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Journal articles on the topic 'PNA-Peptide Conjugate'

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Author: Grafiati

Published: 10 December 2022

Last updated: 29 January 2023

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1

Thompson, Andrew, Mark Prescott, Noorhan Chelebi, John Smith, Tom Brown, and Günter Schmidt. "Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS." Nucleic Acids Research 35, no. 4 (December 9, 2006): e28-e28. http://dx.doi.org/10.1093/nar/gkl1123.

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Abstract The synthesis and characterization of isotopomer tandem nucleic acid mass tag–peptide nucleic acid (TNT–PNA) conjugates is described along with their use as electrospray ionisation-cleavable (ESI-Cleavable) hybridization probes for the detection and quantification of target DNA sequences by electrospray ionisation tandem mass spectrometry (ESI-MS/MS). ESI-cleavable peptide TNT isotopomers were introduced into PNA oligonucleotide sequences in a total synthesis approach. These conjugates were evaluated as hybridization probes for the detection and quantification of immobilized synthetic target DNAs using ESI-MS/MS. In these experiments, the PNA portion of the conjugate acts as a hybridization probe, whereas the peptide TNT is released in a collision-based process during the ionization of the probe conjugate in the electrospray ion source. The cleaved TNT acts as a uniquely resolvable marker to identify and quantify a unique target DNA sequence. The method should be applicable to a wide variety of assays requiring highly multiplexed, quantitative DNA/RNA analysis, including gene expression monitoring, genetic profiling and the detection of pathogens.

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2

Tan, Xin-Xing, Jeffrey K. Actor, and Yin Chen. "Peptide Nucleic Acid Antisense Oligomer as a Therapeutic Strategy against Bacterial Infection: Proof of Principle Using Mouse Intraperitoneal Infection." Antimicrobial Agents and Chemotherapy 49, no. 8 (August 2005): 3203–7. http://dx.doi.org/10.1128/aac.49.8.3203-3207.2005.

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ABSTRACT Antisense oligodeoxynucleotides (ODNs) and their analogs have been successfully utilized to inhibit gene expression and bacterial growth in vitro or in cell culture. In this study, acpP-targeting antisense peptide nucleic acid (PNA) and its peptide conjugate were tested as potential antibacterial agents in two groups of experiments using a mouse model. In the first group, Escherichia coli mutant strain SM101 with a defective outer membrane was used to induce bacteremia and peritonitis in BALB/c mice by intraperitoneal (i.p.) injection. The resulting bacteremia was fatal within 48 h. A single i.p injection of 5 nmol (or more) of PNA administered 30 min before bacterial challenge significantly reduced the bacterial load in mouse blood. Reductions in serum concentrations of the proinflammatory cytokines tumor necrosis factor alpha, interleukin-1β (IL-1β), IL-6, and IL-12 were also observed. PNA treatment was effective in rescuing 100% of infected animals. In the second group, bacteremia in BALB/c mice was induced by i.p. injection of E. coli wild-type strain K-12. The infected mice were treated by a single intravenous injection of peptide-PNA conjugate 30 min after bacterial challenge. Treatment with the peptide-PNA conjugate significantly reduced the K-12 load, with modest reduction in cytokine concentrations. The conjugate treatment was also able to rescue up to 60% of infected animals. This report is the first demonstration of ODNs' antibacterial efficacy in an animal disease model. The ability of PNA and its peptide conjugate to inhibit bacterial growth and to prevent fatal infection demonstrates the potential for this new class of antibacterial agents.

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3

Awasthi, Satish, and Peter Nielsen. "Parallel Synthesis of PNA-Peptide Conjugate Libraries." Combinatorial Chemistry & High Throughput Screening 5, no. 3 (May 1, 2002): 253–59. http://dx.doi.org/10.2174/1386207024607266.

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4

Lee, Eun Kyung, Chan Woo Kim, Hiroyuki Kawanami, Akihiro Kishimura, Takuro Niidome, Takeshi Mori, and Yoshiki Katayama. "Utilization of a PNA-peptide conjugate to induce a cancer protease-responsive RNAi effect." RSC Advances 5, no. 104 (2015): 85816–21. http://dx.doi.org/10.1039/c5ra17737e.

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5

Burlina, Fabienne, David D. Dixson, Robert P. Doyle, Gérard Chassaing, Christopher N. Boddy, Philip Dawson, and John Offer. "Orthogonal ligation: a three piece assembly of a PNA–peptide–PNA conjugate." Chemical Communications, no. 24 (2008): 2785. http://dx.doi.org/10.1039/b801242c.

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6

de Koning, Martijn C., Dmitri V. Filippov, Nico Meeuwenoord, Mark Overhand, Gijsbert A. van der Marel, and Jacques H. van Boom. "Synthesis of a PNA-Peptide Conjugate by Chemical Ligation." Synlett 2001, no. 10 (2001): 1516–18. http://dx.doi.org/10.1055/s-2001-17455.

