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Stachelska-Wierzchowska A, Wieczorek ZJ. Hydrolysis of 5',5'-tri- or tetraphosphate-mRNA 5'-cap analogs promoted by Cu2+ or Zn2+ metal ions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:135-48. [PMID: 21360411 DOI: 10.1080/15257770.2010.551722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Kinetics of the hydrolysis of a P(1)-(7-methylguanosinyl-5') P(3)-(guanosinyl-5') triphosphate (m(7)GpppG), P(1)-(7-methylguanosinyl-5') P(4)- (guanosinyl-5') tetraphosphate (m(7)GppppG), diadenosine-5',5'''-P(1),P(3)-triphosphate (ApppA), and diadenosine-5',5'''-P(1),P(4)-tetraphosphate (AppppA) promoted by Cu(2+) or Zn(2+) has been investigated. Time-dependent products distributions at various metal ion concentrations have been determined by CZE and HPLC-RP. The results show that in acidic conditions, in the presence of metal ion, the predominant hydrolytic reaction is the cleavage of 5',5'-oligophosphate bridge. The 5',5'-oligophosphate bridge of the dinucleotides studied is hydrolyzed by Cu(2+) more efficiently than by Zn(2+). At the catalyst concentration of 2 mM the cleavage of the 5',5'-triphosphate bridge of m(7)GpppG was ∼3.6 times faster, and that of the tetraphosphate bridge of m(7)GppppG ∼2.3-fold faster in the presence of Cu(2+) compared to the Zn(2+) ion, applied as catalysts. Dependence of the rates of hydrolysis on the catalyst concentration was in some instances not linear, interpreted as evidence for participation of more than one metal ion in the transition complex.
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Delehanty JB, Stuart TC, Knight DA, Goldman ER, Thach DC, Bongard JE, Chang EL. RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex. RNA (NEW YORK, N.Y.) 2005; 11:831-836. [PMID: 15840822 PMCID: PMC1370767 DOI: 10.1261/rna.7156805] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 01/18/2005] [Indexed: 05/24/2023]
Abstract
Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.
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Affiliation(s)
- James B Delehanty
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
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Manoharan M. Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2002; 12:103-28. [PMID: 12074364 DOI: 10.1089/108729002760070849] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.
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Affiliation(s)
- Muthiah Manoharan
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc, Carlsbad, CA 92008, USA.
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Abstract
Over the last few years the genes responsible for a number of genetic diseases of the cardiovascular system have been identified. These have included X-linked and autosomal dominant dilated cardiomyopathy, and hypertrophic cardiomyopathy. Genetic heterogeneity has been described in both of these diseases but a commonality of function has been apparent: defects in cytoskeletal proteins cause dilated cardiomyopathy and mutations in sarcomeric proteins cause hypertrophic cardiomyopathy. This led us to develop a 'final common pathway' hypothesis as a framework for selecting candidate genes for mutation screening in families with these diseases. The characterization of gene mutations has led to the development of therapies specifically targeting the defective protein or the pathway in which it is involved. These have included the use of pharmaceutical agents to replace or to antagonize the mutated protein, and replacement of the defective gene with a functional one (gene therapy). While early studies using gene therapy vectors were promising, translating studies in animals to viable therapeutic options for humans has remained problematic. There have been many publications describing the use of vectors to transduce target cells for the correction of gene defects, including recombinant retroviruses, adenoviruses, and adeno-associated viruses, as well as non-viral vectors. In this review we will discuss the identification of gene defects associated with cardiomyopathies, and the potential of gene therapy for the treatment of these diseases, as well as addressing some concerns related to the use of adenovirus-based vectors, a virus known to be an etiologic agent of acquired dilated cardiomyopathy.
