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Shang J, Qiao Y, Mao G, Qian L, Liu G, Wang H. Bleomycin-Fe(II) agent with potentiality for treating drug-resistant H1N1 influenza virus: A study using electrochemical RNA beacons. Anal Chim Acta 2021; 1180:338862. [PMID: 34538316 DOI: 10.1016/j.aca.2021.338862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/27/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
Rapid emergence of new strains of drug-resistant H1N1 influenza viruses calls for effective drugs for the controls prior to their outbreaks. In the present work, electrochemical H1N1 RNA beacons have been newly designed for exploring the potentiality of an anticancer agent of Bleomycin (BLM) with Fe (ΙΙ) ions (BLM-Fe(ΙΙ)) alternatively the treatment of drug-resistant H1N1 strains with H274Y gene mutation. Herein, biotinylated (-) ssRNA of H1N1 virus and its complementary (+) ssRNA were labeled with electrochemical signal probes of ferrocene and anthraquinone, respectively. The resultants were hybridized and conjugated with avidin-modified magnetic beads to create electrochemical RNA beacons. The electrochemical signal variation of the H1N1 RNA beacon treated with the RNA degradation agent of BLM-Fe(ΙΙ) were monitored. Results indicate that the BLM-Fe(ΙΙ) agent could effectively cleave both H1N1 dsRNAs and ssRNAs at selective cutting sites, as evidenced by the mass spectrometry analysis. This indicates that the BLM-Fe(II) agent could be utilized to block the viral-host infection process by curbing the host-cell viral RNA-mRNA transcription or inactivate the viruses through the cleavage of viral genomes. The efficiency of the BLM-Fe(ΙΙ) agent was verified with clinical seasonal H1N1 samples using real-time polymerase chain reaction. The therapeutic gene drug of BLM-Fe(ΙΙ) holds great potential for controlling new strains of H1N1 virus resistant to clinical antiviral drugs. More importantly, the so designed RNA beacons may provide a rapid, sensitive and cost-effective platform of drug screening by monitoring the drug-DNA/RNA interactions.
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Affiliation(s)
- Jizhen Shang
- School of Life Sciences, Huzhou University, Huzhou, Zhejiang Province, 313000, PR China; College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong, 273165, PR China; Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuchun Qiao
- School of Life Sciences, Huzhou University, Huzhou, Zhejiang Province, 313000, PR China; College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong, 273165, PR China
| | - Guojiang Mao
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Key Laboratory of Green Chemical Media and Reactions, School of Chemistry and Chemical Engineering, Ministry of Education, Henan Normal University, Xinxiang, 453007, PR China
| | - Lisheng Qian
- Institute of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui, 233100, PR China.
| | - Guodong Liu
- Institute of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, Anhui, 233100, PR China.
| | - Hua Wang
- School of Life Sciences, Huzhou University, Huzhou, Zhejiang Province, 313000, PR China; College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong, 273165, PR China.
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Walton JC. Dissociations of free radicals to generate protons, electrophiles or nucleophiles: role in DNA strand breaks. Chem Soc Rev 2021; 50:7496-7512. [PMID: 34019058 DOI: 10.1039/d1cs00193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The concept behind the research described in this article was that of marrying the 'soft' methods of radical generation with the effectiveness and flexibility of nucleophile/electrophile synthetic procedures. Classic studies with pulse radiolysis and laser flash photolysis had shown that free radicals could be more acidic than their closed shell counterparts. QM computations harmonised with this and helped to define which radical centres and which structural types were most effective. Radicals based on the sulfonic acid moiety and on the Meldrum's acid moiety (2,2-dimethyl-1,3-dioxane-4,6-dione) were found to be extreme examples in the superacid class. The ethyne unit could be used as a very effective spacer between the radical centre and the site of proton donation. The key factor in promoting acidity was understood to be the thermodynamic stabilisation of the conjugate anion-radicals released on deprotonation. Solvation played a key part in promoting this and theoretical microhydration studies provided notable support. A corollary was that heterolytic dissociations of free radicals to yield either electrophiles or nucleophiles were also enhanced relative to non-radical models. The most effective radical types for spontaneous releases of both these types of reagents were identified. Ethyne units were again effective as spacers. The enhancement of release of phosphate anions by adjacent radical centres was an important special case. Reactive oxygen species and also diradicals from endiyne antibiotics generate C4'-deoxyribose radicals from nucleotides. Radicals of these types spontaneously release phosphate and triphosphate and this is a contributor to DNA and RNA strand breaks.
