1
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Laverty DJ, Greenberg MM. Expanded Substrate Scope of DNA Polymerase θ and DNA Polymerase β: Lyase Activity on 5'-Overhangs and Clustered Lesions. Biochemistry 2018; 57:6119-6127. [PMID: 30299084 PMCID: PMC6200648 DOI: 10.1021/acs.biochem.8b00911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA polymerase θ (Pol θ) is a multifunctional enzyme with double-strand break (DSB) repair, translesion synthesis, and lyase activities. Pol θ lyase activity on ternary substrates containing a 5'-dRP that are produced during base excision repair of abasic sites (AP) is weak compared to that of DNA polymerase β (Pol β), a polymerase integrally involved in base excision repair. This led us to explore whether Pol θ utilizes its lyase activity to remove 5'-dRP and incise abasic sites from alternative substrates that might be produced during DNA damage and repair. We found that Pol θ exhibited lyase activity on abasic lesions near DSB termini and on clustered lesions. To calibrate the Pol θ activity, Pol β reactivity was examined with the same substrates. Pol β excised 5'-dRP from within a 5'-overhang 80 times faster than did Pol θ. Pol θ and Pol β also incised AP within clustered lesions but showed opposite preferences with respect to the polarity of the lesions. AP lesions in 5'-overhangs were typically excised by Pol β 35-50 times faster than those in a duplex substrate but 15-20-fold more slowly than 5'-dRP in a ternary complex. This is the first report of Pol θ exhibiting lyase activity within an unincised strand. These results suggest that bifunctional polymerases may exhibit lyase activity on a greater variety of substrates than previously recognized. A role in DSB repair could potentially be beneficial, while the aberrant activity exhibited on clustered lesions may be deleterious because of their conversion to DSBs.
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Affiliation(s)
- Daniel J. Laverty
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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2
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Muthuramalingam S, Subramaniyan S, Khamrang T, Velusamy M, Mayilmurugan R. Copper(II)-Bioinspired Models for Copper Amine Oxidases: Oxidative Half-Reaction in Water. ChemistrySelect 2017. [DOI: 10.1002/slct.201601786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sethuraman Muthuramalingam
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
| | - Shanmugam Subramaniyan
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
| | - Themmila Khamrang
- Department of Chemistry; North Eastern Hill Universuty; Shillong- 793022 India
| | - Marappan Velusamy
- Department of Chemistry; North Eastern Hill Universuty; Shillong- 793022 India
| | - Ramasamy Mayilmurugan
- Bioinorganic Chemistry Laboratory/Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021, Tamil Nadu India
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3
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Banerjee S, Chakraborty S, Jacinto MP, Paul MD, Balster MV, Greenberg MM. Probing Enhanced Double-Strand Break Formation at Abasic Sites within Clustered Lesions in Nucleosome Core Particles. Biochemistry 2016; 56:14-21. [PMID: 28005342 DOI: 10.1021/acs.biochem.6b01144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA is rapidly cleaved under mild alkaline conditions at apyrimidinic/apurinic sites, but the half-life is several weeks in phosphate buffer (pH 7.5). However, abasic sites are ∼100-fold more reactive within nucleosome core particles (NCPs). Histone proteins catalyze the strand scission, and at superhelical location 1.5, the histone H4 tail is largely responsible for the accelerated cleavage. The rate constant for strand scission at an abasic site is enhanced further in a nucleosome core particle when it is part of a bistranded lesion containing a proximal strand break. Cleavage of this form results in a highly deleterious double-strand break. This acceleration is dependent upon the position of the abasic lesion in the NCP and its structure. The enhancement in cleavage rate at an apurinic/apyrimidinic site rapidly drops off as the distance between the strand break and abasic site increases and is negligible once the two forms of damage are separated by 7 bp. However, the enhancement of the rate of double-strand break formation increases when the size of the gap is increased from one to two nucleotides. In contrast, the cleavage rate enhancement at 2-deoxyribonolactone within bistranded lesions is more modest, and it is similar in free DNA and nucleosome core particles. We postulate that the enhanced rate of double-strand break formation at bistranded lesions containing apurinic/apyrimidinic sites within nucleosome core particles is a general phenomenon and is due to increased DNA flexibility.