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7

Proshkina, Galina, Elena Shramova, Anastasiya Ryabova, Liat Katrivas, Clelia Giannini, Daniele Malpicci, Yael Levi-Kalisman, Sergey Deyev, and Alexander Kotlyar. "Novel Small Multilamellar Liposomes Containing Large Quantities of Peptide Nucleic Acid Selectively Kill Breast Cancer Cells." Cancers 14, no. 19 (September 30, 2022): 4806. http://dx.doi.org/10.3390/cancers14194806.

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Peptide nucleic acid (PNA) may be used in various biomedical applications; however, these are currently limited, due to its low solubility in aqueous solutions. In this study, a methodology to overcome this limitation is demonstrated, as well as the effect of PNA on cell viability. We show that extruding a mixture of natural phospholipids and short (6–22 bases), cytosine-rich PNA through a 100 nm pore size membrane under mild acidic conditions resulted in the formation of small (60–90 nm in diameter) multilamellar vesicles (SMVs) comprising several (3–5) concentric lipid membranes. The PNA molecules, being positively charged under acidic conditions (due to protonation of cytosine bases in the sequence), bind electrostatically to negatively charged phospholipid membranes. The large membrane surface area allowed the encapsulation of thousands of PNA molecules in the vesicle. SMVs were conjugated with the designed ankyrin repeat protein (DARPin_9-29), which interacts with human epidermal growth factor receptor 2 (HER2), overexpressed in human breast cancer. The conjugate was shown to enter HER2-overexpressing cells by receptor-mediated endocytosis. PNA molecules, released from lysosomes, aggregate in the cytoplasm into micron-sized particles, which interfere with normal cell functioning, causing cell death. The ability of DARPin-functionalized SMVs to specifically deliver large quantities of PNA to cancer cells opens a new promising avenue for cancer therapy.

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8

Wen, Cui-jiao, Jia-yuan Gong, Ke-wei Zheng, Yi-de He, Jia-yu Zhang, Yu-hua Hao, and Zheng Tan. "Targeting nucleic acids with a G-triplex-to-G-quadruplex transformation and stabilization using a peptide–PNA G-tract conjugate." Chemical Communications 56, no. 48 (2020): 6567–70. http://dx.doi.org/10.1039/d0cc02102d.

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The synergy between two recognizing units in a bi-functional peptide–PNA G-tract conjugate recognizes a three guanine-tracts motif to form an extra stable bimolecular complex, resulting in highly potent and selective interference to DNA metabolism.

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9

Vázquez, O., and O. Seitz. "Cytotoxic peptide–PNA conjugates obtained by RNA-programmed peptidyl transfer with turnover." Chem. Sci. 5, no. 7 (2014): 2850–54. http://dx.doi.org/10.1039/c4sc00299g.

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10

Soudah, Terese, Saleh Khawaled, Rami I. Aqeilan, and Eylon Yavin. "AntimiR-155 Cyclic Peptide–PNA Conjugate: Synthesis, Cellular Uptake, and Biological Activity." ACS Omega 4, no. 9 (August 12, 2019): 13954–61. http://dx.doi.org/10.1021/acsomega.9b01697.

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11

Kaushik, Neerja, Amartya Basu, Paul Palumbo, Rene L. Myers, and Virendra N. Pandey. "Anti-TAR Polyamide Nucleotide Analog Conjugated with a Membrane-Permeating Peptide Inhibits Human Immunodeficiency Virus Type 1 Production." Journal of Virology 76, no. 8 (April 15, 2002): 3881–91. http://dx.doi.org/10.1128/jvi.76.8.3881-3891.2002.

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ABSTRACT The emergence of drug-resistant variants has posed a significant setback against effective antiviral treatment for human immunodeficiency virus (HIV) infections. The choice of a nonmutable region of the viral genome such as the conserved transactivation response element (TAR element) in the 5′ long terminal repeat (LTR) may potentially be an effective target for drug development. We have earlier demonstrated that a polyamide nucleotide analog (PNA) targeted to the TAR hairpin element, when transfected into cells, can effectively inhibit Tat-mediated transactivation of HIV type 1 (HIV-1) LTR (T. Mayhood et al., Biochemistry 39:11532-11539, 2000). Here we show that this anti-TAR PNA (PNATAR), upon conjugation with a membrane-permeating peptide vector (transportan) retained its affinity for TAR in vitro similar to the unconjugated analog. The conjugate was efficiently internalized into the cells when added to the culture medium. Examination of the functional efficacy of the PNATAR-transportan conjugate in cell culture using luciferase reporter gene constructs resulted in a significant inhibition of Tat-mediated transactivation of HIV-1 LTR. Furthermore, PNATAR-transportan conjugate substantially inhibited HIV-1 production in chronically HIV-1-infected H9 cells. The mechanism of this inhibition appeared to be regulated at the level of transcription. These results demonstrate the efficacy of PNATAR-transportan as a potential anti-HIV agent.

