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Sergeyev DS, Zarytova VF. Interaction of bleomycin and its oligonucleotide derivatives with nucleic acids. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1996v065n04abeh000216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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2
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Ma Q, Xu Z, Schroeder BR, Sun W, Wei F, Hashimoto S, Konishi K, Leitheiser CJ, Hecht SM. Biochemical evaluation of a 108-member deglycobleomycin library: viability of a selection strategy for identifying bleomycin analogues with altered properties. J Am Chem Soc 2007; 129:12439-52. [PMID: 17887752 DOI: 10.1021/ja0722729] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycins (BLMs) are clinically used glycopeptide antitumor antibiotics that have been shown to mediate the sequence-selective oxidative damage of both DNA and RNA. Previously, we described the solid-phase synthesis of a library of 108 unique analogues of deglycoBLM A6, a congener that cleaves DNA analogously to BLM itself. Each member of the library was assayed for its ability to effect single- and double-strand nicking of duplex DNA, sequence-selective DNA cleavage, and RNA cleavage in the presence and absence of a metal ion cofactor. All of the analogues tested were found to mediate concentration-dependent plasmid DNA relaxation to some extent, and a number exhibited double-strand cleavage with an efficiency comparable to or greater than deglycoBLM A6. Further, some analogues having altered linker and metal-binding domains mediated altered sequence-selective cleavage, and a few were found to cleave a tRNA3Lys transcript both in the presence and in the absence of a metal cofactor. The results provide insights into structural elements within BLM that control DNA and RNA cleavage. The present study also permits inferences to be drawn regarding the practicality of a selection strategy for the solid-phase construction and evaluation of large libraries of BLM analogues having altered properties.
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Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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3
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Calafat AM, Marzilli LG. Chiralities of Complexes of BleomycirvType Ligands, a Neglected Feature in Structural Studies Relevant to Anticancer Drug Action. COMMENT INORG CHEM 2006. [DOI: 10.1080/02603599808012255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Vivekananda S, Sadílek M, Chen X, Adams LE, Turecek F. Modeling deoxyribose radicals by neutralization-reionization mass spectrometry. Part 2. Preparation, dissociations, and energetics of 3-hydroxyoxolan-3-yl radical and cation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1068-1079. [PMID: 15234365 DOI: 10.1016/j.jasms.2004.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 03/29/2004] [Accepted: 03/29/2004] [Indexed: 05/24/2023]
Abstract
The title radical (1) is generated in the gas-phase by collisional neutralization of carbonyl-protonated oxolan-3-one. A 1.5% fraction of 1 does not dissociate and is detected following reionization as survivor ions. The major dissociation of 1 (approximately 56%) occurs as loss of the hydroxyl H atom forming oxolan-3-one (2). The competing ring cleavages by O[bond]C-2 and C-4[bond]C-5 bond dissociations combined account for approximately 42% of dissociation and result in the formation of formaldehyde and 2-hydroxyallyl radical. Additional ring-cleavage dissociations of 1 resulting in the formation of C(2)H(3)O and C(2)H(4)O cannot be explained as occurring competitively on the doublet ground (X) electronic state of 1, but are energetically accessible from the A and higher electronic states accessed by vertical electron transfer. Exothermic protonation of 2 also produces 3-oxo-(1H)-oxolanium cation (3(+)) which upon collisional neutralization gives hypervalent 3-oxo-(1H)-oxolanium radical (3). The latter dissociates spontaneously by ring opening and expulsion of hydroxy radical. Experiment and calculations suggest that carbohydrate radicals incorporating the 3-hydroxyoxolan-3-yl motif will prefer ring-cleavage dissociations at low internal energies or upon photoexcitation by absorbing light at approximately 590 and approximately 400 nm.