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Affiliation(s)
- Samya Banerjee
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Supratim Chakraborty
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Marco Paolo Jacinto
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Michael D Paul
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Morgan V Balster
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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4
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Yang B, Jinnouchi A, Usui K, Katayama T, Fujii M, Suemune H, Aso M. Bioconjugation of Oligodeoxynucleotides Carrying 1,4-Dicarbonyl Groups via Reductive Amination with Lysine Residues. Bioconjug Chem 2015. [PMID: 26200210 DOI: 10.1021/acs.bioconjchem.5b00361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We evaluated the efficacy of bioconjugation of oligodeoxynucleotides (ODNs) containing 1,4-dicarbonyl groups, a C4'-oxidized abasic site (OAS), and a newly designed 2'-methoxy analogue, via reductive amination with lysine residues. Dicarbonyls, aldehyde and ketone at C1- and C4-positions of deoxyribose in the ring-opened form of OAS allowed efficient reaction with amines. Kinetic studies indicated that reductive amination of OAS-containing ODNs with a proximal amine on the complementary strand proceeded 10 times faster than the corresponding reaction of an ODN containing an abasic site with C1-aldehyde. Efficient reductive amination between the DNA-binding domain of Escherichia coli DnaA protein and ODNs carrying OAS in the DnaA-binding sequence proceeded at the lysine residue in proximity to the phosphate group at the 5'-position of the OAS, in contrast to unsuccessful conjugation with abasic site ODNs, even though they have similar aldehydes. Theoretical calculation indicated that the C1-aldehyde of OAS was more accessible to the target lysine than that of the abasic site. These results demonstrate the potential utility of cross-linking strategies that use dicarbonyl-containing ODNs for the study of protein-nucleic acid interactions. Conjugation with a lysine-containing peptide that lacked specific affinity for ODN was also successful, further highlighting the advantages of 1,4-dicarbonyls.
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Affiliation(s)
- Bo Yang
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akiko Jinnouchi
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kazuteru Usui
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tsutomu Katayama
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masayuki Fujii
- ‡Department of Biological and Environmental Chemistry, School of Humanity-Oriented Science and Engineering, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Hiroshi Suemune
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Mariko Aso
- †Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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5
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Greenberg MM. Abasic and oxidized abasic site reactivity in DNA: enzyme inhibition, cross-linking, and nucleosome catalyzed reactions. Acc Chem Res 2014; 47:646-55. [PMID: 24369694 DOI: 10.1021/ar400229d] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abasic lesions are a family of DNA modifications that lack Watson-Crick bases. The parent member of this family, the apurinic/apyrimidinic lesion (AP), occurs as an intermediate during DNA repair, following nucleobase alkylation, and from random hydrolysis of native nucleotides. In a given day, each cell produces between 10000 and 50000 AP lesions. A variety of oxidants including γ-radiolysis produce oxidized abasic sites, such as C4-AP, from the deoxyribose backbone. A number of potent, cytotoxic antitumor agents, such as bleomycin and the enediynes (e.g., calicheamicin, esperamicin, and neocarzinostatin) also lead to oxidized abasic sites in DNA. The absence of Watson-Crick bases prevents DNA polymerases from properly determining which nucleotide to incorporate opposite abasic lesions. Consequently, several studies have revealed that (oxidized) abasic sites are highly mutagenic. Abasic lesions are also chemically unstable, are prone to strand scission, and possess electrophilic carbonyl groups. However, researchers have only uncovered the consequences of the inherent reactivity of these electrophiles within the past decade. The development of solid phase synthesis methods for oligonucleotides that both place abasic sites in defined positions and circumvent their inherent alkaline lability has facilitated this research. Chemically synthesized oligonucleotides containing abasic lesions provide substrates that have allowed researchers to discover a range of interesting chemical properties of potential biological importance. For instance, abasic lesions form DNA-DNA interstrand cross-links, a particularly important family of DNA damage because they block replication and transcription absolutely. In addition, bacterial repair enzymes can convert an interstrand cross-link derived from C4-AP into a double-strand break, the most deleterious form of DNA damage. Oxidized abasic lesions can also inhibit DNA repair enzymes that remove damaged nucleotides. DNA polymerase β, an enzyme that is irreversibly inactivated, is vitally important in base excision repair and is overproduced in some tumor cells. Nucleosome core particles, the monomeric components that make up chromatin, accentuate the chemical instability of abasic lesions. In experiments using synthetic nucleosome core particles containing abasic sites, the histone proteins catalyze strand cleavage at the sites that incorporate these lesions. Furthermore, in the presence of the C4-AP lesion, strand scission is accompanied by modification of the histone protein. The reactivity of (oxidized) abasic lesions illustrates how seemingly simple nucleic acid modifications can have significant biochemical effects and may provide a chemical basis for the cytotoxicity of the chemotherapeutic agents that produce them.