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12

Wu, Xinghua, Yu Chen, Herve Aloysius, and Longqin Hu. "A novel high-yield synthesis of aminoacyl p-nitroanilines and aminoacyl 7-amino-4-methylcoumarins: Important synthons for the synthesis of chromogenic/fluorogenic protease substrates." Beilstein Journal of Organic Chemistry 7 (July 27, 2011): 1030–35. http://dx.doi.org/10.3762/bjoc.7.117.

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Aminoacyl p-nitroaniline (aminoacyl-pNA) and aminoacyl 7-amino-4-methylcoumarin (aminoacyl-AMC) are important synthons for the synthesis of chromogenic/fluorogenic protease substrates. A new efficient method was developed to synthesize aminoacyl-pNA and aminoacyl-AMC derivatives in excellent yields starting from either amino acids or their corresponding commercially available N-hydroxysuccinimide esters. The method involved the in situ formation of selenocarboxylate intermediate of protected amino acids and the subsequent non-nucleophilic amidation with an azide. Common protecting groups used in amino acid/peptide chemistry were all well-tolerated. The method was also successfully applied to the synthesis of a dipeptide conjugate, indicating that the methodology is applicable to the synthesis of chromogenic substrates containing short peptides. The method has general applicability to the synthesis of chromogenic and fluorogenic peptide substrates and represents a convenient and high-yield synthesis of N α-protected-aminoacyl-pNAs/AMCs, providing easy access to these important synthons for the construction of chromogenic/fluorogenic protease substrates through fragment condensation or stepwise elongation.

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13

Deuss, Peter J., Andrey A. Arzumanov, Donna L. Williams, and Michael J. Gait. "Parallel synthesis and splicing redirection activity of cell-penetrating peptide conjugate libraries of a PNA cargo." Organic & Biomolecular Chemistry 11, no. 43 (2013): 7621. http://dx.doi.org/10.1039/c3ob41659c.

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14

Rogers, Faye A., Sharon S. Lin, Denise C. Hegan, Diane S. Krause, and Peter M. Glazer. "Targeted Gene Modification of Hematopoietic Progenitor Cells in Mice Following Systemic Administration of a PNA-peptide Conjugate." Molecular Therapy 20, no. 1 (January 2012): 109–18. http://dx.doi.org/10.1038/mt.2011.163.

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15

Fortunati, Simone, Andrea Rozzi, Federica Curti, Marco Giannetto, Roberto Corradini, and Maria Careri. "Single-Walled Carbon Nanotubes as Enhancing Substrates for PNA-Based Amperometric Genosensors." Sensors 19, no. 3 (January 30, 2019): 588. http://dx.doi.org/10.3390/s19030588.

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A new amperometric sandwich-format genosensor has been implemented on single-walled carbon nanotubes screen printed electrodes (SWCNT-SPEs) and compared in terms of performance with analogous genoassays developed using the same methodology on non-nanostructured glassy carbon platforms (GC-SPE). The working principle of the genosensors is based on the covalent immobilization of Peptide Nucleic Acid (PNA) capture probes (CP) on the electrode surface, carried out through the carboxylic functions present on SWCNT-SPEs (carboxylated SWCNT) or electrochemically induced on GC-SPEs. The sequence of the CP was complementary to a 20-mer portion of the target DNA; a second biotin-tagged PNA signalling probe (SP), with sequence complementary to a different contiguous portion of the target DNA, was used to obtain a sandwich hybrid with an Alkaline Phosphatase-streptavidin conjugate (ALP-Strp). Comparison of the responses obtained from the SWCNT-SPEs with those produced from the non-nanostructured substrates evidenced the remarkable enhancement effect given by the nanostructured electrode platforms, achieved both in terms of loading capability of PNA probes and amplification of the electron transfer phenomena exploited for the signal transduction, giving rise to more than four-fold higher sensitivity when using SWCNT-SPEs. The nanostructured substrate allowed to reach limit of detection (LOD) of 71 pM and limit of quantitation (LOQ) of 256 pM, while the corresponding values obtained with GC-SPEs were 430 pM and 1.43 nM, respectively.

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16

Ghavami, Shiraishi, and Nielsen. "Cooperative Cellular Uptake and Activity of Octaarginine Antisense Peptide Nucleic acid (PNA) Conjugates." Biomolecules 9, no. 10 (October 1, 2019): 554. http://dx.doi.org/10.3390/biom9100554.

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Cellular uptake and antisense activity of d-octaarginine conjugated peptide nucleic acids (PNAs) is shown to exhibit pronounced cooperativity in serum-containing medium, in particular by being enhanced by analogous mis-match PNA–cell-penetrating peptide (PNA–CPP) conjugates without inherent antisense activity. This cooperativity does not show cell or PNA sequence dependency, suggesting that it is a common effect in cationic CPP conjugated PNA delivery. Interestingly, our results also indicate that Deca-r8-PNA and r8-PNA could assist each other and even other non-CPP PNAs as an uptake enhancer agent. However, the peptide itself (without being attached to the PNA) failed to enhance uptake and antisense activity. These results are compatible with an endosomal uptake mechanism in which the endocytosis event is induced by multiple CPP–PNA binding to the cell surface requiring a certain CPP density, possibly in terms of nanoparticle number and/or size, to be triggered. In particular the finding that the number of endosomal events is dependent on the total CPP–PNA concentration supports such a model. It is not possible from the present results to conclude whether endosomal escape is also cooperatively induced by CPP–PNA.

