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Kennelly SA, Moorthy R, Otero RS, Harki DA. Expanding Catch and Release DNA Decoy (CRDD) Technology with Pyrimidine Mimics. Chemistry 2022; 28:e202201355. [PMID: 35849314 PMCID: PMC9588621 DOI: 10.1002/chem.202201355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Catch and release DNA decoys (CRDDs) utilize photochemically responsive nucleoside analogues that generate abasic sites upon exposure to light. Herein, we describe the synthesis and evaluation of four candidate CRDD monomers containing nucleobases that mimic endogenous pyrimidines: 2-nitroimidazole (2-NI), 2-nitrobenzene (2-NB), 2-nitropyrrole (2-NP) and 3-nitropyrrole (3-NP). Our studies reveal that 2-NI and 2-NP can function as CRDDs, whereas 3-NP and 2-NB undergo decomposition and transformation to a higher-ordered structure upon photolysis, respectively. When incorporated into DNA, 2-NP undergoes rapid photochemical cleavage of the anomeric bond (1.8 min half-life) to yield an abasic site. Finally, we find that all four pyrimidine mimics show significantly greater stability when base-paired against the previously reported 7-nitroindole CRDD monomer. Our work marks the expansion of CRDD technology to both purine and pyrimidine scaffolds.
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Affiliation(s)
- Samantha A. Kennelly
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ramkumar Moorthy
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ruben Silva Otero
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Daniel A. Harki
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
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2
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Tashiro R, Sugiyama H. Photoreaction of DNA Containing 5-Halouracil and its Products. Photochem Photobiol 2022; 98:532-545. [PMID: 34543451 PMCID: PMC9197447 DOI: 10.1111/php.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-Cyo, Suzuka, Mie, 513-8670, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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3
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Tavakoli A, Min JH. Photochemical modifications for DNA/RNA oligonucleotides. RSC Adv 2022; 12:6484-6507. [PMID: 35424630 PMCID: PMC8982246 DOI: 10.1039/d1ra05951c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022] Open
Abstract
Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
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4
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Zálešák J, Constant JF, Jourdan M. Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions. Biochemistry 2016; 55:3899-906. [PMID: 27322640 DOI: 10.1021/acs.biochem.6b00396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionizing radiation, free radicals, and reactive oxygen species produce hundreds of different DNA lesions. Clustered lesions are typical for ionizing radiation. They compromise the efficiency of the base excision repair (BER) pathway, and as a consequence, they are much more toxic and mutagenic than isolated lesions. Despite their biological relevance, e.g., in cancer radiotherapy and accidental exposure, they are not very well studied from a structural point of view, and while insights provided by structural studies contribute to the understanding of the repair process, only three nuclear magnetic resonance (NMR) studies of DNA containing clusters of lesions were reported. Herein, we report the first NMR solution structure of two DNAs containing a bistranded cluster with the 2'-deoxyribonolactone and 8-oxoguanine lesions. Both DNA duplexes feature a 2'-deoxyribonolactone site in the middle of the sequence of one strand and differ by the relative position of the 8-oxoguanine, staggered 3' or 5' side on the complementary strand at a three-nucleotide distance. Depending on its relative position, the repair of the 8-oxoguanine lesion by the base excision repair protein Fpg is either almost complete or inhibited. We found that the structures of the two DNAs containing a bistranded cluster of two lesions are similar and do not deviate very much from the standard B-form. As no obvious structural deformations were observed between the two duplexes, we concluded that the differences in Fpg activity are not due to differences in their global conformation.
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Affiliation(s)
- Jan Zálešák
- Universite Grenoble Alpes , DCM UMR 5250, F-38000 Grenoble, France.,CNRS , DCM UMR 5250, F-38000 Grenoble, France
| | - Jean-François Constant
- Universite Grenoble Alpes , DCM UMR 5250, F-38000 Grenoble, France.,CNRS , DCM UMR 5250, F-38000 Grenoble, France
| | - Muriel Jourdan
- Universite Grenoble Alpes , DCM UMR 5250, F-38000 Grenoble, France.,CNRS , DCM UMR 5250, F-38000 Grenoble, France
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5
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Struntz NB, Harki DA. Catch and Release DNA Decoys: Capture and Photochemical Dissociation of NF-κB Transcription Factors. ACS Chem Biol 2016; 11:1631-8. [PMID: 27054264 DOI: 10.1021/acschembio.6b00130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Catch and release DNA decoys (CRDDs) are a new class of non-natural DNA probes that capture and dissociate from DNA-binding proteins using a light trigger. Photolytic cleavage of non-natural nucleobases in the CRDD yields abasic sites and truncation products that lower the affinity of the CRDD for its protein target. Herein, we demonstrate the ability of the first-generation CRDD to bind and release NF-κB proteins. This platform technology should be applicable to other DNA-binding proteins by modification of the target sequence.
