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Moriya SS, Shibasaki H, Kohara M, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A, Sugiyama T. Synthesis and characterization of PNA oligomers containing preQ 1 as a positively charged guanine analogue. Bioorg Med Chem Lett 2021; 39:127850. [PMID: 33662538 DOI: 10.1016/j.bmcl.2021.127850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
We report the synthesis of a peptide nucleic acid (PNA) monomer containing preQ1, a positively charged guanine analogue. The new monomer was incorporated into PNA oligomers using standard Fmoc-chemistry-based solid-phase synthesis. The preQ1 unit-containing PNA oligomers exhibited improved affinity for their complementary DNA through electrostatic attraction, and their sequence specificity was not compromised. It could be beneficial to incorporate preQ1 into PNA oligomers instead of guanine when creating antisense/antigene agents or research tools.
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Affiliation(s)
- Shun-Suke Moriya
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hatsune Shibasaki
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Misaki Kohara
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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2
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SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens. Molecules 2020; 25:molecules25040769. [PMID: 32053960 PMCID: PMC7070780 DOI: 10.3390/molecules25040769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
During the treatment of viral or bacterial infections, it is important to evaluate any resistance to the therapeutic agents used. An amino acid substitution arising from a single base mutation in a particular gene often causes drug resistance in pathogens. Therefore, molecular tools that discriminate a single base mismatch in the target sequence are required for achieving therapeutic success. Here, we synthesized peptide nucleic acids (PNAs) derivatized with tolane via an amide linkage at the N-terminus and succeeded in improving the sequence specificity, even with a mismatched base pair located near the terminal region of the duplex. We assessed the sequence specificities of the tolane-PNAs for single-strand DNA and RNA by UV-melting temperature analysis, thermodynamic analysis, an in silico conformational search, and a gel mobility shift assay. As a result, all of the PNA-tolane derivatives stabilized duplex formation to the matched target sequence without inducing mismatch target binding. Among the different PNA-tolane derivatives, PNA that was modified with a naphthyl-type tolane could efficiently discriminate a mismatched base pair and be utilized for the detection of resistance to neuraminidase inhibitors of the influenza A/H1N1 virus. Therefore, our molecular tool can be used to discriminate single nucleotide polymorphisms that are related to drug resistance in pathogens.
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3
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Sawada S, Takao T, Kato N, Kaihatsu K. Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA. Molecules 2017; 22:molecules22111840. [PMID: 29077023 PMCID: PMC6150319 DOI: 10.3390/molecules22111840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/18/2017] [Accepted: 10/21/2017] [Indexed: 11/18/2022] Open
Abstract
DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated azobenzene linker gave a stable 1:1 TC-PNA/ssDNA complex and exhibited good mismatch recognition. Our design for TC-PNA-AZO can be utilized for detecting homopurine sequences in various genes.
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Affiliation(s)
- Shinjiro Sawada
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Toshifumi Takao
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Nobuo Kato
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kunihiro Kaihatsu
- Department of Organic Fine Chemicals, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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4
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Sugiyama T, Hasegawa G, Niikura C, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A. PNA monomers fully compatible with standard Fmoc-based solid-phase synthesis of pseudocomplementary PNA. Bioorg Med Chem Lett 2017; 27:3337-3341. [PMID: 28610975 DOI: 10.1016/j.bmcl.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022]
Abstract
Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies.