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17

DEKONING, M., G. VANDERMAREL, and M. OVERHAND. "Synthetic developments towards PNA?peptide conjugates." Current Opinion in Chemical Biology 7, no. 6 (December 2003): 734–40. http://dx.doi.org/10.1016/j.cbpa.2003.10.006.

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18

Frimodt-Møller, Jakob, Christopher Campion, Peter E. Nielsen, and Anders Løbner-Olesen. "Translocation of non-lytic antimicrobial peptides and bacteria penetrating peptides across the inner membrane of the bacterial envelope." Current Genetics 68, no. 1 (November 8, 2021): 83–90. http://dx.doi.org/10.1007/s00294-021-01217-9.

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AbstractThe increase in multidrug-resistant pathogenic bacteria has become a problem worldwide. Currently there is a strong focus on the development of novel antimicrobials, including antimicrobial peptides (AMP) and antimicrobial antisense agents. While the majority of AMP have membrane activity and kill bacteria through membrane disruption, non-lytic AMP are non-membrane active, internalize and have intracellular targets. Antimicrobial antisense agents such as peptide nucleic acids (PNA) and phosphorodiamidate morpholino oligomers (PMO), show great promise as novel antibacterial agents, killing bacteria by inhibiting translation of essential target gene transcripts. However, naked PNA and PMO are unable to translocate across the cell envelope of bacteria, to reach their target in the cytosol, and are conjugated to bacteria penetrating peptides (BPP) for cytosolic delivery. Here, we discuss how non-lytic AMP and BPP-PMO/PNA conjugates translocate across the cytoplasmic membrane via receptor-mediated transport, such as the cytoplasmic membrane transporters SbmA, MdtM/YjiL, and/or YgdD, or via a less well described autonomous process.

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19

Li, Chengxi, Alex J. Callahan, Kruttika S. Phadke, Bryan Bellaire, Charlotte E. Farquhar, Genwei Zhang, Carly K. Schissel, et al. "Automated Flow Synthesis of Peptide–PNA Conjugates." ACS Central Science 8, no. 2 (November 15, 2021): 205–13. http://dx.doi.org/10.1021/acscentsci.1c01019.

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20

Good, Liam, Satish Kumar Awasthi, Rikard Dryselius, Ola Larsson, and Peter E. Nielsen. "Bactericidal antisense effects of peptide–PNA conjugates." Nature Biotechnology 19, no. 4 (April 2001): 360–64. http://dx.doi.org/10.1038/86753.

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21

Ndeboko, Bénédicte, Olivier Hantz, Guy Lemamy, and Lucyna Cova. "Developments in Cell-Penetrating Peptides as Antiviral Agents and as Vehicles for Delivery of Peptide Nucleic Acid Targeting Hepadnaviral Replication Pathway." Biomolecules 8, no. 3 (July 16, 2018): 55. http://dx.doi.org/10.3390/biom8030055.

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Alternative therapeutic approaches against chronic hepatitis B virus (HBV) infection need to be urgently developed because current therapies are only virostatic. In this context, cell penetration peptides (CPPs) and their Peptide Nucleic Acids (PNAs) cargoes appear as a promising novel class of biologically active compounds. In this review we summarize different in vitro and in vivo studies, exploring the potential of CPPs as vehicles for intracellular delivery of PNAs targeting hepadnaviral replication. Thus, studies conducted in the duck HBV (DHBV) infection model showed that conjugation of (D-Arg)8 CPP to PNA targeting viral epsilon (ε) were able to efficiently inhibit viral replication in vivo following intravenous administration to ducklings. Unexpectedly, some CPPs, (D-Arg)8 and Decanoyl-(D-Arg)8, alone displayed potent antiviral effect, altering late stages of DHBV and HBV morphogenesis. Such antiviral effects of CPPs may affect the sequence-specificity of CPP-PNA conjugates. By contrast, PNA conjugated to (D-Lys)4 inhibited hepadnaviral replication without compromising sequence specificity. Interestingly, Lactose-modified CPP mediated the delivery of anti-HBV PNA to human hepatoma cells HepaRG, thus improving its antiviral activity. In light of these promising data, we believe that future studies will open new perspectives for translation of CPPs and CPP-PNA based technology to therapy of chronic hepatitis B.

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22

Nejad, Alireza Japoni, Nader Shahrokhi, and Peter E. Nielsen. "Targeting of the Essential acpP, ftsZ, and rne Genes in Carbapenem-Resistant Acinetobacter baumannii by Antisense PNA Precision Antibacterials." Biomedicines 9, no. 4 (April 15, 2021): 429. http://dx.doi.org/10.3390/biomedicines9040429.