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Affiliation(s)
- Nicholas B. Struntz
- Department
of Medicinal Chemistry, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
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6
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Greenberg MM. Reactivity of Nucleic Acid Radicals. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2016; 50:119-202. [PMID: 28529390 DOI: 10.1016/bs.apoc.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.
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7
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Ingale SA, Leonard P, Yang H, Seela F. 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts. Org Biomol Chem 2015; 12:8519-32. [PMID: 25236942 DOI: 10.1039/c4ob01478b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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8
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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9
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Berthet N, Crey-Desbiolles C, Kotera M, Dumy P. Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic. Nucleic Acids Res 2009; 37:5237-45. [PMID: 19586934 PMCID: PMC2760783 DOI: 10.1093/nar/gkp562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2'-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation (lambda > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.
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Affiliation(s)
- Nathalie Berthet
- Département de Chimie Moléculaire-Equipe Ingénierie et Interactions BioMoléculaires, UMR-5250, ICMG FR-2607, CNRS, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9, France.
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10
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Huang H, Greenberg MM. Hydrogen bonding contributes to the selectivity of nucleotide incorporation opposite an oxidized abasic lesion. J Am Chem Soc 2008; 130:6080-1. [PMID: 18412345 DOI: 10.1021/ja801715c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability of DNA polymerases to maintain the integrity of the genome even after it has been structurally altered is vital. There is considerable interest in determining the structural properties of the DNA template that polymerases recognize when determining which nucleotide to add to a nascent strand. Mechanistic, synthetic, and structural chemistries have been used to study how DNA polymerase activity is affected by size, shape, pi-stacking, and hydrogen bonds of the template molecules. Herein, we probe the structural aspects of abasic lesions that result in their distinct coding potential in Escherichia coli despite lacking a Watson-Crick base. In particular, we investigate why bypass of 2-deoxyribonolactone (L) results in significant amounts of dG incorporation opposite the lesion, whereas other abasic lesions (e.g., AP) adhere to the "A-rule". Experiments using synthetic analogues reveal that DNA polymerase V bypasses L and increased levels of dG incorporation result from a hydrogen bonding interaction between the carbonyl oxygen and dG. These results show that a DNA polymerase utilizes hydrogen bonding as one structural parameter when decoding an abasic lesion.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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11
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Huang H, Greenberg MM. Synthesis and analysis of oligonucleotides containing abasic site analogues. J Org Chem 2008; 73:2695-703. [PMID: 18324835 DOI: 10.1021/jo702614p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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12
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Usui K, Aso M, Fukuda M, Suemune H. Photochemical generation of oligodeoxynucleotide containing a C4'-oxidized abasic site and its efficient amine modification: dependence on structure and microenvironment. J Org Chem 2007; 73:241-8. [PMID: 18062702 DOI: 10.1021/jo702080r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bleomycin-induced oxidative DNA damage under limited oxygen conditions results in the formation of the C4'-oxidized abasic site (1). We synthesized the oligodeoxynucleotides (ODN) 5, which contains 4'-o-nitrobenzyloxythymidine (3), and 6, which contains 2-nitrobenzyloxy-4'-methoxy-2'-deoxy-d-ribofuranoside (4), as the caged precursors of 7, an ODN containing 1, to study its reactivity with amines. Photoirradiation of the single- and double-stranded 5 led to the formation of 7. Uncaging of the duplex was faster and the yield of 7 was higher with the double-stranded than with the single-stranded ODN. It was suggested that a low dielectric environment of the o-nitrobenzyloxy group in the minor groove of the duplex might accelerate the uncaging rate. Similarly, 6 and its duplex yielded 7 by photoirradiation. However, the yields of 7 were lower than those of 5, and duplex formation slowed the uncaging rate. Reaction of the obtained 7 with an amine resulted in the formation of the lactam 2b in good yield in both single- and double-stranded forms, showing that amine modification of biomolecules by an ODN containing 1 is possible under physiologic conditions.
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Affiliation(s)
- Kazuteru Usui
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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13
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Iwai S. Chemical synthesis of oligonucleotides containing damaged bases for biological studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:561-82. [PMID: 16838846 DOI: 10.1080/15257770600685826] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Since nucleic acids are organic molecules, even DNA, which carries genetic information, is subjected to various chemical reactions in cells. Alterations of the chemical structure of DNA, which are referred to as DNA damage or DNA lesions, induce mutations in the DNA sequences, which lead to carcinogenesis and cell death, unless they are restored by the repair systems in each organism. Formerly, DNA from bacteria and bacteriophages and DNA fragments treated with UV or gamma radiation, alkylating or crosslinking agents, and other carcinogens were used as damaged DNA for biochemical studies. With these materials, however, it is difficult to understand the detailed mechanisms of mutagenesis and DNA repair. Recent progress in the chemical synthesis of oligonucleotides has enabled us to incorporate a specific lesion at a defined position within any sequence context. This method is especially important for studies on mutagenesis and translesion synthesis, which require highly pure templates, and for the structural biology of repair enzymes, which necessitates large amounts of substrate DNA as well as modified substrate analogs. In this review, the various phosphoramidite building blocks for the synthesis of lesion-containing oligodeoxyribonucleotides are described, and some examples of their applications to molecular and structural biology are presented.