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Affiliation(s)
- Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Genki Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Chie Niikura
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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5
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Sugiyama T, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Takano M, Kittaka A. Peptide Nucleic Acid with a Lysine Side Chain at the β-Position: Synthesis and Application for DNA Cleavage. Chem Pharm Bull (Tokyo) 2017; 64:817-23. [PMID: 27373637 DOI: 10.1248/cpb.c16-00191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This paper reports the synthesis of new β-Lys peptide nucleic acid (PNA) monomers and their incorporation into a 10-residue PNA sequence. PNA containing β-Lys PNA units formed a stable hybrid duplex with DNA. However, incorporation of β-Lys PNA units caused destabilization of PNA-DNA duplexes to some extent. Electrostatic attractions between β-PNA and DNA could reduce this destabilization effect. Subsequently, bipyridine-conjugated β-Lys PNA was prepared and exhibited sequence selective cleavage of DNA. Based on the structures of the cleavage products and molecular modeling, we reasoned that bipyridine moiety locates within the minor groove of the PNA-DNA duplexes. The lysine side chain of β-PNA is a versatile handle for attaching various functional molecules.
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Affiliation(s)
- Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University
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6
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Browne EC, Parakh S, Duncan LF, Langford SJ, Atkin JD, Abbott BM. Efficacy of peptide nucleic acid and selected conjugates against specific cellular pathologies of amyotrophic lateral sclerosis. Bioorg Med Chem 2016; 24:1520-7. [PMID: 26935939 DOI: 10.1016/j.bmc.2016.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/09/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Cellular studies have been undertaken on a nonamer peptide nucleic acid (PNA) sequence, which binds to mRNA encoding superoxide dismutase 1, and a series of peptide nucleic acids conjugated to synthetic lipophilic vitamin analogs including a recently prepared menadione (vitamin K) analog. Reduction of both mutant superoxide dismutase 1 inclusion formation and endoplasmic reticulum stress, two of the key cellular pathological hallmarks in amyotrophic lateral sclerosis, by two of the prepared PNA oligomers is reported for the first time.
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Affiliation(s)
- Elisse C Browne
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Sonam Parakh
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia; Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University, Sydney 2109, Australia
| | - Luke F Duncan
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | | | - Julie D Atkin
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia; Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University, Sydney 2109, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia.
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7
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Ostromohov N, Schwartz O, Bercovici M. Focused upon hybridization: rapid and high sensitivity detection of DNA using isotachophoresis and peptide nucleic acid probes. Anal Chem 2015; 87:9459-66. [PMID: 26278590 DOI: 10.1021/acs.analchem.5b02547] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a novel assay for rapid and high sensitivity detection of nucleic acids without amplification. Utilizing the neutral backbone of peptide nucleic acids (PNA), our method is based on the design of low electrophoretic mobility PNA probes, which do not focus under isotachophoresis (ITP) unless bound to their target sequence. Thus, background noise associated with free probes is entirely eliminated, significantly improving the signal-to-noise ratio while maintaining a simple single-step assay requiring no amplification steps. We provide a detailed analytical model and experimentally demonstrate the ability to detect targets as short as 17 nucleotides (nt) and a limit of detection of 100 fM with a dynamic range of 5 decades. We also demonstrate that the assay can be successfully implemented for detection of DNA in human serum without loss of signal. The assay requires 15 min to complete, and it could potentially be used in applications where rapid and highly sensitive amplification-free detection of nucleic acids is desired.
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Affiliation(s)
- Nadya Ostromohov
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Ortal Schwartz
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology , Haifa 3200003, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
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8
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Amirkhanov RN, Mazurkova NA, Amirkhanov NV, Zarytova VF. [Composites of Peptide Nucleic Acids with Titanium Dioxide Nanoparticles. IV+. Antiviral Activity of Nanocomposites Containing DNA/PNA Duplexes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:162-9. [PMID: 26165123 DOI: 10.1134/s1068162015020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antiviral activity of TiO2 · PL · DNA/PNA nanobiocomposites was studied on the MDCK cell culture infected with influenza A virus (subtype H3N2). PNA fragment in nanocomposites as a DNA/PNA heteroduplex is electrostatically bound to titanium dioxide nanoparticles precovered with polylysine (TiO2 · PL). It was shown that TiO2 · PL · DNA1/PNA1 nanobiocomposit bearing PNA1 fragment targeted to the 3'-end of the noncoding region of segment 5 of viral RNA specifically inhibited the virus reproduction with the efficiency of 99.8%. It was determined that the 50% cytotoxic concentration (TC50) of the TiO2 · PL · DNA1/PNA1 nanocomposite is more than 1200 mg/mL. And 50% effective inhibitory concentration (IC50) is less than 0.003 mg/mL. Based on these data, the selectivity index (SI) for TiO2 · PL · DNA1/PNA1 nanobiocomposite defined as the ratio TC50/LC50, is more than 400. Thus TiO2 · PL · DNA/PNA nanobiocomposites can not only penatrate through cell membrane, but and are able to exhibit a high specific antisense activity, without causing toxic effects on the living cells.