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Infections by carbapenem-resistant A. baumannii (CRAB), a widespread nosocomial pathogen, are becoming increasingly difficult to prevent and treat. Therefore, there is an urgent need for discovery of novel antibiotics against CRAB. Programmable, precision antisense antibiotics, e.g., based on the nucleic acid mimic PNA (peptide nucleic acid) have shown promise in this respect in the form of PNA-BPP (bacteria penetrating peptide) conjugates targeting essential bacterial genes. In the present study, we designed and synthesized a series of PNA-BPPs targeting the translation initiation region of the ftsZ, acpP, or rne gene of CRAB strains. The antimicrobial activity of the compounds and effects on gene expression level was compared to that of analogous mismatch PNA controls. Three antisense conjugates (KFF)3K-eg1-(acpP)PNA (5639), (KFF)3K-eg1-(ftsZ)PNA (5612), and (KFF)3-K-eg1-(rne)PNA (5656) exhibited complete growth inhibition against several CRAB strains at 1–2, 2–8, and 2 µM, respectively, and the compounds were bactericidal at 1–2× MIC. The bactericidal effect was correlated to reduction of target gene mRNA level using RT-qPCR, and the compounds showed no bacterial membrane disruption activity at 1–2× MIC. PNA5612 was tested against a series of 12 CRAB isolates and all were sensitive at 2–8 µM. In addition, the conjugates exhibited no cellular toxicity in the HepG2 cell line (up to 20 μM) and did not shown significant antibacterial activity against other Gram negatives (E. coli, P. aeruginosa). These results provide a starting point for discovery of antisense precision designer antibiotics for specific treatment of CRAB infections.

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23

Koppelhus, Uffe, Satish Kumar Awasthi, Vladimir Zachar, Henrik Uffe Holst, Peter Ebbesen, and Peter Eigil Nielsen. "Cell-Dependent Differential Cellular Uptake of PNA, Peptides, and PNA-Peptide Conjugates." Antisense and Nucleic Acid Drug Development 12, no. 2 (April 2002): 51–63. http://dx.doi.org/10.1089/108729002760070795.

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24

Bøe, S., and E. Hovig. "Photochemically Induced Gene Silencing Using PNA-Peptide Conjugates." Oligonucleotides 16, no. 2 (June 2006): 145–57. http://dx.doi.org/10.1089/oli.2006.16.145.

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25

Svensen, Nina, Juan José Díaz-Mochón, and Mark Bradley. "Microwave-assisted orthogonal synthesis of PNA–peptide conjugates." Tetrahedron Letters 49, no. 46 (November 2008): 6498–500. http://dx.doi.org/10.1016/j.tetlet.2008.08.104.

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26

Simmons, Carla G., Anne E. Pitts, Lynn D. Mayfield, Jerry W. Shay, and David R. Corey. "Synthesis and membrane permeability of PNA-peptide conjugates." Bioorganic & Medicinal Chemistry Letters 7, no. 23 (December 1997): 3001–6. http://dx.doi.org/10.1016/s0960-894x(97)10136-6.

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27

Ivanova, G. D., M. M. Fabani, A. A. Arzumanov, R. Abes, H. Yin, B. Lebleu, M. Wood, and M. J. Gait. "PNA-peptide conjugates as intracellular gene control agents." Nucleic Acids Symposium Series 52, no. 1 (September 1, 2008): 31–32. http://dx.doi.org/10.1093/nass/nrn016.

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28

Yokoi, Yasuhito, Yugo Kawabuchi, Abdullah Adham Zulmajdi, Reiji Tanaka, Toshiyuki Shibata, Takahiro Muraoka, and Tetsushi Mori. "Cell-Penetrating Peptide–Peptide Nucleic Acid Conjugates as a Tool for Protein Functional Elucidation in the Native Bacterium." Molecules 27, no. 24 (December 15, 2022): 8944. http://dx.doi.org/10.3390/molecules27248944.

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Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or hard-to-transform bacteria. In this report, we employed cell-penetrating peptide (CPP) –peptide nucleotide acid (PNA) conjugates to elucidate the function of such uncharacterized proteins in vivo within the native bacterium. Paenibacillus, a hard-to-transform bacterial genus, was used as a model. Two hypothetical genes showing amino acid sequence similarity to ι-carrageenases, termed cgiA and cgiB, were identified from the draft genome of Paenibacillus sp. strain YYML68, and CPP–PNA probes targeting the mRNA of the acyl carrier protein gene, acpP, and the two ι-carrageenase candidate genes were synthesized. Upon direct incubation of CPP–PNA targeting the mRNA of the acpP gene, we successfully observed growth inhibition of strain YYML68 in a concentration-dependent manner. Similarly, both the function of the candidate ι-carrageenases were also inhibited using our CPP–PNA probes allowing for the confirmation and characterization of these hypothetical proteins. In summary, we believe that CPP–PNA conjugates can serve as a simple and efficient alternative approach to characterize proteins in the native bacterium.

