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Kaplanskiy MV, Kruglov ML, Vanin AA, Tupikina EY. Dynamics of non-covalent interactions during the P-O bond cleavage reaction by ribonuclease A. Phys Chem Chem Phys 2024; 26:21061-21073. [PMID: 39054927 DOI: 10.1039/d4cp01888e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
In this work, an atomistic-scale investigation of the phosphodiester P-O bond cleavage reaction by the enzyme ribonuclease A was carried out using computer simulation techniques. It is shown that during the reaction the network of non-covalent interactions in the active center of the ribonuclease changes significantly, while the role of these non-covalent interactions is different: coordination of the corresponding groups, electron density transfer, and ligand holding in the active center. It is shown that the process of proton transfer from Asp121 to His119 is the first stage of this reaction; at the same time, the hydrogen bond between the phosphate ligand and the imino group of Arg39 is broken, which, although keeping the ligand in the active center, does not allow the ligand to orient itself more conveniently for subsequent proton transfers. Furthermore, the key step of this reaction occurs: proton transfer with the participation of imidazole rings His12 and His119, in which the guiding role is played by several hydrogen bonds with the participation of Phe120, and the role of an electron density carrier is played by the pnictogen bond between the oxygen of the phosphate ligand and the pyridine-like nitrogen of the imidazole ring His119, which was detected for the first time.
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Affiliation(s)
- Mark V Kaplanskiy
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Maxim L Kruglov
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Aleksandr A Vanin
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Elena Yu Tupikina
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
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Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
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Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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4
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Kuah E, Toh S, Yee J, Ma Q, Gao Z. Enzyme Mimics: Advances and Applications. Chemistry 2016; 22:8404-30. [PMID: 27062126 DOI: 10.1002/chem.201504394] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.
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Affiliation(s)
- Evelyn Kuah
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Seraphina Toh
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Jessica Yee
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Qian Ma
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax.
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Dogandzhiyski P, Ghidini A, Danneberg F, Strömberg R, Göbel MW. Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques. Bioconjug Chem 2015; 26:2514-9. [PMID: 26544527 DOI: 10.1021/acs.bioconjchem.5b00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
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Affiliation(s)
- Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
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Danneberg F, Ghidini A, Dogandzhiyski P, Kalden E, Strömberg R, Göbel MW. Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole). Beilstein J Org Chem 2015; 11:493-8. [PMID: 25977723 PMCID: PMC4419560 DOI: 10.3762/bjoc.11.55] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/02/2015] [Indexed: 12/19/2022] Open
Abstract
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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Affiliation(s)
- Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Alice Ghidini
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, SE-141 83 Huddinge, Sweden
| | - Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Elisabeth Kalden
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
| | - Roger Strömberg
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, SE-141 83 Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany
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Stephan H, Foerster C, Gasser G. Synthesis, characterization, and evaluation of radiometal-containing peptide nucleic acids. Methods Mol Biol 2014; 1050:37-54. [PMID: 24297349 DOI: 10.1007/978-1-62703-553-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide nucleic acids (PNAs) have very attractive properties for applications in nuclear medicine. Because PNAs have high selectivity for DNA/RNA recognition, resistance to nuclease/protease degradation, and high thermal and radiolytic stabilities, PNA bioconjugates could transform the areas of diagnostic and therapeutic nuclear medicine. In this book chapter, we report on the current developments towards the preparation of radiometal-containing PNA constructs and summarize the protocols for labeling these probes with (99m)Tc, (111)In, (64)Cu, (90)Y, and (177)Lu.
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Affiliation(s)
- Holger Stephan
- Institute of Radiopharmaceutical Cancer Research, Helmholtz- Zentrum Dresden-Rossendorf, Dresden, Germany
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8
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Joshi T, Patra M, Spiccia L, Gasser G. Di-heterometalation of thiol-functionalized peptide nucleic acids. ARTIFICIAL DNA, PNA & XNA 2013; 4:11-8. [PMID: 23422249 PMCID: PMC3654725 DOI: 10.4161/adna.24019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 12/21/2022]
Abstract
As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium(II) polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru(II)-polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone (H-a-a-g-t-c-t-g-c-linker-cys-NH 2) has been performed by standard peptide coupling method. As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 (H-gly-a-a-g-t-c-t-g-c-linker-cys-NH 2) and PNA2 (C1-a-a-g-t-c-t-g-c-linker-cys-NH 2) to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed. The synthesized ruthenium(II)-cymantrenyl PNA oligomers have been characterized by mass spectrometry (ESI-MS) and IR spectroscopy. The distinct Mn-CO vibrational IR stretches, between 1,924-2,074 cm (-1) , have been used as markers to confirm the presence of cymantrenyl units in the PNA sequences and the purity of the HPLC-purified PNA thioethers assessed using LC-MS.