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Meunier S, Desage-El Murr M, Nowaczyk S, Le Gall T, Pin S, Renault JP, Boquet D, Créminon C, Saint-Aman E, Valleix A, Taran F, Mioskowski C. A Powerful Antiradiation Compound Revealed by a New High-Throughput Screening Method. Chembiochem 2004; 5:832-40. [PMID: 15174167 DOI: 10.1002/cbic.200300787] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a new high-throughput screening method for the selection of powerful water-soluble antiradiation compounds. This method, which uses conventional immunoassay techniques, allowed the capacity of a given compound to protect thymidine from irradiation to be evaluated. By applying this assay to an antioxidant library, we showed for the first time that norbadione A, a well-known mushroom pigment, has pronounced atypical antiradiation properties.
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Affiliation(s)
- Stéphane Meunier
- Service de Marquage Moléculaire et de Chimie Bio-Organique, DBJC/DSV CEA Saclay, 91191 Gif sur Yvette Cedex, France
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6
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Kelly JJ, Chernov BK, Tovstanovsky I, Mirzabekov AD, Bavykin SG. Radical-generating coordination complexes as tools for rapid and effective fragmentation and fluorescent labeling of nucleic acids for microchip hybridization. Anal Biochem 2002; 311:103-18. [PMID: 12470669 DOI: 10.1016/s0003-2697(02)00388-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA microchip technology is a rapid, high-throughput method for nucleic acid hybridization reactions. This technology requires random fragmentation and fluorescent labeling of target nucleic acids prior to hybridization. Radical-generating coordination complexes, such as 1,10-phenanthroline-Cu(II) (OP-Cu) and Fe(II)-EDTA (Fe-EDTA), have been commonly used as sequence nonspecific "chemical nucleases" to introduce single-strand breaks in nucleic acids. Here we describe a new method based on these radical-generating complexes for random fragmentation and labeling of both single- and double-stranded forms of RNA and DNA. Nucleic acids labeled with the OP-Cu and the Fe-EDTA protocols revealed high hybridization specificity in hybridization with DNA microchips containing oligonucleotide probes selected for identification of 16S rRNA sequences of the Bacillus group microorganisms. We also demonstrated cDNA- and cRNA-labeling and fragmentation with this method. Both the OP-Cu and Fe-EDTA fragmentation and labeling procedures are quick and inexpensive compared to other commonly used methods. A column-based version of the described method does not require centrifugation and therefore is promising for the automation of sample preparations in DNA microchip technology as well as in other nucleic acid hybridization studies.
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Affiliation(s)
- John J Kelly
- Northwestern University, Department of Civil Engineering, 2145 Sheridan Road, Evanston, IL 60208, USA
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7
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Zou Y, Fahmi NE, Vialas C, Miller GM, Hecht SM. Total synthesis of deamido bleomycin a(2), the major catabolite of the antitumor agent bleomycin. J Am Chem Soc 2002; 124:9476-88. [PMID: 12167044 DOI: 10.1021/ja012741l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic inactivation of the antitumor antibiotic bleomycin is believed to be mediated exclusively via the action of bleomycin hydrolase, a cysteine proteinase that is widely distributed in nature. While the spectrum of antitumor activity exhibited by the bleomycins is believed to reflect the anatomical distribution of bleomycin hydrolase within the host, little has been done to characterize the product of the putative inactivation at a chemical or biochemical level. The present report describes the synthesis of deamidobleomycin demethyl A(2) (3) and deamido bleomycin A(2) (4), as well as the respective aglycones. These compounds were all accessible via the key intermediate N(alpha)-Boc-N(beta)-[1-amino-3(S)-(4-amino-6-carboxy-5-methylpyrimidin-2-yl)propion-3-yl]-(S)-beta-aminoalanine tert-butyl ester (16). Synthetic deamido bleomycin A(2) was shown to be identical to the product formed by treatment of bleomycin A(2) with human bleomycin hydrolase, as judged by reversed-phase HPLC analysis and (1)H NMR spectroscopy. Deamido bleomycin A(2) was found to retain significant DNA cleavage activity in DNA plasmid relaxation assays and had the same sequence selectivity of DNA cleavage as bleomycin A(2). The most significant alteration of function noted in this study was a reduction in the ability of deamido bleomycin A(2) to mediate double-strand DNA cleavage, relative to that produced by BLM A(2).