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9
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Amirkhanov NV, Amirkhanov RN, Zarytova VF. [Composites of peptide nucleic acids with titanium dioxide nanoparticles. I. Construction of nanocomposites containing DNA/PNA duplexes and their delivery into HeLa cells]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 38:691-705. [PMID: 23547473 DOI: 10.1134/s1068162012060027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to investigate the possibility of using titanium dioxide (TiO2) nanoparticles to transport peptide nucleic acids (PNA) in eukaryotic cells, a PNA oligomer has been synthesized, and method of PNA immobilization in the form of hybrid DNA/PNA duplexes on the surface of TiO2 nanoparticles covered with polylysine (PL) has been designed. Attaching of DNA/PNA duplex on TiO2 x PL nanoparticles occurred due to electrostatic interactions between the negatively charged DNA chain and the positively charged amino groups of PL. Binding of the PNA with the nanocomposite achieved through noncovalent Watson-Crick interactions between the PNA and complementary DNA. The capacity of obtained TiO2 x PL x DNA/PNA nanocomposites depending on immobilization conditions was 10-30 nmol PNA per 1 mg of TiO2 particles, which corresponds to -1-3 PNA molecules per one TiO2 particle with size of 4-6 nm. By method ofconfocal laser scanning microscopy on the example of the fluorescein labeled PNA oligomer (Flu)PNA it has been shown that the PNA molecules in composition of TiO2 x PL x DNA/(Flu)PNA nanocomposites effectively penetrate and accumulate in HeLa cells without the use oftransfection agents, electroporation, or other auxiliary procedures has been shown.
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10
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Kaihatsu K, Sawada S, Nakamura S, Nakaya T, Yasunaga T, Kato N. Sequence-specific and visual identification of the influenza virus NS gene by azobenzene-tethered bis-peptide nucleic acid. PLoS One 2013; 8:e64017. [PMID: 23704970 PMCID: PMC3660326 DOI: 10.1371/journal.pone.0064017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/07/2013] [Indexed: 11/21/2022] Open
Abstract
To rapidly and specifically identify highly virulent influenza virus strains, we prepared an azobenzene-tethered hairpin-type peptide nucleic acid, bisPNA-AZO, which has a complementary sequence against a highly conserved genomic RNA sequence within the ribonucleoprotein complex of the 2009 pandemic influenza A virus, H1N1 subtype. bisPNA-AZO recognizes the conserved virus genome sequence in a sequence-specific manner. Immobilization of bisPNA-AZO on a plate allowed capture of the target virus gene and the generation of a visual colour signal.
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Affiliation(s)
- Kunihiro Kaihatsu
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
- * E-mail:
| | - Shinjiro Sawada
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Teruo Yasunaga
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
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11
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β-PNA: peptide nucleic acid (PNA) with a chiral center at the β-position of the PNA backbone. Bioorg Med Chem Lett 2011; 21:7317-20. [PMID: 22050888 DOI: 10.1016/j.bmcl.2011.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 10/04/2011] [Accepted: 10/07/2011] [Indexed: 11/22/2022]
Abstract
Peptide nucleic acid (PNA) monomers with a methyl group at the β-position have been synthesized. The modified monomers were incorporated into PNA oligomers using Fmoc chemistry for solid-phase synthesis. Thermal denaturation and circular dichroism (CD) studies have shown that PNA containing the S-form monomers was well suited to form a hybrid duplex with DNA, whose stability was comparable to that of unmodified PNA-DNA duplex, whereas PNA containing the R-form monomers was not.