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Affiliation(s)
- Tanmaya Joshi
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
| | - Malay Patra
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
| | - Leone Spiccia
- ARC Centre of Excellence for Electromaterials Science and School of Chemistry; Monash University; Clayton, VIC Australia
| | - Gilles Gasser
- Institute of Inorganic Chemistry; University of Zurich; Zurich, Switzerland
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9
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Gasser G, Neumann S, Ott I, Seitz M, Heumann R, Metzler-Nolte N. Preparation and Biological Evaluation of Di-Hetero-Organometallic-Containing PNA Bioconjugates. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100734] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Gasser G, Sosniak AM, Metzler-Nolte N. Metal-containing peptide nucleic acid conjugates. Dalton Trans 2011; 40:7061-76. [PMID: 21541385 DOI: 10.1039/c0dt01706j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA·DNA hybrid stability, and last but not least as probes for molecular and cell biology.
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Affiliation(s)
- Gilles Gasser
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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12
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Murtola M, Strömberg R. PNA based artificial nucleases displaying catalysis with turnover in the cleavage of a leukemia related RNA model. Org Biomol Chem 2008; 6:3837-42. [PMID: 18843415 DOI: 10.1039/b810106j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several peptide nucleic acid based artificial nucleases (PNAzymes) are designed to create a bulge in the target RNA, which is a short model of the leukemia related bcr/abl mRNA. The target RNA is cleaved by the PNAzymes with a half-life of down to 11 h (using a 1 : 1 ratio of PNA-conjugate to target) and only upon base-pairing with the substrate. The PNA based systems are also shown to act in a catalytic fashion with turnover of substrate and are thus the first reported peptide nucleic acid based artificial RNA-cleaving enzymes.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet Novum, 14157 Huddinge, Sweden
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Murtola M, Ossipov D, Sandbrink J, Strömberg R. RNA cleavage by 2,9-diamino-1,10-phenanthroline PNA conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1479-83. [PMID: 18066810 DOI: 10.1080/15257770701542769] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report on the synthesis of 2,9-diamino-1,10-phenanthroline PNA conjugates as well as on their action in cleavage of a target RNA. Synthesis of the PNA conjugates are performed on solid support and the phenanthroline derivative is conjugated either to the amino-end or to a centrally positioned diaminopropionic acid in the PNA via a urea linker. Cleavage of the target RNA is achieved and compared to cleavage with the corresponding 2,9-dimethyl-1,10-phenanthroline and glycine conjugates.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, S-14157 Huddinge, Sweden
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Chaubey B, Tripathi S, Désiré J, Baussanne I, Décout JL, Pandey VN. Mechanism of RNA cleavage catalyzed by sequence specific polyamide nucleic acid-neamine conjugate. Oligonucleotides 2007; 17:302-13. [PMID: 17854270 DOI: 10.1089/oli.2007.0085] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In earlier studies, we found that a conjugate of neamine-polyamide nucleic acid targeting transactivation response element of HIV-1 RNA genome (HIV-1 TAR) displayed anti-HIV-1 activity and sequence-specific cleavage of the target RNA in vitro. Here we show that both the position of conjugation of polyamide nucleic acid (PNA) on neamine and the length of the spacer are critical parameters for conferring cleavage activity to the conjugate. The conjugation of PNA via a spacer incorporating 11 atoms to the 5-position of ring I of the neamine core conferred sequence-specific RNA cleavage activity on the conjugate, while conjugation to the 4'-position of ring II abolished this activity. Similarly, 5-neamine PNA complementary to TAR sequence of HIV-1 genome (PNA(TAR)) conjugates having either a 23-atom spacer or a bulky dansyl group between PNA and the neamine core also resulted in complete loss of cleavage activity. Based on these observations, we propose a mechanism for the observed RNA cleavage catalyzed by the conjugate involving unprotonated and protonated amino groups at the 3-position of ring I and the 6'-position of ring II of the neamine core, respectively.
