycles capable of exponential growth. The first one relies on mixing nucleobase- and peptide-based building blocks, where the ligation of these two gives rise to highly specific chimeric ring structures. The second one starts from peptide nucleic acid (PNA) building blocks in which nucleobases are already linked to amino acids from the start. While previously reported nucleic acid-based self-replicating systems rely on ...
DNA-directed chemical ligations enable the highly sequence specific analysis of mutations in DNA. The full diagnostic potential of DNAdirected chemistry can be harvested when DNA-analogues that provide new opportunities such as improved affinity and selectivity in DNA-binding and/or ease and accuracy of detection are employed. It is shown that peptide nucleic acid (PNA) conjugates, non-ionic biostable DNA analogues, can be ligated by using native chemical ligation. This reaction proceeds as rapidly and more selective than T4-ligase mediated oligonucleotide ligations. The selectivity is higher than 3000-fold in discriminating matched from single mismatched DNA. This high selectivity is the result of a particular ligation architecture which involves an unpaired DNA-base opposite to the ligation site. It is suggested that the high sequence specificity of this so-called abasic ligation architecture facilitates the analysis of early cancer onset. As an example it is shown that as little as 0.2% of ...
PNA and single-strand-specific nuclease were used here for SNPs detection. After treatment by single-strand-specific nuclease such as S1 and mung bean, the DNA strand in PNA/DNA duplex, which involves a one-base mismatch, was completely digested. However,
Fluorescence in situ hybridization (FISH) is an efficient technique for the identification of specific bacteria in tissue of both experimental and spontaneous infections. The method detects specific sequences of nucleic acids by hybridization of fluorescently labeled probes to complementary target sequences within intact cells. FISH allows direct histological localization of the bacteria in the tissue and thereby a correlation between the infection and the histopathological changes present. This chapter presents protocols for FISH identification of bacterial pathogens in fixed deparaffinized tissue samples mounted on glass slides. Two different methods are presented: one is illustrated with the use of peptide nucleic acid (PNA) that is carried out directly on glass slides (Method I), whereas the other is exemplified by using a DNA probe in a Shandon rack (Method II). In the two methods, both PNA and DNA probes can be used ...
Affibody molecules are small proteins engineered using a nonanti-body scaffold. Radiolabeled Affibody molecules are excellent imaging probes, but their application to radionuclide therapy has been prevented by high renal reabsorption. The aim of this study was to test the hypothesis that Affibody-based peptide nucleic acid (PNA)-mediated pretargeted therapy of human epidermal growth factor receptor 2 (HER2)-expressing cancer extends survival without accompanying renal toxicity.. Methods: A HER2-targeting Affibody molecule ligated with an AGTCGTGATGTAGTC PNA hybridization probe (Z(HER2:342)-SR-HP1) was used as the primary pretargeting agent. A complementary AGTCGTGATGTAGTC PNA conjugated to the chelator DOTA and labeled with the radionuclide Lu-177 (Lu-177-HP2) was used as the secondary agent. The influence of different factors on pretargeting was investigated. Experimental radionuclide therapy in mice bearing SKOV-3 xenografts was performed in 6 cycles separated by 7 d.. Results: Optimal tumor ...