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Affiliation(s)
- John C Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, UK.
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Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
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Chitrapriya N, Shin JH, Hwang IH, Kim Y, Kim C, Kim SK. Synthesis, DNA binding profile and DNA cleavage pathway of divalent metal complexes. RSC Adv 2015. [DOI: 10.1039/c5ra10695h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Divalent metal complexes of dipyridylamine ligand with an anthracene moiety induced considerable oxidative DNA cleavage in the presence hydrogen peroxide and dioxygen.
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Affiliation(s)
| | - Jong Heon Shin
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
| | - In Hong Hwang
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Youngmee Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Republic of Korea
| | - Cheal Kim
- Department of Fine Chemistry and Department of Interdisciplinary Bio IT Materials
- Seoul National University of Science and Technology
- Seoul 139-743
- Republic of Korea
| | - Seog K. Kim
- Department of Chemistry
- Yeungnam University
- Gyeongsan
- Republic of Korea
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5
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Bozeman TC, Nanjunda R, Tang C, Liu Y, Segerman ZJ, Zaleski PA, Wilson WD, Hecht SM. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA. J Am Chem Soc 2012; 134:17842-5. [PMID: 23072568 PMCID: PMC3840713 DOI: 10.1021/ja306233e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.
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Affiliation(s)
- Trevor C. Bozeman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Chenhong Tang
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zachary J. Segerman
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul A. Zaleski
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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6
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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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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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Tao ZF, Konishi K, Keith G, Hecht SM. An Efficient Mammalian Transfer RNA Target for Bleomycin. J Am Chem Soc 2006; 128:14806-7. [PMID: 17105281 DOI: 10.1021/ja066187x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The antitumor antibiotic bleomycin has long been believed to exert its therapeutic effects at the level of DNA cleavage. Recently, evidence has been presented to suggest that RNA cleavage may also be important and that one or more transfer RNAs may be involved. To define those tRNAs that may represent important loci for the action of bleomycin, we have fractionated chicken liver tRNAs and identified those isoacceptors most susceptible to oxidative cleavage by Fe(II).BLM. Two chicken liver tRNAs, tRNA3Lys and tRNAPhe, were found to be cleaved with exceptional facility by Fe(II).BLM, and both were cleaved predominantly at U66. The cleavage of tRNA3Lys was shown to be minimally affected by physiological concentrations of Mg2+. Chicken liver tRNA3Lys is identical in sequence with human tRNA3Lys. These findings support a possible role for a critical tRNA such as tRNA3Lys in the mechanism by which bleomycin mediates its antitumor activity.
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Affiliation(s)
- Zhi-Fu Tao
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, USA
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9
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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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10
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Abstract
DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
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Affiliation(s)
- John SantaLucia
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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Papakyriakou A, Mouzopoulou B, Katsaros N. The solution structure of the Ga(III)-bleomycin A2 complex resolved by NMR and molecular modeling; interaction with d(CCAGGCCTGG). J Biol Inorg Chem 2003; 8:549-559. [PMID: 12632272 DOI: 10.1007/s00775-003-0448-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Accepted: 01/23/2003] [Indexed: 10/18/2022]
Abstract
The solution structure of the Ga(III)-bleomycin A2 complex (GaBLM) has been determined using 2D NMR methods in combination with molecular dynamics calculations. Complete assignment of the amide and amine protons, observation of 80 NOEs and measurement of 15 (3)JH(-H) coupling constants provided us with a well-defined structure using a restrained simulated annealing protocol. On the basis of distance and dihedral angle constraints agreement, along with potential energy considerations, the favored model is a five-coordinate complex with the primary amine of beta-aminoalanine holding the axial position of a distorted tetragonal pyramid. The disaccharide moiety of GaBLM is not a ligand, sharing the same side of the equatorial plane with the axial amine ligand. Titration of the self-complementary oligonucleotide d(CCAGGCCTGG) with GaBLM results in the formation of only one 1:1 complex in slow exchange on the NMR time scale. Our data indicate that the bithiazole moiety intercalates between the C6*G15 and C7*G14 base pairs, in a similar mode to that reported by earlier studies. Structural implications and comparisons to other metallo-bleomycins are discussed.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute of Physical Chemistry, NCSR "Demokritos", 153-10 Ag. Paraskevi Attikis, Athens, Greece
| | - Barbara Mouzopoulou
- Institute of Physical Chemistry, NCSR "Demokritos", 153-10 Ag. Paraskevi Attikis, Athens, Greece
| | - Nikos Katsaros
- Institute of Physical Chemistry, NCSR "Demokritos", 153-10 Ag. Paraskevi Attikis, Athens, Greece.
