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Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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2
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Amato NJ, Wang Y. Epimeric 2-deoxyribose lesions: Products from the improper chemical repair of 2-deoxyribose radicals. Chem Res Toxicol 2014; 27:470-9. [PMID: 24517165 PMCID: PMC4002128 DOI: 10.1021/tx400430g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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Genomic
integrity is constantly challenged by DNA damaging agents
such as reactive oxygen species (ROS). Consequently, DNA damage can
compromise the fidelity and efficiency of essential DNA metabolic
processes, including replication and transcription, which may contribute
significantly to the etiology of many human diseases. Here, we review
one family of DNA lesions, the epimeric 2-deoxyribose lesions, which
arise from the improper chemical repair of the 2-deoxyribose radicals.
Unlike most other DNA lesions, the epimeric 2-deoxyribose lesions
are indistinguishable from their corresponding unmodified nucleosides
in both molecular mass and chemical reactivity. We placed our emphasis
of discussion on the formation of these lesions, their impact on the
structure and stability of duplex DNA, their biological consequences,
their potential therapeutic relevance, and future research directions
about these modified nucleosides.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, University of California , 900 University Avenue, Riverside, California 92521, United States
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3
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Amato NJ, Bryant-Friedrich AC. The impact of structure on oxidatively generated DNA damage products resulting from the C3'-thymidinyl radical. Chembiochem 2012; 14:187-90. [PMID: 23280951 DOI: 10.1002/cbic.201200723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Indexed: 11/05/2022]
Abstract
What's the damage? Trapping the C3'-thymidinyl radical in biologically significant architectures delivers both the repaired oligomer and 1-(2'-deoxy-β-D-threo-pentofuranosyl)thymidine-containing substrates. The stereoselectivity of the reduction was found to be dependent upon the DNA structure.
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Affiliation(s)
- Nicholas J Amato
- Department of Chemistry, The University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606-3390, USA
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4
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Fate of DNA Sugar Radicals. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1872-0854(10)04004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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5
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Minakawa N, Ogata S, Takahashi M, Matsuda A. Selective recognition of unnatural imidazopyridopyrimidine:naphthyridine base pairs consisting of four hydrogen bonds by the Klenow fragment. J Am Chem Soc 2009; 131:1644-5. [PMID: 19146369 DOI: 10.1021/ja807391g] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we investigated how thermally stable ImO(N):NaN(O) and ImN(O):NaO(N) pairs are recognized by the Klenow fragment (KF). As a result, these complementary base pairs, especially the ImN(O):NaO(N) pair, were recognized selectively due to the four hydrogen bonds between the nucleobases and the shape complementarity of the Im:Na pair similar to the purine:pyrimidine base pair.
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Affiliation(s)
- Noriaki Minakawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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6
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Abstract
Phototriggered bod cleavage has found wide application in chemistry as well as in biology. Nevertheless, there are only a few methods available for site-specific photochemical induction of DNA strand scission despite numerous potential applications. In this study we report the development of new photocleavable nucleotides based on the photochemistry of o-nitrobenzyl esters. The light-sensitive moieties were generated through introduction of o-nitrophenyl groups at the 5'C position of the nucleoside sugar backbone. The newly synthesized, modified nucleosides were incorporated in oligonucleotides and are able to build stable DNA duplexes. In such a way modified oligonucleotides ca cleaved site-specifically upon irradiation with > 360 nm light with high efficiency. Furthermore, we show that these modifications can be bypassed in DNA synthesis promoted by Thermus aquaticus DNA polymerase.
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Affiliation(s)
- Adrian Dussy
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse I, 53121 Bonn, Germany
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7
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Horhota A, Zou K, Ichida JK, Yu B, McLaughlin LW, Szostak JW, Chaput JC. Kinetic analysis of an efficient DNA-dependent TNA polymerase. J Am Chem Soc 2005; 127:7427-34. [PMID: 15898792 PMCID: PMC5042361 DOI: 10.1021/ja0428255] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
α-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives
and potential progenitors of present-day β-d-2‘-deoxyribofuranosyl nucleoside triphosphates (dNTPs).
Therminator DNA polymerase, a variant of the 9°N DNA polymerase, is an efficient DNA-directed threosyl
nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed
TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and
dNTPs from a DNA primer−template complex and carried out parallel experiments with a chimeric DNA−TNA primer−DNA template containing five TNA residues at the primer 3‘-terminus. Remarkably, no drop
in the rate of TNA incorporation was observed in comparing the DNA−TNA primer to the all-DNA primer,
suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the
catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a
difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible
when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl2. These results indicate
that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective
catalyst of TNA polymerization despite changes in the geometry of the reactants.