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Affiliation(s)
- Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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14
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Greenberg MM. Elucidating DNA damage and repair processes by independently generating reactive and metastable intermediates. Org Biomol Chem 2006; 5:18-30. [PMID: 17164902 DOI: 10.1039/b612729k] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA damage is a double-edged sword. The modifications produced in the biopolymer are associated with aging, and give rise to a variety of diseases, including cancer. DNA is also the target of anti-tumor agents and the most generally used nonsurgical treatment of cancer, ionizing radiation. Agents that damage DNA produce a variety of radicals. Elucidating the chemistry of individual DNA radicals is challenging due to the availability of multiple reactive pathways and complexities inherent with carrying out mechanistic studies on a heterogeneous polymer. The ability to independently generate radicals and their metastable products at defined sites in DNA has greatly facilitated understanding this biologically important chemistry.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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15
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Crey-Desbiolles C, Kotera M. Synthesis of 3-deaza-3-nitro-2′-deoxyadenosine. Bioorg Med Chem 2006; 14:1935-41. [PMID: 16290164 DOI: 10.1016/j.bmc.2005.10.040] [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] [Received: 08/18/2005] [Revised: 10/18/2005] [Accepted: 10/25/2005] [Indexed: 11/25/2022]
Abstract
Photoactivable deoxyadenosine mimic, 3-deaza-3-nitro-2'-deoxyadenosine (2), was prepared using two different synthetic routes. The first route involved base catalyzed glycosylation of 3-deaza-3-nitroadenine, which was prepared by regioselective nitration of 3-deazaadenine. In the second route, the convertible nucleoside 6-O-(2,4,6-trimethylphenyl)-3-deaza-2'-deoxyadenosine (28) was used to introduce 6-NH2 group in the last step.
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16
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Abstract
[reaction: see text] A general method for the photochemical generation of ribose abasic sites within RNA oligonucleotides is reported. Photochemically caged nucleoside phosphoramidite analogues were prepared and incorporated into RNA oligonucleotides by automated RNA synthesis. Irradiation of the modified RNA at 350 nm efficiently produced ribose abasic sites at specific sites within RNA sequences. The current approach offers a chemical route to RNA abasic lesions for RNA biochemical studies.
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Affiliation(s)
- John D Trzupek
- Department of Chemistry and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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17
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Faure V, Saparbaev M, Dumy P, Constant JF. Action of multiple base excision repair enzymes on the 2'-deoxyribonolactone. Biochem Biophys Res Commun 2005; 328:1188-95. [PMID: 15708002 DOI: 10.1016/j.bbrc.2005.01.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Indexed: 01/25/2023]
Abstract
Free radical attack on the sugar-phosphate backbone generates oxidized apurinic/apyrimidinic (AP) residues in DNA. 2'-deoxyribonolactone (dL) is a C1'-oxidized AP site damage generated by UV and gamma-irradiation, and certain anticancer drugs. If not repaired dL produces G-->A transitions in Escherichia coli. In the base excision repair (BER) pathway, AP endonucleases are the major enzymes responsible for 5'-incision of the regular AP site (dR) and dL. DNA glycosylases with associated AP lyase activity can also efficiently cleave regular AP sites. Here, we report that dL is a substrate for AP endonucleases but not for DNA glycosylases/AP lyases. The kinetic parameters of the dL-incision were similar to those of the dR. DNA glycosylases such as E. coli formamidopyrimidine-DNA glycosylase, mismatch-specific uracil-DNA glycosylase, and human alkylpurine-DNA N-glycosylase bind strongly to dL without cleaving it. We show that dL cross-links with the human proteins 8-oxoguanine-DNA (hOGG1) and thymine glycol-DNA glycosylases (hNth1), and dR cross-links with Nth and hNth1. These results suggest that dL and dR induced genotoxicity might be strengthened by BER pathway in vivo.
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Affiliation(s)
- Virginie Faure
- LEDSS-UMR 5616, ICMG-FR 2607, BP 53, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
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18
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Kim J, Weledji YN, Greenberg MM. Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides. J Org Chem 2004; 69:6100-4. [PMID: 15373495 DOI: 10.1021/jo049033d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.