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12
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Nonekowski ST, Kung FL, Garcia GA. The Escherichia coli tRNA-guanine transglycosylase can recognize and modify DNA. J Biol Chem 2002; 277:7178-82. [PMID: 11751936 DOI: 10.1074/jbc.m111077200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNA-guanine transglycosylase (TGT) catalyzes the exchange of queuine (or a precursor) for guanine 34 in tRNA. The minimal RNA recognition motif for TGT has been found to involve a UGU sequence in the anticodon loop of the queuine-cognate tRNAs. Recent studies have shown that the enzyme is capable of recognizing the UGU sequence in alternative contexts (Kung, F. L., Nonekowski, S., and Garcia, G. A. (2000) RNA 6, 233-244) and have investigated the role of the first U of the UGU sequence in tRNA recognition by TGT (Nonekowski, S. T., and Garcia, G. A. (2001) RNA 7, 1432-1441). The TGT reaction involves the breakage and re-formation of a glycosidic bond. To rule out a potential chemical mechanism involving the 2'-hydroxyl at position 34, we synthesized and evaluated an RNA minihelix with 2'-deoxy-G at 34. The high level of activity exhibited by this analogue indicates that the 2'-hydroxyl of G(34) is not required for catalysis. Furthermore, we find that TGT can recognize analogues composed entirely of DNA, but only when 2'-deoxyuridines replace the thymidines in the DNA. The requirement for uridine bases for recognition is perhaps not surprising given the UGU recognition motif for TGT. However, it is not clear if the uracil requirement is due to specific recognition by TGT or due to the effect of uracils on the conformation of the oligonucleotide.
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Affiliation(s)
- Susanne T Nonekowski
- Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-1065, USA
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13
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Rajani C, Kincaid JR, Petering DH. Raman spectroscopy of an O(2)-Co(II)bleomycin-calf thymus DNA adduct: alternate polymer conformations. Biophys Chem 2001; 94:219-36. [PMID: 11804732 DOI: 10.1016/s0301-4622(01)00237-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bleomycin (Blm) is an antitumor agent which binds to specific sequences of DNA and as HO(2)-Fe(III)Blm causes single and double strand cleavage. In the present investigation, binding of O(2)-Co(II)Blm to a native DNA polymer, calf thymus DNA, was examined using conventional Raman spectroscopy. O(2)-Co(II)Blm is a model for O(2)-Fe(II)Blm, the direct precursor of HO(2)-Fe(III)Blm. Although the DNA polymer retained a predominant B-form structure, Raman spectral evidence was obtained for localized structural changes to A, C and Z-DNA forms. The presence of these alternate DNA forms within B-DNA implied the presence of B/A, B/C and B/Z junctions. The observed changes in DNA secondary structure were attributed to perturbation of structural water resulting from binding of O(2)-Co(II)Blm within the minor groove.