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Affiliation(s)
- Allen Horhota
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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8
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Abstract
DNA polymerase enzymes process their natural substrates with very high specificity. Yet recent experiments have shown that these enzymes can also process DNA in which the backbone or bases are modified to a surprising degree. Such experiments have important implications in understanding the mechanisms of DNA replication, and suggest important biotechnological uses as well.
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Affiliation(s)
- E T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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9
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Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
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Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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10
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Smith CA, Baeten J, Taylor JS. The ability of a variety of polymerases to synthesize past site-specific cis-syn, trans-syn-II, (6-4), and Dewar photoproducts of thymidylyl-(3'-->5')-thymidine. J Biol Chem 1998; 273:21933-40. [PMID: 9705333 DOI: 10.1074/jbc.273.34.21933] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of photoproduct structure, 3' --> 5' exonuclease activity, and processivity on polynucleotide synthesis past photoproducts of thymidylyl-(3' --> 5')-thymidine was investigated. Both Moloney murine leukemia virus reverse transcriptase and 3' --> 5' exonuclease-deficient (exo-) Vent polymerase were blocked by all photoproducts, whereas Taq polymerase could slowly bypass the cis-syn dimer. T7 RNA polymerase was able to bypass all the photoproducts in the order cis-syn > Dewar > (6-4) > trans-syn-II. Klenow fragment could not bypass any of the photoproducts, but an exo- mutant could bypass the cis-syn dimer to a greater extent than the others. Likewise T7 DNA polymerase, composed of the T7 gene 5 protein and Escherichia coli thioredoxin, was blocked by all the photoproducts, but the exo- mutant Sequenase 2.0 was able to bypass them all in the order cis-syn > Dewar > trans-syn-II > (6-4). No bypass occurred with an exo- gene 5 protein in the absence of the thioredoxin processivity factor. Bypass of the cis-syn and trans-syn-II products by Sequenase 2.0 was essentially non-mutagenic, whereas about 20% dTMP was inserted opposite the 5'-T of the Dewar photoproduct. A mechanism involving a transient abasic site is proposed to account for the preferential incorporation of dAMP opposite the 3'-T of the photoproducts.
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Affiliation(s)
- C A Smith
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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11
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Wenzel T, Nair V. Novel oligodeoxyribonucleotides incorporating L-related isodeoxynucleosides: Solid phase synthesis, enzymology, and CD studies. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)10183-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Giese B, Dussy A, Meggers E, Petretta M, Schwitter U. Conformation, Lifetime, and Repair of 4‘-DNA Radicals. J Am Chem Soc 1997. [DOI: 10.1021/ja972769q] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernd Giese
- Department of Chemistry, University of Basel St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Adrian Dussy
- Department of Chemistry, University of Basel St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Eric Meggers
- Department of Chemistry, University of Basel St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Mario Petretta
- Department of Chemistry, University of Basel St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Urs Schwitter
- Department of Chemistry, University of Basel St. Johanns-Ring 19, CH-4056 Basel, Switzerland
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Hess MT, Schwitter U, Petretta M, Giese B, Naegeli H. Bipartite substrate discrimination by human nucleotide excision repair. Proc Natl Acad Sci U S A 1997; 94:6664-9. [PMID: 9192622 PMCID: PMC21215 DOI: 10.1073/pnas.94.13.6664] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian nucleotide excision repair (NER) eliminates carcinogen-DNA adducts by double endonucleolytic cleavage and subsequent release of 24-32 nucleotide-long single-stranded fragments. Here we manipulated the deoxyribose-phosphate backbone of DNA to analyze the mechanism by which damaged strands are discriminated as substrates for dual incision. We found that human NER is completely inactive on DNA duplexes containing single C4'-modified backbone residues. However, the same C4' backbone variants, which by themselves do not perturb complementary hydrogen bonds, induced strong NER reactions when incorporated into short segments of mispaired bases. No oligonucleotide excision was detected when DNA contained abnormal base pairs without concomitant changes in deoxyribose-phosphate composition. Thus, neither C4' backbone lesions nor improper base pairing stimulated human NER, but the combination of these two substrate alterations constituted an extremely potent signal for double DNA incision. In summary, we used C4'-modified backbone residues as molecular tools to dissect DNA damage recognition by human NER into separate components and identified a bipartite discrimination mechanism that requires changes in DNA chemistry with concurrent disruption of Watson-Crick base pairing.
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Affiliation(s)
- M T Hess
- Institute of Pharmacology and Toxicology, University of Zürich-Tierspital, Winterthurerstrasse 260, 8057 Zürich, Switzerland
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