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Affiliation(s)
- Jaeseung Kim
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA
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19
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Crey-Desbiolles C, Lhomme J, Dumy P, Kotera M. 3-nitro-3-deaza-2'-deoxyadenosine as a versatile photocleavable 2'-deoxyadenosine mimic. J Am Chem Soc 2004; 126:9532-3. [PMID: 15291544 DOI: 10.1021/ja047976m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new photocleavable 2'-deoxyadenosine mimic, 3-nitro-3-deaza-2'-deoxyadenosine (NidA), was prepared and introduced into DNA fragments via its 6-O-trimethylphenyl precursor phophoramidite. Photocleavage of the resulting oligonucleotide is highly efficient in single and double strands. Hybridization properties of NidA are very similar to those of deoxyadenosine.
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20
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Zheng Y, Sheppard TL. Half-life and DNA strand scission products of 2-deoxyribonolactone oxidative DNA damage lesions. Chem Res Toxicol 2004; 17:197-207. [PMID: 14967007 DOI: 10.1021/tx034197v] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species lead to oxidative damage of the nucleobase and sugar components of nucleotides in double-stranded DNA. The 2-deoxyribonolactone (or oxidized abasic site) lesion results from oxidation of the C-1' position of DNA nucleotides and has been implicated in DNA strand scission, mutagenesis, and covalent cross-linking to DNA binding proteins. We previously described a strategy for the synthesis of DNA-containing deoxyribonolactone lesions. We now report an improved method for the site specific photochemical generation of deoxyribonolactone sites within DNA oligonucleotides and utilize these synthetic oligonucleotides to characterize the products and rates of DNA strand scission at the lactone lesion under simulated physiological conditions. A C-1' nitroveratryl cyanohydrin phosphoramidite analogue was synthesized and used for the preparation of DNA containing a photochemically "caged" lactone precursor. Irradiation at 350 nm quantitatively converted the caged analogue into the deoxyribonolactone lesion. The methodology was validated by RP-HPLC and MALDI-TOF mass spectrometry. Incubation of deoxyribonolactone-containing DNA under simulated physiological conditions gave rise to DNA fragmentation by two consecutive elimination reactions. The DNA-containing products resulting from DNA cleavage at the deoxyribonolactone site were isolated by PAGE and unambiguously characterized by MALDI-TOF MS and chemical fingerprinting assays. The rate of DNA strand scission at the deoxyribonolactone site was measured in single- and double-stranded DNA under simulated physiological conditions: DNA cleavage occurred with a half-life of approximately 20 h in single-stranded DNA and 32-54 h in duplex DNA, dependent on the identity of the deoxynucleotide paired opposite the lesion site. The initial alpha,beta-elimination reaction was shown to be the rate-determining step for the formation of methylene furanone and phosphorylated DNA products. These investigations demonstrated that the deoxyribonolactone site represents a labile lesion under simulated physiological conditions and forms the basis for further studies of the biological effects of this oxidative DNA damage lesion.
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Affiliation(s)
- Yan Zheng
- Department of Chemistry and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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21
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Greenberg MM, Weledji YN, Kim J, Bales BC. Repair of oxidized abasic sites by exonuclease III, endonuclease IV, and endonuclease III. Biochemistry 2004; 43:8178-83. [PMID: 15209514 DOI: 10.1021/bi0496236] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Deoxyribonolactone (L) and the C4'-oxidized abasic site (C4-AP) are produced by a variety of DNA-damaging agents. If not repaired, these lesions can be mutagenic. Exonuclease III and endonuclease IV are the major enzymes in E. coli responsible for 5'-incision of abasic sites (APs), the first steps in AP repair. Endonuclease III efficiently excises AP lesions via intermediate Schiff-base formation. Incision of L and C4-AP lesions by exonuclease III and endonuclease IV was determined under steady-state conditions using oligonucleotide duplexes containing the lesions at defined sites. An abasic lesion (AP) in an otherwise identical DNA sequence was incised by exonuclease III or endonuclease IV approximately 6-fold more efficiently than either of the oxidized abasic sites (L, C4-AP). Endonuclease IV incision efficiency of 2-deoxyribonolactone or C4-AP was independent of whether the lesion was opposite dA or dG. 2-Deoxyribonolactone is known to cross-link to endonuclease III (Hashimoto, M. (2001) J. Am. Chem. Soc. 123, 3161.). However, the C4-AP lesion is efficiently excised by endonuclease III. Oxidized abasic site repair by endonuclease IV and endonuclease III (C4-AP only) is approximately 100-fold less efficient than repair by exonuclease III. These results suggest that the first step of C4-AP and L oxidized abasic site repair will be the same as that of regular AP lesions in E. coli.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
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22