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Affiliation(s)
- C Rajani
- Department of Chemistry, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53211, USA
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Thorp HH. The importance of being r: greater oxidative stability of RNA compared with DNA. CHEMISTRY & BIOLOGY 2000; 7:R33-6. [PMID: 10662699 DOI: 10.1016/s1074-5521(00)00080-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The 2'-hydroxyl group of ribose imparts hydrolytic lability on RNA, which provides a mechanism for numerous biological functions. Recent evidence from chemical cleavage studies shows that this hydroxyl group also stabilizes the sugar moiety in RNA towards oxidation relative to DNA. Is this just because RNA needs to be distinguishable from DNA or does it have other evolutionary significance?
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Affiliation(s)
- H H Thorp
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
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Das GK, Bhattacharyya D, Burma DP. A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase. J Theor Biol 1999; 200:193-205. [PMID: 10504285 DOI: 10.1006/jtbi.1999.0987] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosome, the ubiquitous organelle, is the site for protein synthesis in all types of cells. The consecutive peptide bonds are formed by the transpeptidation reaction between carboxyl group of peptidyl moiety and the amino group of the aminoacyl moiety. Both the moieties are attached to the appropiate tRNAs positioned on the ribosome at P and A sites, respectively, through codon-anticodon recognition directed by messenger RNA. The reaction seems to proceed by the nucleophillic attack of the amino group of the aminoacyl tRNA at the A site and on the carboxyl of the ester group of the tRNA at P-site of ribosome. The configuration of the carbon atom of the tetrahedral intermediate may be R or S depending on the direction of the nucleophillic attack. After selecting the favorable conformation of this tetrahedral intermediate quantum mechanical calculations have been carried out to determine the energy needed for its formation. A cyclic intermediate where 2'-OH of the ribose sugar of the P-site tRNA is a member of the ring can be formed from the tetrahedral intermediate. This cyclic intermediate produces a free tRNA and a tRNA attached to a planar peptide unit. Analysis of the energetics using semiempirical method for the formation of a cyclic intermediate indicates that the peptide bond formation through the tetrahedral intermediate in S configuration may not need assistance from any outside agent like an enzyme
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Affiliation(s)
- G K Das
- Department of Chemistry, Visva-Bharati, Santiniketan, 731235, India
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Strittmatter H, Dussy A, Schwitter U, Giese B. Unterschiede zwischen 4′-RNA- und 4′-DNA-Radikalen beim anaeroben und aeroben Strangbruch. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990115)111:1/2<238::aid-ange238>3.0.co;2-j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Ciftan SA, Theil EC, Thorp HH. Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies. CHEMISTRY & BIOLOGY 1998; 5:679-87. [PMID: 9862796 DOI: 10.1016/s1074-5521(98)90661-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms. RESULTS Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern. CONCLUSIONS The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.
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Affiliation(s)
- S A Ciftan
- Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599-3290 USA
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Katano K, An H, Aoyagi Y, Overhand M, Sucheck SJ, Stevens WC, Hess CD, Zhou X, Hecht SM. Total Synthesis of Bleomycin Group Antibiotics. Total Syntheses of Bleomycin Demethyl A2, Bleomycin A2, and Decarbamoyl Bleomycin Demethyl A2. J Am Chem Soc 1998. [DOI: 10.1021/ja9819458] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kiyoaki Katano
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Haoyun An
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Yoshiaki Aoyagi
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Mark Overhand
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Steven J. Sucheck
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - William C. Stevens
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Cynthia D. Hess
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Xiang Zhou
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
| | - Sidney M. Hecht
- Contribution from the Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901
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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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21
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Beckwith ALJ, Crich D, Duggan PJ, Yao Q. Chemistry of beta-(Acyloxy)alkyl and beta-(Phosphatoxy)alkyl Radicals and Related Species: Radical and Radical Ionic Migrations and Fragmentations of Carbonminus signOxygen Bonds. Chem Rev 1997; 97:3273-3312. [PMID: 11851491 DOI: 10.1021/cr950207o] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Athelstan L. J. Beckwith
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia, Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, and Department of Chemistry, Monash University, Clayton, Victoria 3168, Australia
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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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23
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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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24
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Xu H, Johnston S. Yeast bleomycin hydrolase is a DNA-binding cysteine protease. Identification, purification, biochemical characterization. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31945-2] [Citation(s) in RCA: 14] [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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25
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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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