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Affiliation(s)
- Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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6
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Akopiants K, Mohapatra S, Menon V, Zhou T, Valerie K, Povirk LF. Tracking the processing of damaged DNA double-strand break ends by ligation-mediated PCR: increased persistence of 3'-phosphoglycolate termini in SCAN1 cells. Nucleic Acids Res 2013; 42:3125-37. [PMID: 24371269 PMCID: PMC3950721 DOI: 10.1093/nar/gkt1347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To track the processing of damaged DNA double-strand break (DSB) ends in vivo, a method was devised for quantitative measurement of 3′-phosphoglycolate (PG) termini on DSBs induced by the non-protein chromophore of neocarzinostatin (NCS-C) in the human Alu repeat. Following exposure of cells to NCS-C, DNA was isolated, and labile lesions were chemically stabilized. All 3′-phosphate and 3′-hydroxyl ends were enzymatically capped with dideoxy termini, whereas 3′-PG ends were rendered ligatable, linked to an anchor, and quantified by real-time Taqman polymerase chain reaction. Using this assay and variations thereof, 3′-PG and 3′-phosphate termini on 1-base 3′ overhangs of NCS-C-induced DSBs were readily detected in DNA from the treated lymphoblastoid cells, and both were largely eliminated from cellular DNA within 1 h. However, the 3′-PG termini were processed more slowly than 3′-phosphate termini, and were more persistent in tyrosyl-DNA phosphodiesterase 1-mutant SCAN1 than in normal cells, suggesting a significant role for tyrosyl-DNA phosphodiesterase 1 in removing 3′-PG blocking groups for DSB repair. DSBs with 3′-hydroxyl termini, which are not directly induced by NCS-C, were formed rapidly in cells, and largely eliminated by further processing within 1 h, both in Alu repeats and in heterochromatic α-satellite DNA. Moreover, absence of DNA-PK in M059J cells appeared to accelerate resolution of 3′-PG ends.
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Affiliation(s)
- Konstantin Akopiants
- Department of Pharmacology and Toxicology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA and Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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7
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Zhou C, Sczepanski JT, Greenberg MM. Mechanistic studies on histone catalyzed cleavage of apyrimidinic/apurinic sites in nucleosome core particles. J Am Chem Soc 2012; 134:16734-41. [PMID: 23020793 DOI: 10.1021/ja306858m] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Duplex DNA containing an apurinic/apyrimidinic (AP) lesion undergoes cleavage significantly more rapidly in nucleosome core particles (NCPs) than it does when free. The mechanism of AP cleavage within NCPs was studied through independently generating lesions within them. AP mediated DNA cleavage within NCPs is initiated by DNA-protein cross-link (DPC(un)) formation followed by β-elimination to give DPCs containing cleaved DNA (DPC(cl)). Hydrolysis of DPC(cl) produces a DNA single strand break (SSB). C2-dideuteration of AP showed that deprotonation from this position is involved in the rate-determining step. Experiments utilizing NCPs containing mutated histone H4 proteins indicated that lysine residues in the amino terminal tail are involved in both DPC formation and β-elimination steps. Lysines 16 and 20 seem to play a greater role in reacting with AP at superhelical location 1.5, but other amino acids (e.g., lysines 5, 8, and 12) compensate in their absence. The mechanism of rapid double strand breaks in bistranded, clustered AP lesions was studied by independently preparing reaction intermediates within model NCPs. A single strand break on one strand enhances the cleavage of a proximal AP on the opposite strand.