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Kroeger KM, Jiang YL, Kow YW, Goodman MF, Greenberg MM. Mutagenic effects of 2-deoxyribonolactone in Escherichia coli. An abasic lesion that disobeys the A-rule. Biochemistry 2004; 43:6723-33. [PMID: 15157106 DOI: 10.1021/bi049813g] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abasic sites are often referred to as noninstructive lesions. The C1'-oxidized abasic site (2-deoxyribonolactone, L) is produced by several DNA damaging agents, including gamma-radiolysis and the neocarzinostatin chromophore (NCS). The effects of a C1'-oxidized abasic site incorporated at a defined site in single-stranded plasmid were examined in SOS polymerase-proficient and -deficient Escherichia coli. For comparison, experiments utilizing plasmids containing an abasic site (AP) were carried out side by side. In contrast to plasmid containing AP, dA and dG were incorporated most often when plasmid containing L was replicated. The ratio of dG:dA incorporation depended upon local sequence and varied from 0.9 to 2.2. High levels of translesion incorporation of dA are consistent with previous observations that treatment of DNA with the neocarzinostatin chromophore resulted in large amounts of G.C --> A.T transitions [Povirk and Goldberg (1986) Nucleic Acids Res. 14, 1417] and support the proposal that L is the source of these mutations. Both abasic lesions were 100% lethal in triple knockout cells lacking pol II, pol IV, and pol V. Analysis of translesion synthesis in repair-deficient cells revealed that pol V played a significant role in replication of L and AP. Significant levels of -1 frameshifts were formed in 5'-d(CL) sequences in the presence of pol V and were the exclusive product in pol V-deficient cells. Frameshift products were not formed when the nucleotide on the 5'-side of L was either dT or dG. Deleting pol II or pol IV had only modest effects on replication of L-containing plasmid but significantly decreased the amount of -1 frameshift product formed from an AP lesion. Experiments carried out side by side using otherwise identical plasmids containing an AP site illustrate the distinct properties of these two abasic lesions and that neither should be thought of as noninstructive.
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Affiliation(s)
- Kelly M Kroeger
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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23
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Greenberg MM, Weledji YN, Kroeger KM, Kim J, Goodman MF. In vitro effects of a C4'-oxidized abasic site on DNA polymerases. Biochemistry 2004; 43:2656-63. [PMID: 14992603 DOI: 10.1021/bi036028f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidative damage to DNA produces abasic sites resulting from the formal hydrolysis of the nucleotides' glycosidic bonds, along with a variety of oxidized abasic sites. The C4'-oxidized abasic site (C4-AP) is produced by several DNA-damaging agents. This lesion accounts for approximately 40% of the DNA damage produced by bleomycin. The effect of a C4'-oxidized abasic site incorporated at a defined site in a template was examined on Klenow fragments with and without 3' --> 5' exonuclease activity. Both enzymes preferentially incorporated dA > dG >> dC, T opposite C4-AP. Neither enzyme is able to extend the primer past the lesion. Experiments with regular AP sites in an otherwise identical template indicate that Klenow does not differentiate between these two disparate abasic sites. Extension of the primer by alternative polymerases pol II, pol II exo(-), pol IV, and pol V was examined. Pol II exo(-) was most efficient. Qualitative translesion synthesis experiments showed that pol II exo(-) preferentially incorporates T opposite C4-AP, followed in order by dG, dA, and dC. Thymidine incorporation opposite C4'-AP is distinct from the pol II exonuclease interaction with a regular AP site in an otherwise identical template. These in vitro experiments suggest that bypass polymerases may play a crucial role in survival of cells in which C4-AP is produced, and unlike a typical AP site, the C4-AP lesion may not follow the "A-rule". The interaction between bypass polymerases and a C4-AP lesion could explain the high levels of G:C --> T:A transversions in cells treated with bleomycin.
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Affiliation(s)
- Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
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24
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Crey C, Dumy P, Lhomme J, Kotera M. Deoxyribonolactone lesion in DNA: synthesis of fluorinated analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1093-5. [PMID: 14565352 DOI: 10.1081/ncn-120022744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mono- and difluorinated derivatives of 2-deoxyribonolactone were synthesized using diastereoselective Reformatski reaction as a key step.
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Affiliation(s)
- Caroline Crey
- LEDSS-UMR5616 associé au CNRS, BP53, Université Joseph Fourier, Grenoble, France
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25
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Kroeger KM, Hashimoto M, Kow YW, Greenberg MM. Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes. Biochemistry 2003; 42:2449-55. [PMID: 12600212 DOI: 10.1021/bi027168c] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Deoxyribonolactone (3) is produced in DNA as a result of reaction with a variety of DNA damaging agents. The lesion undergoes beta-elimination to form a second metastable electrophilic product (4). In this study, DNA containing 2-deoxyribonolactone (3) and its beta-elimination product (4) are generated at specific sites using a photolabile nucleotide precursor. 2-Deoxyribonolactone is not incised by any of the 8 AP lyases tested. One enzyme, Escherichia coli endonuclease III, cross-links to 3, and the lesion strongly inhibits excision of typical abasic sites by this enzyme. Two of the enzymes, FPG and NEIL1 known to cleave normal abasic sites (1) by effecting beta,delta-elimination form cross-links to the butenolide lesion (4). The observed results are ascribable to characteristics of the enzymes and the lesions. These enzymes are also important for the removal of oxidative base lesions. These results suggest that high concentrations of 3 and 4 may exert significant effects on the repair of normal AP site and oxidative base lesions in cells by reducing the cellular activity of these BER enzymes either via cross-linking or competing with binding to the BER enzymes.