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29

Huang, Yi-Chao, Cheng Cao, Xiang-Long Tan, Xiaoyu Li, and Lei Liu. "Facile solid-phase synthesis of PNA–peptide conjugates using pNZ-protected PNA monomers." Org. Chem. Front. 1, no. 9 (September 5, 2014): 1050–54. http://dx.doi.org/10.1039/c4qo00217b.

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30

Sato, Takaya, Yusuke Sato, Kenta Iwai, Shusuke Kuge, Seiichi Nishizawa, and Norio Teramae. "Synthetic fluorescent probes capable of selective recognition of 3′-overhanging nucleotides for siRNA delivery imaging." Chemical Communications 51, no. 8 (2015): 1421–24. http://dx.doi.org/10.1039/c4cc08800j.

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Peptide nucleic acid (PNA)–thiazole orange (TO) conjugates are developed as fluorescent probes capable of selective recognition of 3′-overhanging nucleotides of siRNAs for an accurate analysis of the siRNA delivery process.

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31

Harrison, Joseph G., Christelle Frier, Ronald Laurant, Regina Dennis, Kevin D. Raney, and Shankar Balasubramanian. "Inhibition of human telomerase by PNA-cationic peptide conjugates." Bioorganic & Medicinal Chemistry Letters 9, no. 9 (May 1999): 1273–78. http://dx.doi.org/10.1016/s0960-894x(99)00170-5.

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32

Bialy, Laurent, Juan José Díaz-Mochón, Edgar Specker, Lise Keinicke, and Mark Bradley. "Dde-protected PNA monomers, orthogonal to Fmoc, for the synthesis of PNA–peptide conjugates." Tetrahedron 61, no. 34 (August 2005): 8295–305. http://dx.doi.org/10.1016/j.tet.2005.06.003.

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33

Popella, Linda, Jakob Jung, Kristina Popova, Svetlana Ðurica-Mitić, Lars Barquist, and Jörg Vogel. "Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics." Nucleic Acids Research 49, no. 8 (April 13, 2021): 4705–24. http://dx.doi.org/10.1093/nar/gkab242.

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Abstract Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.

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34

Noguchi, Eri, Narumi Shigi, and Makoto Komiyama. "Intracellular Localization of PNA in Human Cells upon its Introduction by Electroporation." Natural Product Communications 7, no. 3 (March 2012): 1934578X1200700. http://dx.doi.org/10.1177/1934578x1200700316.

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Peptide nucleic acid (PNA) is one of the most useful DNA analogs in a wide variety of gene analysis in human cells. In order to exhibit its maximal functions, PNA must be localized to a desired place (e.g., nucleus, cytoplasm and other organelles). Here, we introduced PNAs into HeLa cells by electroporation and examined their localization at various time points. The PNA which binds to the mitochondrial COII gene was initially accumulated in the nucleus, and thereafter mostly transferred to cytoplasm. This time-dependent intracellular localization of PNA is ascribed to the breakdown of the nuclear envelope in the cell division. On the other hand, another PNA that binds to telomere repeat sequence mostly remained in the nucleus, even after the cell division occurred. The retention of this PNA in the nucleus was further enhanced when it was conjugated with Cy3.

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Fabani, M. M., and M. J. Gait. "miR-122 targeting with LNA/2'-O-methyl oligonucleotide mixmers, peptide nucleic acids (PNA), and PNA-peptide conjugates." RNA 14, no. 2 (December 14, 2007): 336–46. http://dx.doi.org/10.1261/rna.844108.

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Tassinari, Martina, Michela Zuffo, Matteo Nadai, Valentina Pirota, Adriana Carolina Sevilla Montalvo, Filippo Doria, Mauro Freccero, and Sara N. Richter. "Selective targeting of mutually exclusive DNA G-quadruplexes: HIV-1 LTR as paradigmatic model." Nucleic Acids Research 48, no. 9 (April 13, 2020): 4627–42. http://dx.doi.org/10.1093/nar/gkaa186.

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Abstract Targeting of G-quadruplexes, non-canonical conformations that form in G-rich regions of nucleic acids, has been proposed as a novel therapeutic strategy toward several diseases, including cancer and infections. The unavailability of highly selective molecules targeting a G-quadruplex of choice has hampered relevant applications. Herein, we describe a novel approach, based on naphthalene diimide (NDI)-peptide nucleic acid (PNA) conjugates, taking advantage of the cooperative interaction of the NDI with the G-quadruplex structure and hybridization of the PNA with the flanking region upstream or downstream the targeted G-quadruplex. By biophysical and biomolecular assays, we show that the NDI-PNA conjugates are able to specifically recognize the G-quadruplex of choice within the HIV-1 LTR region, consisting of overlapping and therefore mutually exclusive G-quadruplexes. Additionally, the conjugates can induce and stabilize the least populated G-quadruplex at the expenses of the more stable ones. The general and straightforward design and synthesis, which readily apply to any G4 target of choice, together with both the red-fluorescent emission and the possibility to introduce cellular localization signals, make the novel conjugates available to selectively control G-quadruplex folding over a wide range of applications.