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Affiliation(s)
- Chuanzheng Zhou
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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8
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Jiang S, Sheng J, Huang Z. Synthesis of the tellurium-derivatized phosphoramidites and their incorporation into DNA oligonucleotides. ACTA ACUST UNITED AC 2012; Chapter 1:Unit 1.25.1-16. [PMID: 22147418 DOI: 10.1002/0471142700.nc0125s47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this unit, an efficient method for the synthesis of 2'-tellerium-modified phosphoramidite and its incorporation into oligonucleotide are presented. We choose 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine nucleosides (S.1, S.2) as starting materials due to their easy preparation. The 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine can be converted to the corresponding 2'-tellerium-derivatized nucleosides by treating with the telluride nucleophiles. Subsequently, the 2'-Te-nucleosides can be transformed into 3'-phosphoramidites, which are the building blocks for DNA/RNA synthesis. The DNA synthesis, purification, and applications of oligonucleotides containing 2'-Te-U or 2'-Te-T are described in the protocol.
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Affiliation(s)
- Sibo Jiang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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9
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Resendiz MJE, Pottiboyina V, Sevilla MD, Greenberg MM. Direct strand scission in double stranded RNA via a C5-pyrimidine radical. J Am Chem Soc 2012; 134:3917-24. [PMID: 22335525 DOI: 10.1021/ja300044e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase radicals are the major family of reactive intermediates produced when nucleic acids are exposed to γ-radiolysis. The 5,6-dihydrouridin-5-yl radical (1), the formal product of hydrogen atom addition and a model for hydroxyl radical addition, was independently generated from a ketone precursor via Norrish Type I photocleavage in single and double stranded RNA. Radical 1 produces direct strand breaks at the 5'-adjacent nucleotide and only minor amounts of strand scission are observed at the initial site of radical generation. Strand scission occurs preferentially in double stranded RNA and in the absence of O(2). The dependence of strand scission efficiency from the 5,6-dihydrouridin-5-yl radical (1) on secondary structure under anaerobic conditions suggests that this reactivity may be useful for extracting additional RNA structural information from hydroxyl radical reactions. Varying the identity of the 5'-adjacent nucleotide has little effect on strand scission. Internucleotidyl strand scission occurs via β-elimination of the 3'-phosphate following C2'-hydrogen atom abstraction by 1. The subsequently formed olefin cation radical yields RNA fragments containing 3'-phosphate or 3'-deoxy-2'-ketonucleotide termini from competing deprotonation pathways. The ketonucleotide end group is favored in the presence of low concentrations of thiol, presumably by reducing the cation radical to the enol. Competition studies with thiol show that strand scission from the 5,6-dihydrouridin-5-yl radical (1) is significantly faster than from the 5,6-dihydrouridin-6-yl radical (2) and is consistent with computational studies using the G3B3 approach that predict the latter to be more stable than 1 by 2.8 kcal/mol.
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Affiliation(s)
- Marino J E Resendiz
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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10
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Sczepanski JT, Hiemstra CN, Greenberg MM. Probing DNA interstrand cross-link formation by an oxidized abasic site using nonnative nucleotides. Bioorg Med Chem 2011; 19:5788-93. [PMID: 21903404 DOI: 10.1016/j.bmc.2011.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 08/08/2011] [Accepted: 08/11/2011] [Indexed: 11/17/2022]
Abstract
The C4'-oxidized abasic site (C4-AP) forms two types of interstrand cross-links with the adjacent nucleotides in DNA. Previous experiments revealed that dG does not react with the lesion and that formation of one type of cross-link is catalyzed by the opposing dA. iso-Guanosine·dC and 2-aminopurine·dT base pairs were used to determine why dG does not cross-link with C4-AP despite its well known reactivity with other bis-electrophiles. 7-Deaza-2'-deoxyadenosine was used to probe the role of the nucleotide opposite C4-AP in the catalysis of interstrand cross-link formation.