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12
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Brown EMB, Paunesku T, Wu A, Thurn KT, Haley B, Clark J, Priester T, Woloschak GE. Methods for assessing DNA hybridization of peptide nucleic acid-titanium dioxide nanoconjugates. Anal Biochem 2008; 383:226-35. [PMID: 18786502 DOI: 10.1016/j.ab.2008.08.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/28/2008] [Accepted: 08/09/2008] [Indexed: 12/25/2022]
Abstract
We describe the synthesis of peptide nucleic acid (PNA)-titanium dioxide (TiO(2)) nanoconjugates and several novel methods developed to investigate the DNA hybridization behaviors of these constructs. PNAs are synthetic DNA analogs resistant to degradation by cellular enzymes that hybridize to single-stranded DNA (ssDNA) with higher affinity than DNA oligonucleotides, invade double-stranded DNA (dsDNA), and form different PNA/DNA complexes. Previously, we developed a DNA-TiO(2) nanoconjugate capable of hybridizing to target DNA intracellularly in a sequence-specific manner with the ability to cleave DNA when excited by electromagnetic radiation but susceptible to degradation that may lower its intracellular targeting efficiency and retention time. PNA-TiO(2) nanoconjugates described in the current article hybridize to target ssDNA, oligonucleotide dsDNA, and supercoiled plasmid DNA under physiological-like ionic and temperature conditions, enabling rapid, inexpensive, sequence-specific concentration of nucleic acids in vitro. When modified by the addition of imaging agents or peptides, hybridization capabilities of PNA-TiO(2) nanoconjugates are enhanced, providing essential benefits for numerous in vitro and in vivo applications. The series of experiments shown here could not be done with either TiO(2)-DNA nanoconjugates or PNAs alone, and the novel methods developed will benefit studies of numerous other nanoconjugate systems.
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Affiliation(s)
- Eric M B Brown
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Avenue, Ward-13-002, Chicago, IL 60611, USA
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13
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Braasch DA, Nulf CJ, Corey DR. Synthesis and purification of peptide nucleic acids. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.11. [PMID: 18428893 DOI: 10.1002/0471142700.nc0411s09] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peptide nucleic acids (PNAs) are DNA analogs in which the normal phosphodiester backbone is replaced by 2-aminoethyl glycine linkages. Hybridization of PNAs with RNA or DNA follows normal rules for Watson-Crick base pairing and occurs with high affinity. Thus, PNAs are a promising choice for applications that benefit from high-affinity hybridization. They are assembled using techniques adapted from peptide chemistry. Protocols are given for both automated and manual synthesis of PNAs as well as their purification. The advantages of each method are discussed, as are the different monomers and reagents that are required. Additionally, protocols are given for adding peptides to PNAs (which can enhance hybridization or cell uptake of the PNA) and for adding a biotin label.