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Jenkins LA, Bashkin JK, Pennock JD, Florián J, Warshel A. Catalytic Hydrolysis of Adenosine 2‘,3‘-Cyclic Monophosphate by CuII Terpyridine. Inorg Chem 1999. [DOI: 10.1021/ic990228r] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisa A. Jenkins
- Department of Chemistry, Washington University, Box 1134, 1 Brookings Drive, St. Louis, Missouri 63130-4899, and Department Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - James K. Bashkin
- Department of Chemistry, Washington University, Box 1134, 1 Brookings Drive, St. Louis, Missouri 63130-4899, and Department Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Jennifer D. Pennock
- Department of Chemistry, Washington University, Box 1134, 1 Brookings Drive, St. Louis, Missouri 63130-4899, and Department Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Jan Florián
- Department of Chemistry, Washington University, Box 1134, 1 Brookings Drive, St. Louis, Missouri 63130-4899, and Department Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Arieh Warshel
- Department of Chemistry, Washington University, Box 1134, 1 Brookings Drive, St. Louis, Missouri 63130-4899, and Department Chemistry, University of Southern California, Los Angeles, California 90089-1062
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Trawick BN, Daniher AT, Bashkin JK. Inorganic Mimics of Ribonucleases and Ribozymes: From Random Cleavage to Sequence-Specific Chemistry to Catalytic Antisense Drugs. Chem Rev 1998; 98:939-960. [PMID: 11848920 DOI: 10.1021/cr960422k] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bobby N. Trawick
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
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Oivanen M, Kuusela S, Lönnberg H. Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases. Chem Rev 1998; 98:961-990. [PMID: 11848921 DOI: 10.1021/cr960425x] [Citation(s) in RCA: 358] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikko Oivanen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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Daniher AT, Xie J, Mathur S, Bashkin JK. Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects. Bioorg Med Chem 1997; 5:1037-42. [PMID: 9222496 DOI: 10.1016/s0968-0896(97)00040-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have previously prepared ribozyme mimics and chemical nucleases from modified DNA containing pendant bipyridine and terpyridine groups. The ability of these modified DNA probes to support RNase H cleavage of complementary RNA is described. DNA/RNA duplexes were formed using DNA probes designed to deliver metal complexes via either the major groove or the minor groove of the duplex. The duplexes were treated with Escherichia coli RNase H. Modifications in the major groove produced the same RNA cleavage pattern as unmodified DNA probes. However, minor groove substituents inhibited RNA cleavage over a four-base region. Comparison was made with a DNA probe containing a 2'-OMe modification. Our results support enzyme binding in the minor groove of a DNA/RNA duplex. We do not observe cleavage directly across from the modified nucleoside. The RNA cleavage efficiency effected by RNase H and a DNA probe decreases as follows: unmodified DNA > or = C-5 modified DNA >> c2'-modified DNA > C1'-modified DNA. Results with 28-mer RNA substrates roughly parallel those obtained with a 159-mer RNA target. The differences observed between low and high MW RNA substrates can be explained by a much higher enzyme-substrate binding constant for the high MW target.
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Affiliation(s)
- A T Daniher
- Department of Chemistry, Washington University, St Louis, MO 63130, USA
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Corey MJ, Corey E. On the failure of de novo-designed peptides as biocatalysts. Proc Natl Acad Sci U S A 1996; 93:11428-34. [PMID: 8876152 PMCID: PMC38074 DOI: 10.1073/pnas.93.21.11428] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
While the elegance and efficiency of enzymatic catalysis have long tempted chemists and biochemists with reductionist leanings to try to mimic the functions of natural enzymes in much smaller peptides, such efforts have only rarely produced catalysts with biologically interesting properties. However, the advent of genetic engineering and hybridoma technology and the discovery of catalytic RNA have led to new and very promising alternative means of biocatalyst development. Synthetic chemists have also had some success in creating nonpeptide catalysts with certain enzyme-like characteristics, although their rates and specificities are generally much poorer than those exhibited by the best novel biocatalysts based on natural structures. A comparison of the various approaches from theoretical and practical viewpoints is presented. It is suggested that, given our current level of understanding, the most fruitful methods may incorporate both iterative selection strategies and rationally chosen small perturbations, superimposed on frameworks designed by nature.
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Affiliation(s)
- M J Corey
- Urology Department, University of Washington School of Medicine, Seattle 98195, USA
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Jenkins LA, Bashkin JK, Autry ME. The Embedded Ribonucleotide Assay: A Chimeric Substrate for Studying Cleavage of RNA by Transesterification. J Am Chem Soc 1996. [DOI: 10.1021/ja960191z] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisa A. Jenkins
- Contribution from the Department of Chemistry, Washington University, Campus Box 1134, 1 Brookings Drive, St. Louis Missouri 63130
| | - James K. Bashkin
- Contribution from the Department of Chemistry, Washington University, Campus Box 1134, 1 Brookings Drive, St. Louis Missouri 63130
| | - Mark E. Autry
- Contribution from the Department of Chemistry, Washington University, Campus Box 1134, 1 Brookings Drive, St. Louis Missouri 63130
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Bashkin JK, Xie J, Daniher AT, Sampath U, Kao JLF. Building Blocks for Ribozyme Mimics: Conjugates of Terpyridine and Bipyridine with Nucleosides. J Org Chem 1996. [DOI: 10.1021/jo9518213] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James K. Bashkin
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899
| | - Jin Xie
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899
| | - Andrew T. Daniher
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899
| | - UmaShanker Sampath
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899
| | - Jeffrey L.-F. Kao
- Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899
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Kuusela S, Guzaev A, Lönnberg H. Acceleration of the Zn2+-promoted phosphodiester hydrolysis of oligonucleotides by the 3′-terminal monophosphate group: intrastrand participation over several nucleoside units. ACTA ACUST UNITED AC 1996. [DOI: 10.1039/p29960001895] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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