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Affiliation(s)
- Jonathan T Sczepanski
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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11
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Jacobs AC, Resendiz MJE, Greenberg MM. Product and mechanistic analysis of the reactivity of a C6-pyrimidine radical in RNA. J Am Chem Soc 2011; 133:5152-9. [PMID: 21391681 PMCID: PMC3071645 DOI: 10.1021/ja200317w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleobase radicals are the major reactive intermediates produced when hydroxyl radical reacts with nucleic acids. 5,6-Dihydrouridin-6-yl radical (1) was independently generated from a ketone precursor via Norrish Type I photocleavage in a dinucleotide, single-stranded, and double-stranded RNA. This radical is a model of the major hydroxyl radical adduct of uridine. Tandem lesions resulting from addition of the peroxyl radical derived from 1 to the 5'-adjacent nucleotide are observed by ESI-MS. Radical 1 produces direct strand breaks at the 5'-adjacent nucleotide and at the initial site of generation. The preference for cleavage at these two positions depends upon the secondary structure of the RNA and whether O(2) is present or not. Varying the identity of the 5'-adjacent nucleotide has little effect on strand scission. In general, strand scission is significantly more efficient under anaerobic conditions than when O(2) is present. Strand scission is more than twice as efficient in double-stranded RNA than in a single-stranded oligonucleotide under anaerobic conditions. Internucleotidyl strand scission occurs via β-fragmentation following C2'-hydrogen atom abstraction by 1. The subsequently formed olefin cation radical ultimately yields products containing 3'-phosphate or 3'-deoxy-2'-ketouridine termini. These end groups are proposed to result from competing deprotonation pathways. The dependence of strand scission efficiency from 1 on secondary structure under anaerobic conditions suggests that this reactivity may be useful for extracting additional RNA structural information from hydroxyl radical reactions.
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Affiliation(s)
| | | | - Marc M. Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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12
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Sheng J, Hassan AEA, Huang Z. Synthesis of the first tellurium-derivatized oligonucleotides for structural and functional studies. Chemistry 2010; 15:10210-6. [PMID: 19691067 DOI: 10.1002/chem.200900774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report here the first synthesis of Te-nucleoside phosphoramidites and Te-modified oligonucleotides. We protected the 2'-tellurium functionality by alkylation and found that the Te functionality is compatible with solid-phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te-DNA can also be site-specifically fragmented oxidatively or reductively when 2'-TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2'-TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, 50 Decatur Street, Atlanta, GA 30303-3083, USA
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13
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Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
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14
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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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15
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Chowdhury G, Guengerich FP. Tandem mass spectrometry-based detection of c4'-oxidized abasic sites at specific positions in DNA fragments. Chem Res Toxicol 2009; 22:1310-9. [PMID: 19496605 DOI: 10.1021/tx900115z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Oxidative damage to DNA has been linked to aging, cancer, and other biological processes. Reactive oxygen species and various antitumor agents including bleomycin and ionizing radiation have been shown to cause oxidative DNA sugar damage. Detection of DNA lesions is important for understanding the toxicological or therapeutic consequences associated with such agents. C4'-oxidized abasic sites (C4-AP) are produced by the antitumor drug bleomycin and ionizing radiation. The currently available methods for the detection of C4-AP cannot provide both structural and sequence information. We have developed an LC-ESI-MS-based approach for specific detection and mapping of C4-AP from a mixture of lesions. We show using Fe-bleomycin-damaged DNA that C4-AP can be detected at cytosine and thymine sites by direct MS analysis. Our results reveal that collision-induced dissociation of C4-AP-containing oligonucleotides results in preferential fragmentation at C4-AP sites with the formation of the unique a* ions (18 amu more than the a-B ions) that allow mapping of the C4-AP sites. Various chemical modification strategies (e.g., reduction with NaBH4 and NaBD4 and derivatization with methoxyamine and hydrazine, followed by LC-MS analysis) were also used for unambiguous detection of C4-AP sites. Finally, we show that the methods described here can detect the presence of C4-AP at specific sites in a complex sample such as hydroxyl radical-damaged DNA. The LC-MS approach was also used for the simultaneous detection of the other C4'-oxidation end product, 3'-phosphoglycolate, at a specific site in hydroxyl radical-damaged DNA. Thus, LC-MS provides a rapid and direct approach for the detection and mapping of oxidative DNA lesions.