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Affiliation(s)
- Kelly M Kroeger
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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26
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27
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Roupioz Y, Lhomme J, Kotera M. Chemistry of the 2-deoxyribonolactone lesion in oligonucleotides: cleavage kinetics and products analysis. J Am Chem Soc 2002; 124:9129-35. [PMID: 12149017 DOI: 10.1021/ja025688p] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deoxyribonolactone in DNA is an oxidized abasic site damage that is produced by a variety of physical and chemical agents such as gamma-irradiation and ene-diyne antibiotics. The extent and biological significance of the lesion are poorly documented due to the high lability of the damaged DNA. The chemistry of degradation of deoxyribonolactone-containing DNA was investigated using oligonucleotides of different length (5-, 11-, 23-, 34-mers) in which the lactone was photochemically generated, as already reported, from oligonucleotide precursors containing a photoactive nitroindole residue. The procedure was successfully extended to double-strand synthesis by irradiation of the preformed duplex in which one strand contained the nitroindole residue. The degradation kinetics were investigated as a function of pH, temperature, length, and ionic strength. The cleavage fragments resulting from beta- and delta-eliminations were isolated and identified by (1)H NMR. It was found that the lesion is extremely sensitive to pH and temperature while slightly dependent upon ionic strength, length, and sequence. The cleavage rates for the beta- and delta-elimination steps are of the same order of magnitude. The deoxyribonolactone site leads to greater instability of DNA than the "regular" deoxyribose abasic site.
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Affiliation(s)
- Yoann Roupioz
- Chimie Bioorganique, L.E.D.S.S., Associé au CNRS, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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28
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Lenox HJ, McCoy CP, Sheppard TL. Site-specific generation of deoxyribonolactone lesions in DNA oligonucleotides. Org Lett 2001; 3:2415-8. [PMID: 11463330 DOI: 10.1021/ol016255e] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] An efficient method for the site-specific generation of 2-deoxyribonolactone oxidative DNA damage lesions from a "photocaged" nucleoside analogue was developed. A nucleoside phosphoramidite bearing a C-1' nitrobenzyl cyanohydrin was prepared and incorporated into DNA oligonucleotides using automated DNA synthesis. The caged analogue, which was stable in aqueous solution, was converted to the 2-deoxyribonolactone lesion by UV irradiation. DNA containing the caged analogue and the deoxyribonolactone site were characterized by electrospray mass spectrometry (ES-MS).
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Affiliation(s)
- H J Lenox
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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29
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Tallman KA, Greenberg MM. Oxygen-dependent DNA damage amplification involving 5,6-dihydrothymidin-5-yl in a structurally minimal system. J Am Chem Soc 2001; 123:5181-7. [PMID: 11457379 DOI: 10.1021/ja010180s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5,6-Dihydrothymidin-5-yl (1) was independently generated in a dinucleotide from a phenyl selenide precursor (4). Under free radical chain propagation conditions, the products resulting from hydrogen atom donation and radical-pair reaction are the major observed products in the absence of O(2). The stereoselectivity of the trapping process is dependent on the structure of the hydrogen atom donor. No evidence for internucleotidyl hydrogen atom abstraction by 1 was detected. The tandem lesion (17) resulting from hydrogen atom abstraction from the C1' position of the adjacent 2'-deoxyuridine by the peroxyl radical derived from 1 (3) is observed under aerobic conditions. The structure of this product is confirmed by independent synthesis and its transformation into a second independently synthesized product (24). Internucleotidyl hydrogen atom abstraction is effected selectively by the 5S-diastereomer of the peroxyl radical. The formation of dinucleotide 17 provides further support for the novel O(2)-dependent DNA damage amplification mechanism involving 1 reported previously (Greenberg, M. M.; et al. J. Am. Chem. Soc. 1997, 119, 1828).