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Affiliation(s)
- Dwaine A Braasch
- University of Texas Southwestern Medical Center at Dallas, Dallas, USA
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14
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Dömling A. A Novel Concept for the Combinatorial Synthesis of Peptide Nucleic Acids. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004699] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Alexander Dömling
- a Technische Universität München, Institut für Organische Chemie und Biochemie , Lichtenbergstr. 4, D-85747 , Garching , Germany
- b MORPHOCHEM GmbH , Am Klopferspitz 19, D-82152 , Martinsried , Germany Phone: Fax: E-mail:
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15
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Chiarantini L, Cerasi A, Millo E, Sparnacci K, Laus M, Riccio M, Santi S, Ballestri M, Spaccasassi S, Tondelli L. Enhanced antisense effect of modified PNAs delivered through functional PMMA microspheres. Int J Pharm 2006; 324:83-91. [PMID: 16926075 DOI: 10.1016/j.ijpharm.2006.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2006] [Revised: 07/03/2006] [Accepted: 07/06/2006] [Indexed: 11/26/2022]
Abstract
Peptide nucleic acids (PNA) are very promising antisense agents, but their in vivo application is often hampered by their low bioavailability, mainly due to their limited uptake through cellular and nuclear membranes. However, PNA chemical synthesis easily allows modification with functional structures able to improve the intrinsically low permeability and great interest is arising in finding specific and efficient delivery protocols. Polymeric core-shell microspheres with anionic functional groups on the surface were tested for their ability to reversibly bind lysine modified PNA sequences, whose antisense activity against COX-2 mRNA was already demonstrated in murine macrophages.
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16
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Sharma S, Raymond E, Soda H, Von Hoff DD. Telomerase and telomere inhibitors in preclinical development. Expert Opin Investig Drugs 2005; 6:1179-85. [PMID: 15991892 DOI: 10.1517/13543784.6.9.1179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Telomerase is an enzyme required by actively dividing cells to maintain the ends of chromosomes (telomeres). It is present in germline tissue, stem cells and cancer cells, but is repressed in somatic cells. Efforts are underway to exploit this selective expression of telomerase in cancer therapeutics. This review describes the status of telomerase research, which although at present predominantly preclinical, has the potential to enter clinical research.
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Affiliation(s)
- S Sharma
- Institute for Drug Development, Cancer Therapy and Research Center, 14960 Omicron Drive, San Antonio, TX 78245, USA
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17
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Robaczewska M, Narayan R, Seigneres B, Schorr O, Thermet A, Podhajska AJ, Trepo C, Zoulim F, Nielsen PE, Cova L. Sequence-specific inhibition of duck hepatitis B virus reverse transcription by peptide nucleic acids (PNA). J Hepatol 2005; 42:180-7. [PMID: 15664242 DOI: 10.1016/j.jhep.2004.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 09/17/2004] [Accepted: 10/04/2004] [Indexed: 01/02/2023]
Abstract
BACKGROUND/AIMS Peptide nucleic acids (PNAs) appear as promising new antisense agents, that have not yet been examined as hepatitis B virus (HBV) inhibitors. Our aim was to study the ability of PNAs targeting the duck HBV (DHBV) encapsidation signal epsilon to inhibit reverse transcription (RT) and to compare their efficacy with phosphorothioate oligodeoxynucleotides (S-ODNs). METHODS The effect of two partly overlapping PNAs targeting epsilon and of analogous S-ODNs was tested in cell-free transcription and translation system for DHBV RT expression. In addition their antiviral effect was investigated in primary duck hepatocytes (PDH). RESULTS Both PNAs reproducibly inhibited DHBV RT in a dose-dependent manner with IC(50) of 10nM, whereas up to 600-fold higher concentration of S-ODNs was required for similar inhibition. The PNA targeting the bulge and upper stem of epsilon appeared as more efficient RT inhibitor than the PNA targeting only the bulge. Importantly, the inhibition was highly sequence-specific since double-mismatched PNA had no effect on the RT reaction. Moreover, in PDH the PNA coupled to Arg(7) cationic delivery peptide decreased DHBV replication. CONCLUSIONS We provide the first evidence that PNAs targeting the bulge and upper stem of epsilon can efficiently and in a sequence-specific manner inhibit DHBV RT.
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Abstract
The recognition of cellular nucleic acids by synthetic oligonucleotides is a versatile strategy for regulating biological processes. The vast majority of published studies have focused on antisense oligonucleotides that target mRNA, but it is also possible to design antigene oligonucleotides that are complementary to chromosomal DNA. Antigene oligomers could be used to inhibit the expression of any gene or analyze promoter structure and the mechanisms governing gene regulation. Other potential applications of antigene oligomers include activation of expression of chosen genes or the introduction of mutations to correct genetic disease. Peptide nucleic acid (PNA) is a nonionic DNA/RNA mimic that possesses outstanding potential for recognition of duplex DNA. Here we describe properties of PNAs and the challenges for their development as robust antigene agents.