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Affiliation(s)
- Goutam Chowdhury
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, Tennessee 37232-0146, USA
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16
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Cui Z, Theruvathu JA, Farrel A, Burdzy A, Sowers LC. Characterization of synthetic oligonucleotides containing biologically important modified bases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2008; 379:196-207. [PMID: 18485883 PMCID: PMC3985270 DOI: 10.1016/j.ab.2008.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 04/11/2008] [Accepted: 04/18/2008] [Indexed: 11/16/2022]
Abstract
Oligonucleotides containing modified bases are commonly used for biochemical and biophysical studies to assess the impact of specific types of chemical damage on DNA structure and function. In contrast to the synthesis of oligonucleotides with normal DNA bases, oligonucleotide synthesis with modified bases often requires modified synthetic or deprotection conditions. Furthermore, several modified bases of biological interest are prone to further damage during synthesis and oligonucleotide isolation. In this article, we describe the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the characterization of a series of modified synthetic oligonucleotides. The potential for and limits in obtaining high mass accuracy for confirming oligonucleotide composition are discussed. Examination of the isotope cluster is also proposed as a method for confirming oligonucleotide elemental composition. MALDI-TOF-MS analysis of the unpurified reaction mixture can be used to confirm synthetic sequence and to reveal potential problems during synthesis. Analysis during and after purification can yield important information on depurination and base oxidation. It can also reveal unexpected problems that can occur with nonstandard synthesis, deprotection, or purification strategies. Proper characterization of modified oligonucleotides is essential for the correct interpretation of experiments performed with these substrates, and MALDI-TOF-MS analysis provides a simple yet extensive method of characterization that can be used at multiple stages of oligonucleotide production and use.
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Affiliation(s)
- Zhengfang Cui
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Jacob A. Theruvathu
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Alvin Farrel
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Artur Burdzy
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Lawrence C. Sowers
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
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17
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Affiliation(s)
- Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, NE47-277, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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18
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Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J. DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res 2007; 36:253-62. [PMID: 18025040 PMCID: PMC2248740 DOI: 10.1093/nar/gkm622] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs with three different bases (G, C or T) opposite an abasic site have been synthesized in the same sequence context (5′-CCA AAG6 XA8C CGG G-3′, where X denotes the abasic site) and characterized by 2D NMR spectroscopy. Studies on a duplex DNA with an A opposite the abasic site in the same sequence has recently been reported [Chen,J., Dupradeau,F.-Y., Case,D.A., Turner,C.J. and Stubbe,J. (2007) Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4′-oxidized abasic sites. Biochemistry, 46, 3096–3107]. Molecular modeling based on NMR-derived distance and dihedral angle restraints and molecular dynamics calculations have been applied to determine structural models and conformational flexibility of each duplex. The results indicate that all four duplexes adopt an overall B-form conformation with each unpaired base stacked between adjacent bases intrahelically. The conformation around the abasic site is more perturbed when the base opposite to the lesion is a pyrimidine (C or T) than a purine (G or A). In both the former cases, the neighboring base pairs (G6-C21 and A8-T19) are closer to each other than those in B-form DNA. Molecular dynamics simulations reveal that transient H-bond interactions between the unpaired pyrimidine (C20 or T20) and the base 3′ to the abasic site play an important role in perturbing the local conformation. These results provide structural insight into the dynamics of abasic sites that are intrinsically modulated by the bases opposite the abasic site.