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Affiliation(s)
- K A Tallman
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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30
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Hashimoto M, Greenberg MM, Kow YW, Hwang JT, Cunningham RP. The 2-deoxyribonolactone lesion produced in DNA by neocarzinostatin and other damaging agents forms cross-links with the base-excision repair enzyme endonuclease III. J Am Chem Soc 2001; 123:3161-2. [PMID: 11457038 DOI: 10.1021/ja003354z] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Pirrung MC, Zhao X, Harris SV. A universal, photocleavable DNA base: nitropiperonyl 2'-deoxyriboside. J Org Chem 2001; 66:2067-71. [PMID: 11300902 DOI: 10.1021/jo001594r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A universal, photochemically cleavable DNA base analogue would add desirable versatility to a number of methods in molecular biology. A novel C-nucleoside, nitropiperonyl deoxyriboside (NPdR, P), has been investigated for this purpose. NPdR can be converted to its 5'-DMTr-3'-CE-phosphoramidite and was incorporated into pentacosanucleotides by conventional synthesis techniques. The destabilizing effect on hybrid formation with a complementary strand when this P base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 min) of DNA containing the P base and piperidine treatment causes strand cleavage giving the 3'- and 5'-phosphates. Two significant recent interests, universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a light-based DNA scissors.
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Affiliation(s)
- M C Pirrung
- Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, USA.
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32
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Kotera M, Roupioz Y, Defrancq E, Bourdat AG, Garcia J, Coulombeau C, Lhomme J. The 7-nitroindole nucleoside as a photochemical precursor of 2'-deoxyribonolactone: access to DNA fragments containing this oxidative abasic lesion. Chemistry 2000; 6:4163-9. [PMID: 11128280 DOI: 10.1002/1521-3765(20001117)6:22<4163::aid-chem4163>3.0.co;2-k] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
On the basis of molecular modeling studies, the 7-nitroindole nucleoside 1 was selected as a suitable photochemical precursor for photochemical generation of the C1' deoxyribosyl radical under irradiation, which led to 2'-deoxyribonolactone. The nitro-indole nucleoside derivatives 1a and 1b were prepared and their conformation was determined by X-ray crystallography and NMR spectroscopy. The photoreaction of these nucleosides gave the corresponding deoxyribonolactone derivatives efficiently, with release of 7-nitrosoindole. This reaction was successfully applied to synthesis of oligonucleotides containing the deoxyribonolactone lesion.
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Affiliation(s)
- M Kotera
- LEDSS, Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier, Grenoble, France.
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33
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Abstract
Loss of a base in DNA, i.e., creation of an abasic site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously, or under the action of radiations and alkylating agents, or enzymatically as an intermediate in the repair of modified or abnormal bases. The abasic site lesion is mutagenic or lethal if not repaired. From a chemical point of view,the abasic site is an alkali-labile residue that leads to strand breakage through beta- and delta- elimination. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of synthetic abasic duplexes. Several efficient synthetic methods have thus been developed to introduce the lesion (or a stable analogue) at defined position in the sequence. Physicochemical and spectroscopic examination of such duplexes, including calorimetry, melting temperature, high-field nmr and molecular modeling indicate that the lesion strongly destabilizes the duplex, although remaining in the canonical B-form with structural modifications strictly located at the site of the lesion. Probes have been developed to titrate the damage in DNA in vitro. Series of molecules have been devised to recognize specifically the abasic site, exhibiting a cleavage activity and mimicking the AP nucleases. Others have been prepared that bind strongly to the abasic site and show promise in potentiating the cytotoxic and antitumor activity of the clinically used nitrosourea (bis-chloroethylnitrosurea).
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Affiliation(s)
- J Lhomme
- LEDSS, Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier, Grenoble Cedex 9, France.
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34
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Oyoshi T, Sugiyama H. Mechanism of DNA Strand Scission Induced by (1,10-Phenanthroline)copper Complex: Major Direct DNA Cleavage Is Not through 1‘,2‘-Dehydronucleotide Intermediate nor β-Elimination of Forming Ribonolactone. J Am Chem Soc 2000. [DOI: 10.1021/ja9919130] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takanori Oyoshi
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda Tokyo 101-0062, Japan
| | - Hiroshi Sugiyama
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda Tokyo 101-0062, Japan
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35
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Abstract
Ionizing radiation and radiomimetic drugs such as bleomycin, calichieamycin, neocarzinostatin chromophore, and other synthetic agents can produce both single and double strand breaks in DNA. The ability to study the structure-activity relationships of single and double-strand break repair, lethality, and mutagenesis in vivo is complicated by the numerous types and sites of DNA cleavage products that can be induced by such agents. The ability to "cage" such breaks in DNA might help to further such studies and additionally afford a mechanism for activating and deactivating nucleic acid based drugs and probes. The major type of single strand break induced by ionizing radiation is a 3'- and 5'-phosphate terminated single nucleotide gap. Previously, a caged strand break of this type had been developed that was designed to produce the 5'-phosphate directly upon irradiation with 366 nm light, and the 3'-phosphate by a subsequent beta-elimination reaction [Ordoukhanian, P., and Taylor, J.-S. (1995) J. Am. Chem. Soc. 117, 9570]. Unfortunately, the release of the 3'-phosphate group was quite slow at pH 7. To circumvent this problem, a second caged strand break has been developed that produces the 3'-phosphate directly upon irradiation, and the 5'-phosphate by a subsequent beta-elimination reaction. When this caged strand break was used in tandem with the previous caged strand break, 5'- and 3'-phosphate terminated gaps could be directly produced by irradiation with 366 nm light. These caged single strand breaks were also incorporated in tandem into hairpin substrates to demonstrate that they could be used to cage double strand breaks. These caged single strand breaks should be generally useful for generating site-specific DNA single and double strand breaks and gaps, using wavelengths and doses of light that are nondetrimental to biological systems. Because the position of the single strand break can be varied, it should now be possible to examine the effect of the sequence context and cleavage pattern of single and double strand breaks on the lethality and mutagenicity of this important class of DNA damage.