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Affiliation(s)
- Kunihiro Kaihatsu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 USA
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Hamilton SE, Simmons CG, Kathiriya IS, Corey DR. Cellular delivery of peptide nucleic acids and inhibition of human telomerase. CHEMISTRY & BIOLOGY 1999; 6:343-51. [PMID: 10375543 DOI: 10.1016/s1074-5521(99)80046-5] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Human telomerase has an essential RNA component and is an ideal target for developing rules correlating oligonucleotide chemistry with disruption of biological function. Similarly, peptide nucleic acids (PNAs), DNA analogs that bind complementary sequences with high affinity, are outstanding candidates for inducing phenotypic changes through hybridization. RESULTS We identify PNAs directed to nontemplate regions of the telomerase RNA that can overcome RNA secondary structure and inhibit telomerase by intercepting the RNA component prior to holoenzyme assembly. Relative potencies of inhibition delineate putative structural domains. We describe a novel protocol for introducing PNAs into eukaryotic cells and report efficient inhibition of cellular telomerase by PNAs. CONCLUSIONS PNAs directed to nontemplate regions are a new class of telomerase inhibitor and may contribute to the development of novel antiproliferative agents. The dependence of inhibition by nontemplate-directed PNAs on target sequence suggests that PNAs have great potential for mapping nucleic acid structure and predictably regulating biological processes. Our simple method for introducing PNAs into cells will not only be useful for probing the complex biology surrounding telomere length maintenance but can be broadly applied for controlling gene expression and functional genomics.
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Affiliation(s)
- S E Hamilton
- Howard Hughes Medical Institute Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235-9050, USA
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Simmons CG, Pitts AE, Mayfield LD, Shay JW, Corey DR. Synthesis and membrane permeability of PNA-peptide conjugates. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)10136-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Good L, Nielsen PE. Progress in developing PNA as a gene-targeted drug. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:431-7. [PMID: 9303195 DOI: 10.1089/oli.1.1997.7.431] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Peptide nucleic acid (PNA) is a DNA mimic in which the nucleobases are attached to a pseudopeptide backbone. This achiral, uncharged, and rather flexible peptide backbone permits more stable hybridization to DNA and RNA oligomers with uncompromised or even improved sequence selectivity. Additional advantages of PNA are stability against nucleases and proteases and convenient solid phase synthesis. At the RNA level, PNA can be targeted to mRNA to block protein synthesis in an antisense strategy. PNA can also be targeted to the RNA component of ribonucleoproteins (RNPs) to inhibit their enzymatic activities. At the DNA level, the unique ability of PNA to bind DNA by duplex invasion can be used to arrest transcription within a gene sequence or to provide an artificial open complex to promote transcription. This review focuses on recent progress toward the development of PNA as a sequence-targeted drug.
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Affiliation(s)
- L Good
- Department of Medical Biochemistry and Genetics, University of Copenhagen, Panum Institute, Copenhagen, Denmark
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Abstract
Peptide nucleic acids (PNAs) are DNA analogs containing neutral amide backbone linkages. PNAs are stable to degradation by enzymes and hybridize to complementary sequences with higher affinity than analogous DNA oligomers. PNA synthesis employs protocols derived from solid-phase peptide synthesis, making the methodology straightforward and flexible. PNAs are being incorporated into an expanding set of applications, including genome mapping, the identification of mutations and measurement of telomere length. The growth in the popularity of PNAs as a tool for nucleic acid recognition should accelerate as the properties of PNAs become more familiar.
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Affiliation(s)
- D R Corey
- Howard Hughes Medical Institute, Dallas, TX, USA.
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