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Affiliation(s)
- Jingyang Chen
- Department of Chemistry Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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19
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Chen B, Zhou X, Taghizadeh K, Chen J, Stubbe J, Dedon PC. GC/MS methods to quantify the 2-deoxypentos-4-ulose and 3'-phosphoglycolate pathways of 4' oxidation of 2-deoxyribose in DNA: application to DNA damage produced by gamma radiation and bleomycin. Chem Res Toxicol 2007; 20:1701-8. [PMID: 17944541 PMCID: PMC2529375 DOI: 10.1021/tx700164y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA oxidation plays a substantive role in the pathophysiology of human diseases, such as cancer. While the chemistry of nucleobase lesions has dominated studies of DNA damage, there is growing evidence that the oxidation of 2-deoxyribose in DNA plays a critical role in the genetic toxicology of oxidative stress. As part of an effort to define the spectrum of 2-deoxyribose oxidation products arising in vitro and in vivo, we now describe methods for quantifying products arising from 4' oxidation of 2-deoxyribose in DNA. The chemistry of 4' oxidation partitions between either of two pathways to form either a 2-deoxypentos-4-ulose abasic site (oxAB) or a strand break comprised of a 3'-phosphoglycolate (3PG) residue and a 5'-phosphate, with the release of either malondialdehyde and free base or a base propenal. Highly sensitive gas chromatography/mass spectrometry (GC/MS) methods were developed to quantify both lesions. The abasic site was converted to a 3'-phosphoro-3-pyridazinylmethylate derivative by treatment of the damaged DNA with hydrazine, which was released from DNA as 3-hydroxymethylpyridazine (HMP) by enzymatic hydrolysis. Similarly, 3PG was released as 2-phosphoglycolic acid (PG) by enzymatic hydrolysis. Following HPLC prepurification, both PG and HMP were silylated and quantified by GC/MS, with limits of detection of 100 and 200 fmol and sensitivities of 2 and 4 lesions per 10(6) nucleotides (nt) in 250 microg of DNA, respectively. Following validation of the methods with oligodeoxynucleotides containing the two lesions, the methods were applied to DNA damage produced by bleomycin and gamma radiation. As expected for an agent known to produce only 4' oxidation of DNA, the quantities of 3PG and oxAB accounted for all 2-deoxyribose oxidation events, as indicated by slopes of 0.8 and 0.3, respectively, in plots of the lesion frequency against total 2-deoxyribose oxidation events, with the latter determined by a plasmid-nicking assay. 3PG residues and oxAB were produced at the rate of 32 and 12 lesions per 10(6) nt per microM, respectively. For gamma radiation, on the other hand, 4' oxidation was found to comprise only 13% of 2-deoxyribose oxidation chemistry, with 3% oxAB (4 per 10(6) nt per Gy) and 10% 3PG (13 per 10(6) nt per Gy).
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Affiliation(s)
- Bingzi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Xinfeng Zhou
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Koli Taghizadeh
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA
| | - Jingyang Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA
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20
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Kim J, Kreller CR, Greenberg MM. Preparation and analysis of oligonucleotides containing the c4'-oxidized abasic site and related mechanistic probes. J Org Chem 2006; 70:8122-9. [PMID: 16277338 PMCID: PMC1382185 DOI: 10.1021/jo0512249] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The C4'-oxidized abasic site (C4-AP) is produced by a variety of DNA damaging agents. This alkali labile lesion can exist in up to four diastereomeric cyclic forms, in addition to the acyclic keto-aldehyde. Synthetic oligonucleotides containing the lesion were prepared from a stable photochemical precursor. Chemical integrity of the lesion containing oligonucleotides was probed using phosphodiesterase lability. Analysis of the 3',5'-phosphate diester of the monomeric lesion released from single diastereomers of photolabile precursors by 1H NMR indicates that isomerization of the hemiacetal and/or hemiketal is rapid. The syntheses and characterization of oligonucleotides containing configurationally stable analogues of C4-AP, which serve as mechanistic probes for deciphering the structural basis of the biochemical and biological effects of the C4'-oxidized abasic lesion, are also described.
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21
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Kodama T, Greenberg MM. Preparation and analysis of oligonucleotides containing lesions resulting from C5'-oxidation. J Org Chem 2006; 70:9916-24. [PMID: 16292822 PMCID: PMC1657062 DOI: 10.1021/jo051666k] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Hydrogen atom abstraction from the C5'-position of nucleotides in DNA results in direct strand scission. The newly formed 5'-termini of the cleaved DNA consists of alkali-labile fragments of the oxidized nucleotide. One terminus contains a 5'-aldehyde as part of an otherwise undamaged nucleotide (T-al). A second more structurally distinct product that is produced in lower yields results from cleavage of the C4'-C5' carbon-carbon bond. The 1,4-dioxo-2-phosphorylbutane (DOB) is a precursor of the alkylating agent but-2-ene-1,4-dial. To facilitate studies on these lesions, methods for synthesizing oligodeoxynucleotides containing DOB or T-al at their 5'-termini were developed. The effects of these lesions on the UV-melting temperatures of duplex DNA, and their cleavage labilities were determined. T-al cleaves very slowly (t(1/2) = 100.7 h), whereas DOB has a half-life at 37 degrees C (pH 7.2) of less than 11 h. In addition, DOB forms a stable adduct very efficiently with Tris, which protects the abasic site against cleavage.
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Affiliation(s)
- Tetsuya Kodama
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, USA
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