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Affiliation(s)
- P Ordoukhanian
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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36
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Voituriez L, Cadet J. Isolation and Characterization of Two Furan-side Photoadducts of 7-Methylpyrido[3,4-c] Psoralen to the Sugar Moiety of 2-Deoxyadenosine. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb07983.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Papageorgiou G, Ogden DC, Barth A, Corrie JET. Photorelease of Carboxylic Acids from 1-Acyl-7-nitroindolines in Aqueous Solution: Rapid and Efficient Photorelease of l-Glutamate1. J Am Chem Soc 1999. [DOI: 10.1021/ja990931e] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George Papageorgiou
- National Institute for Medical Research, The Ridgeway Mill Hill, London NW7 1AA, UK Institut für Biophysik, Johann Wolfgang Goethe Universität D-60590 Frankfurt, Germany
| | - David C. Ogden
- National Institute for Medical Research, The Ridgeway Mill Hill, London NW7 1AA, UK Institut für Biophysik, Johann Wolfgang Goethe Universität D-60590 Frankfurt, Germany
| | - Andreas Barth
- National Institute for Medical Research, The Ridgeway Mill Hill, London NW7 1AA, UK Institut für Biophysik, Johann Wolfgang Goethe Universität D-60590 Frankfurt, Germany
| | - John E. T. Corrie
- National Institute for Medical Research, The Ridgeway Mill Hill, London NW7 1AA, UK Institut für Biophysik, Johann Wolfgang Goethe Universität D-60590 Frankfurt, Germany
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38
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Ito T, Shinohara H, Hatta H, Nishimoto SI. Stereoisomeric C5−C5‘-Linked Dihydrothymine Dimers Produced by Radiolytic One-Electron Reduction of Thymine Derivatives in Anoxic Aqueous Solution: Structural Characteristics in Reference to Cyclobutane Photodimers. J Org Chem 1999; 64:5100-5108. [DOI: 10.1021/jo990059s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideki Shinohara
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Hatta
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sei-ichi Nishimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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39
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Jourdan M, Garcia J, Defrancq E, Kotera M, Lhomme J. 2'-deoxyribonolactone lesion in DNA: refined solution structure determined by nuclear magnetic resonance and molecular modeling. Biochemistry 1999; 38:3985-95. [PMID: 10194310 DOI: 10.1021/bi982743r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution conformation of the DNA duplex d(C1G2C3A4C5L6C7A8C9G10C11).d(G12C13G14T15G16T17G18T19G20C21G22 ) containing the 2'-deoxyribonolactone lesion (L6) in the middle of the sequence has been investigated by NMR spectroscopy and restrained molecular dynamics calculations. Interproton distances have been obtained by complete relaxation matrix analysis of the NOESY cross-peak intensities. These distances, along with torsion angles for sugar rings and additional data derived from canonical A- and B-DNA, have been used for structure refinement by restrained molecular dynamics (rMD). Six rMD simulations have been carried out starting from both regular A- and B-DNA forms. The pairwise rms deviations calculated for each refined structure are <1 A, indicating convergence to essentially the same geometry. The accuracy of the rMD structures has been assessed by complete relaxation matrix back-calculation. The average sixth-root residual index (Rx = 0.052 +/- 0.003) indicated that a good fit between experimental and calculated NOESY spectra has been achieved. Detailed analysis revealed a right-handed DNA conformation for the duplex in which both the T17 nucleotide opposite the abasic site and the lactone ring are located inside the helix. No kinking is observed for this molecule, even at the abasic site step. This structure is compared to that of the oligonucleotide with the identical sequence containing the stable tetrahydrofuran abasic site analogue that we reported previously [Coppel, Y., Berthet, N., Coulombeau, C., Coulombeau, Ce., Garcia, J., and Lhomme, J. (1997) Biochemistry 36, 4817-4830].
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Affiliation(s)
- M Jourdan
- LEDSS, Chimie Bioorganique, UMR CNRS 5616, Université Joseph Fourier, BP 53, Grenoble, France
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