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Danneberg, Friederike, Alice Ghidini, Plamena Dogandzhiyski, Elisabeth Kalden, Roger Strömberg, and Michael W. Göbel. "Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)." Beilstein Journal of Organic Chemistry 11 (April 16, 2015): 493–98. http://dx.doi.org/10.3762/bjoc.11.55.

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Tris(2-aminobenzimidazole) conjugates with antisense oligonucleotides are effective site-specific RNA cleavers. Their mechanism of action is independent of metal ions. Here we investigate conjugates with peptide nucleic acids (PNA). RNA degradation occurs with similar rates and substrate specificities as in experiments with DNA conjugates we performed earlier. Although aggregation phenomena are observed in some cases, proper substrate recognition is not compromised. While our previous synthesis of 2-aminobenzimidazoles required an HgO induced cyclization step, a mercury free variant is described herein.

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Turner, John J., Simon Jones, Martin M. Fabani, Gabriela Ivanova, Andrey A. Arzumanov, and Michael J. Gait. "RNA targeting with peptide conjugates of oligonucleotides, siRNA and PNA." Blood Cells, Molecules, and Diseases 38, no. 1 (January 2007): 1–7. http://dx.doi.org/10.1016/j.bcmd.2006.10.003.

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Díaz-Mochón, Juan J., Laurent Bialy, Jon Watson, Rosario M. Sánchez-Martín, and Mark Bradley. "Synthesis and cellular uptake of cell delivering PNA–peptide conjugates." Chemical Communications, no. 26 (2005): 3316. http://dx.doi.org/10.1039/b503777h.

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Shiraishi, Takehiko, and Peter E. Nielsen. "Photochemically enhanced cellular delivery of cell penetrating peptide-PNA conjugates." FEBS Letters 580, no. 5 (January 31, 2006): 1451–56. http://dx.doi.org/10.1016/j.febslet.2006.01.077.

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41

Mier, Walter, Ramon Eritja, Ashour Mohammed, Uwe Haberkorn, and Michael Eisenhut. "Peptide–PNA Conjugates: Targeted Transport of Antisense Therapeutics into Tumors." Angewandte Chemie International Edition 42, no. 17 (April 29, 2003): 1968–71. http://dx.doi.org/10.1002/anie.200219978.

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42

de Koning, Martijn C., Dmitri V. Filippov, Nico Meeuwenoord, Mark Overhand, Gijs A. van der Marel, and Jacques H. van Boom. "An approach to the synthesis of peptide–PNA–peptide conjugates via native ligation." Tetrahedron Letters 43, no. 45 (November 2002): 8173–76. http://dx.doi.org/10.1016/s0040-4039(02)01856-7.

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Soofi, Muhammad A., and Mohamed N. Seleem. "Targeting Essential Genes in Salmonella enterica Serovar Typhimurium with Antisense Peptide Nucleic Acid." Antimicrobial Agents and Chemotherapy 56, no. 12 (September 24, 2012): 6407–9. http://dx.doi.org/10.1128/aac.01437-12.

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ABSTRACTWe investigated the capability of antisense peptide nucleic acids (PNAs) conjugated to the (KFF)3K cell-penetrating peptide to target possible essential genes (ligA,rpoA,rpoD,engA,tsf, andkdtA) inSalmonella entericaserovar Typhimurium and inhibit bacterial growthin vitro and in cell culture. All targeted PNA-based gene inhibition has shown great potency in gene expression inhibition in a sequence-specific and dose-dependent manner at micromolar concentrations. Among tested PNAs, the anti-rpoAand -rpoDPNAs showed the greatest potency.

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Scheibe, Christian, and Oliver Seitz. "PNA–sugar conjugates as tools for the spatial screening of carbohydrate–lectin interactions." Pure and Applied Chemistry 84, no. 1 (December 8, 2011): 77–85. http://dx.doi.org/10.1351/pac-con-11-08-07.

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Multivalent carbohydrate–lectin interactions are essential for a multitude of biological recognition events. Much effort has been spent in the synthesis of potent multivalent scaffolds in order to mimic or inhibit biological carbohydrate–protein interactions. However, the defined spatial presentation of carbohydrates remained a challenging task. Peptide nucleic acid (PNA)- and DNA-based double helices are useful scaffolds that enable the controlled display of carbohydrate ligands in a modular approach. The hybridization of PNA-sugar conjugates with complementary DNA strands provides multivalent complexes with defined spatial presentation of carbohydrates, which facilitates the spatial screening of carbohydrate–lectin interactions with Ångström-scale precision.

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Didion, B. A., and R. Bleher. "263 LABELING BOVINE SPERM Y-CHROMOSOME SEQUENCE USING DNA MIMICS." Reproduction, Fertility and Development 21, no. 1 (2009): 229. http://dx.doi.org/10.1071/rdv21n1ab263.