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Affiliation(s)
- Ying Zou
- Contribution from the Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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8
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Bose RN, Moghaddas S, Mazzer PA, Dudones LP, Joudah L, Stroup D. Oxidative damage of DNA by chromium(V) complexes: relative importance of base versus sugar oxidation. Nucleic Acids Res 1999; 27:2219-26. [PMID: 10219096 PMCID: PMC148443 DOI: 10.1093/nar/27.10.2219] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chromium(V)-mediated oxidative damage of deoxy-ribonucleic acids was investigated at neutral pH in aqueous solution by utilizing bis(2-ethyl-2-hydroxy-butanato)oxochromate(V) (I) and bis(hydroxyethyl)-amino-tris(hydroxymethyl)methane)oxochromate(V) (II). Single-stranded and double-stranded (ds) calf thymus and human placenta DNA, as well as two oligomers, 5'-GATCTAGTAGGAGGACAAATAGTGTTTG-3' and 5'-GATCCAAGCAAACACTATTTGTCCTCCTACTA-3', were reacted with the chromium(V) complexes. Most products were separated and characterized by chroma-tographic and spectroscopic methods. Polyacrylamide gel electrophoresis experiments reveal more damage at G sites in comparison to other bases. Three primary oxidation products, 5-methylene-2-furanone (5-MF), furfural and 8-oxo-2'-deoxyguanosine, were characterized. A minor product, which appears to be thymine propenal, was also observed. The dsDNA produces more furfural than furanone. The formation of these two products resulted from hydrogen ion or hydride transfer from C1' and C5' positions of the ribose to the oxo-chromium(V) center. Since no enhancements of these products (except propenal) were observed in the presence of oxygen, mechanisms pertaining to the participation of activated oxygen species may be ruled out. The oxidation of the G base is most likely associated with an oxygen atom transfer from the oxo-metallates to the double bond between C8 and N7 of the purine ring. The formation of the propenal may be associated with an oxygen-activated species, since a marginal enhancement of this product was observed in the presence of oxygen. The formation of furfural in higher abundance over 5-MF for dsDNA was attributed to the ease of hydrogen ion (or hydride transfer) from the C5' compared to C1' position of the ribose within a Cr(V)-DNA intermediate in which the metal center is bound to the phosphate diester moiety.
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Affiliation(s)
- R N Bose
- Department of Chemistry, Kent State University, Kent, OH 44242, USA.
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Kittaka A, Kato H, Tanaka H, Nonaka Y, Amano M, Nakamura KT, Miyasaka T. Face selective 6,1′-(1-oxo)ethano bridge formation of uracil nucleosides under hypoiodite reaction conditions. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00232-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pogozelski WK, Tullius TD. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chem Rev 1998; 98:1089-1108. [PMID: 11848926 DOI: 10.1021/cr960437i] [Citation(s) in RCA: 841] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wendy Knapp Pogozelski
- Department of Chemistry, State University of New York at Geneseo, Geneseo, New York 14454, and Department of Chemistry, Boston University, Boston, Massachusetts 02215
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12
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Affiliation(s)
- Richard M. Burger
- Public Health Research Institute, 455 First Avenue, New York, New York 10016
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Holmes CE, Duff RJ, van der Marel GA, van Boom J, Hecht SM. On the chemistry of RNA degradation by Fe.bleomycin. Bioorg Med Chem 1997; 5:1235-48. [PMID: 9222517 DOI: 10.1016/s0968-0896(97)00038-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The chemistry of RNA degradation by Fe.bleomycin was studied using two RNA substrates that are modified efficiently at a small number of sites by the antitumor antibiotic. Cleavage of tRNAHis precursor transcript by Fe(II).BLM A2 was shown to require O2; cleavage was also observed when the same substrate was treated with Fe(III).BLM A2 + H2O2. Consistent with earlier observations made for DNA, the extent of tRNAHis precursor cleavage was greater for Fe(II).BLM A5 than for Fe(II).BLM A2; the least cleavage was obtained using Fe(II).BLM demethyl A2. By the use of 32P end labeled tRNAHis precursor transcript that was also 3H labeled within the uracil moieties, it was shown that release of uracil was nearly stoichiometric with tRNA strand scission by Fe(II).BLM A2. Nonetheless, treatment of the tRNAHis with hydrazine following BLM-mediated cleavage indicated formation of a new product that must have derived from a BLM-induced lesion. Also employed for characterization of BLM cleavage of RNA were the octanucleotides CGCTAGCG, C3-ribo-CGCTAGCG and C3-ara-CGCTAGCG. Analysis of the products of cleavage indicates that Fe.BLM is capable of mediating cleavage by abstraction of a H atom either from C-4' H or c-1' H of the chimeric oligonucleotides.