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Affiliation(s)
- Binay Chaubey
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA
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15
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Mancin F, Tecilla P. Zinc(ii) complexes as hydrolytic catalysts of phosphate diester cleavage: from model substrates to nucleic acids. NEW J CHEM 2007. [DOI: 10.1039/b703556j] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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de Koning MC, Petersen L, Weterings JJ, Overhand M, van der Marel GA, Filippov DV. Synthesis of thiol-modified peptide nucleic acids designed for post-assembly conjugation reactions. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.01.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kersebohm T, Kirin SI, Metzler-Nolte N. Insertion of an internal dipeptide into PNA oligomers: thermal melting studies and further functionalization. Bioorg Med Chem Lett 2006; 16:2964-8. [PMID: 16546386 DOI: 10.1016/j.bmcl.2006.02.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/23/2006] [Accepted: 02/25/2006] [Indexed: 11/24/2022]
Abstract
The solid phase synthesis of PNA oligomers with the internal dipeptide Gly-Phe is presented and the interaction with complementary DNA investigated. UV absorbance melting experiments with different but complementary DNA sequences show that stable PNA x DNA duplexes are only obtained when there is no DNA base opposite the dipeptide unit. Instead, the dipeptide spacer forms a loop-like structure within the duplex. Further functionalization with N-heterocyclic ligands is described. p-Nitro-phenylalanine is introduced in place of Phe during solid phase synthesis and subsequently reduced to p-amino-phenylalanine. Reaction with activated acids provides the ligand conjugates in high yield and purity. This strategy opens a universal route to a large number of internal substitutions in PNA chemistry.
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Affiliation(s)
- Tim Kersebohm
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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Abstract
A series of small model complexes made from Ni(II) and the ligands ethylenediamine (en), histamine (hist), and histidylleucine (HisLeu) were prepared and studied as potential hydrolytic DNA-cleavage agents. The stability constants and species-distribution curves for these complexes were determined as a function of pH. The 1 : 1 : 1 ternary complexes [Ni(II)(en)(HisLeu)] (1) and [Ni(II)(hist)(HisLeu)] (2) were the only major species present at the physiologically relevant pH of 6-7, as further corroborated by ESI-MS analysis. The complex geometries of 1 and 2 were analyzed by UV/VIS experiments and molecular dynamics (MD) simulations. Both ternary complexes were found to intercalate with DNA, as shown by UV/VIS, thermal-denaturation, and fluorescence-titration studies with ethidium bromide (EB). The intrinsic binding constants (K(b)) for the bound complexes 1DNA and 2DNA were determined as 150 and 290, resp. Gel-electrophoresis experiments revealed that 1 and 2 cleave supercoiled (type-I) to nicked-circular (type-II) DNA at physiological pH, with rate constants of 0.64 and 0.75 h(-1), resp. A tentative mechanism for this hydrolytic cleavage is proposed.
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Küsel A, Zhang J, Alvariño Gil M, Stückl AC, Meyer-Klaucke W, Meyer F, Diederichsen U. Metal Binding Within a Peptide-Based Nucleobase Stack with Tuneable Double-Strand Topology. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500464] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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Reddy PR, Mohan SK, Rao KS. Ternary Zinc(II)-Dipeptide Complexes for the Hydrolytic Cleavage of DNA at Physiological pH. Chem Biodivers 2005; 2:672-83. [PMID: 17192010 DOI: 10.1002/cbdv.200590043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A series of Zn(II) complexes with cysteinylglycine (CysGly) and histidylserine (HisSer), and of CysGly and histidylphenylalanine (HisPhe) were investigated. Complex stabilities were determined potentiometrically, and binding geometries were probed by means of 1H-NMR spectroscopy, using Co(II) instead of Zn(II) as a spectroscopic marker. The ternary 1:1:1 complexes [Zn(II)(CysGly)(HisSer)] and [Zn(II)(CysGly)(HisPhe)] were shown by UV experiments, fluorescence titration, and gel electrophoresis to intercalate with DNA, and to hydrolytically cleave supercoiled DNA (form-I), partly also circular (form-II) DNA, under physiological conditions (37 degrees, H2O, pH 7.5).
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