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Flow cytometric separation of X- and Y-chromosome bearing bovine sperm is an accepted technology for use at the commercial level. Nevertheless it is important to continue researching the area of gender-preselected sperm for improved efficiencies. We used a synthetic DNA mimic conjugated to a fluorescent dye for in situ detection of Y chromosomes in metaphase preparations of bovine somatic cells and spermatozoa. Peptide nucleic acids (PNA) are a type of DNA mimic having a higher affinity and stability than conventional DNA probes and are used as hybridization probes to complementary DNA. Using male bovine somatic cells and the Y-chromosome as a template, we arranged for the synthesis of a CY3-conjugated PNA to bind 13 to 15 base pairs of unique, Y-chromosome sequence. By testing different labeling conditions, we found that brief incubation (~1 h) of metaphase chromosomes with the PNA produced a localized signal on the Y-chromosome. No signals were observed when chromosomes of female bovine somatic cells were incubated with the same PNA probe. Because chromosomes occupy non-random territories in all cell nuclei, including sperm, we proposed to find centrally-located signals in 50% of fixed bovine sperm when treated with the same PNA as used for the somatic cells. As expected, we found the PNA signals present in 50% sperm (23/43) existing as a single, centrally-located, round fluorescent dot in the sperm head. Validation studies were also conducted using bovine sperm previously flow sorted into X or Y populations, and we found the signals in accordance to an expected signal present using the PNA (146/165 or 88.5% with PNA signal in presorted Y sperm heads and 13/174 or 7.5% with PNA signal in presorted X sperm heads).

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Hong, Seungpyo, Hyon Chang Kim, Hosang Jeon, Dong Soon Choi, Churl K. Min, Seongjo Kim, Hyun Joo, and Han Jip Kim. "A Bioinformatics Approach to Ribosomal Antibiotics Research Using Peptide-Peptide Nucleic Acid (PNA) Conjugates." Interdisciplinary Bio Central 1, no. 3 (October 31, 2006): 207–12. http://dx.doi.org/10.4051/ibce.2009.3.0019.

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Hu, Jiaxin, and David R. Corey. "Inhibiting Gene Expression with Peptide Nucleic Acid (PNA)−Peptide Conjugates That Target Chromosomal DNA†." Biochemistry 46, no. 25 (June 2007): 7581–89. http://dx.doi.org/10.1021/bi700230a.

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Kurupati, Prathiba, Kevin Shyong Wei Tan, Gamini Kumarasinghe, and Chit Laa Poh. "Inhibition of Gene Expression and Growth by Antisense Peptide Nucleic Acids in a Multiresistant β-Lactamase-Producing Klebsiella pneumoniae Strain." Antimicrobial Agents and Chemotherapy 51, no. 3 (December 11, 2006): 805–11. http://dx.doi.org/10.1128/aac.00709-06.

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ABSTRACT Klebsiella pneumoniae causes common and severe hospital- and community-acquired infections with a high incidence of multidrug resistance. The emergence and spread of β-lactamase-producing K. pneumoniae strains highlight the need to develop new therapeutic strategies. In this study, we developed antisense peptide nucleic acids (PNAs) conjugated to the (KFF)3K peptide and investigated whether they could mediate gene-specific antisense effects in K. pneumoniae. No outer membrane permeabilization was observed with antisense PNAs when used alone. Antisense peptide-PNAs targeted at two essential genes, gyrA and ompA, were found to be growth inhibitory at concentrations of 20 μM and 40 μM, respectively. Mismatched antisense peptide-PNAs with sequence variations of the gyrA and ompA genes when used as controls were not growth inhibitory. Bactericidal effects exerted by peptide-anti-gyrA PNA and peptide-anti-ompA PNA on cells were observed within 6 h of treatment. The antisense peptide-PNAs specifically inhibited expression of DNA gyrase subunit A and OmpA from the respective targeted genes in a dose-dependent manner. Both antisense peptide-PNAs cured IMR90 cell cultures that were infected with K. pneumoniae (104 CFU) in a dose-dependent manner without any noticeable toxicity to the human cells.

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Cogoi, Susanna, Andrea Codognotto, Valentina Rapozzi, and Luigi E. Xodo. "ANTIGENE PROPERTY OF PNA CONJUGATED TO THE NUCLEAR LOCALIZATION SIGNAL PEPTIDE." Nucleosides, Nucleotides & Nucleic Acids 24, no. 5-7 (April 1, 2005): 971–74. http://dx.doi.org/10.1081/ncn-200059333.

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Patil, Nitin A., John A. Karas, Bradley J. Turner, and Fazel Shabanpoor. "Thiol-Cyanobenzothiazole Ligation for the Efficient Preparation of Peptide–PNA Conjugates." Bioconjugate Chemistry 30, no. 3 (January 15, 2019): 793–99. http://dx.doi.org/10.1021/acs.bioconjchem.8b00908.

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