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Affiliation(s)
- C E Holmes
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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Greenberg MM, Barvian MR, Cook GP, Goodman BK, Matray TJ, Tronche C, Venkatesan H. DNA Damage Induced via 5,6-Dihydrothymid-5-yl in Single-Stranded Oligonucleotides. J Am Chem Soc 1997. [DOI: 10.1021/ja9533510] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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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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Goodman BK, Greenberg MM. Independent Generation and Reactivity of 2‘-Deoxyurid-1‘-yl. J Org Chem 1996. [DOI: 10.1021/jo951769a] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gimisis T, Ialongo G, Zamboni M, Chatgilialoglu C. Radical transformations of nucleosides with (Me3Si)3SiH. Generation of a C-1’ radical through 1,2-migration of an acyloxy group. Tetrahedron Lett 1995. [DOI: 10.1016/00404-0399(50)1340-n] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pratviel G, Bernadou J, Meunier B. Die CH-Bindungen der Zuckerbausteine von DNA als Angriffspunkte für chemische Nucleasen und Wirkstoffe. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951070705] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Electron-, Energy-, and Atom-Transfer Reactions Between Metal Complexes and Dna. ADVANCES IN INORGANIC CHEMISTRY 1995. [DOI: 10.1016/s0898-8838(08)60117-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Abstract
The effect of iron(II) bleomycin on a DNA-RNA heteroduplex was investigated using a substrate formed by reverse transcription of Escherichia coli 5S ribosomal RNA. Both strands of the heteroduplex were cleaved by FeII.BLM A2 at comparable concentrations; complete digestion of both strands was observed using 5 microM FeII.BLM A2. The DNA strand of the heteroduplex was cleaved predominantly at 5'-G-pyr-3' sites; the sites of cleavage of the DNA strand were a subset of those observed for the corresponding DNA strand of a DNA duplex of identical sequence. The sites of cleavage of the RNA strand of the heteroduplex involved both purines and pyrimidines and were found to be different than the sites of cleavage of the 5S rRNA alone, demonstrating that cleavage of the former must actually have involved heteroduplex recognition by FeII.BLM A2. Both the DNA and RNA strands of the heteroduplex were cleaved by FeII.BLM A2 in the presence of physiological concentrations of Mg2+, consistent with the possibility that DNA-RNA heteroduplexes may be therapeutically relevant targets for bleomycin.
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MESH Headings
- Base Sequence
- Binding Sites
- Bleomycin/chemistry
- Bleomycin/pharmacology
- DNA, Bacterial/chemistry
- DNA, Bacterial/drug effects
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/drug effects
- DNA, Ribosomal/genetics
- Escherichia coli/genetics
- Molecular Sequence Data
- Molecular Structure
- Nucleic Acid Heteroduplexes/chemistry
- Nucleic Acid Heteroduplexes/drug effects
- Nucleic Acid Heteroduplexes/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/drug effects
- RNA, Bacterial/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/drug effects
- RNA, Ribosomal, 5S/genetics
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Affiliation(s)
- M A Morgan
- Department of Chemistry, University of Virginia, Charlottesville 22901
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Kane SA, Hecht SM. Polynucleotide recognition and degradation by bleomycin. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 49:313-52. [PMID: 7532315 DOI: 10.1016/s0079-6603(08)60054-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- S A Kane
- Department of Chemistry, University of Virginia, Charlottesville 22901
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Holmes CE, Hecht SM. Fe.bleomycin cleaves a transfer RNA precursor and its “transfer DNA” analog at the same major site. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74473-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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