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Hutchings ML, Alpha-Cobb CJ, Hiller DA, Berro J, Strobel SA. Mycofumigation through production of the volatile DNA-methylating agent N-methyl- N-nitrosoisobutyramide by fungi in the genus Muscodor. J Biol Chem 2017; 292:7358-7371. [PMID: 28283571 DOI: 10.1074/jbc.m117.779009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/05/2017] [Indexed: 01/31/2023] Open
Abstract
Antagonistic microorganisms produce antimicrobials to inhibit the growth of competitors. Although water-soluble antimicrobials are limited to proximal interactions via aqueous diffusion, volatile antimicrobials are able to act at a distance and diffuse through heterogeneous environments. Here, we identify the mechanism of action of Muscodor albus, an endophytic fungus known for its volatile antimicrobial activity toward a wide range of human and plant pathogens and its potential use in mycofumigation. Proposed uses of the Muscodor species include protecting crops, produce, and building materials from undesired fungal or bacterial growth. By analyzing a collection of Muscodor isolates with varying toxicity, we demonstrate that the volatile mycotoxin, N-methyl-N-nitrosoisobutyramide, is the dominant factor in Muscodor toxicity and acts primarily through DNA methylation. Additionally, Muscodor isolates exhibit higher resistance to DNA methylation compared with other fungi. This work contributes to the evaluation of Muscodor isolates as potential mycofumigants, provides insight into chemical strategies that organisms use to manipulate their environment, and provokes questions regarding the mechanisms of resistance used to tolerate constitutive, long-term exposure to DNA methylation.
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Affiliation(s)
| | | | - David A Hiller
- Molecular Biophysics and Biochemistry, Chemical Biology Institute, and
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Nanobiology Institute, Yale University, West Haven, Connecticut 06516
| | - Scott A Strobel
- Molecular Biophysics and Biochemistry, Chemical Biology Institute, and
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2
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Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry 2013; 52:7659-68. [PMID: 24131376 PMCID: PMC3812902 DOI: 10.1021/bi400695r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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A cationic
7-aminomethyl-7-deaza-2′-deoxyguanosine (7amG)
was incorporated site-specifically into the self-complementary duplex
d(G1A2G3A4X5C6G7C8T9C10T11C12)2 (X = 7amG). This construct placed two positively charged amines adjacent
to the major groove edges of two symmetry-related guanines, providing
a model for probing how cation binding in the major groove modulates
the structure and stability of DNA. Molecular dynamics calculations
restrained by nuclear magnetic resonance (NMR) data revealed that
the tethered cationic amines were in plane with the modified base
pairs. The tethered amines did not form salt bridges to the phosphodiester
backbone. There was also no indication of the amines being capable
of hydrogen bonding to flanking DNA bases. NMR spectroscopy as a function
of temperature revealed that the X5 imino resonance remained
sharp at 55 °C. Additionally, two 5′-neighboring base
pairs, A4:T9 and G3:C10, were stabilized with respect to the exchange of their imino protons
with solvent. The equilibrium constant for base pair opening at the
A4:T9 base pair determined by magnetization
transfer from water in the absence and presence of added ammonia base
catalyst decreased for the modified duplex compared to that of the
A4:T9 base pair in the unmodified duplex, which
confirmed that the overall fraction of the A4:T9 base pair in the open state of the modified duplex decreased. This
was also observed for the G3:C10 base pair,
where αKop for the G3:C10 base pair in the modified duplex was 3.0 × 106 versus 4.1 × 106 for the same base pair in
the unmodified duplex. In contrast, equilibrium constants for base
pair opening at the X5:C8 and C6:G7 base pairs did not change at 15 °C. These results argue
against the notion that electrostatic interactions with DNA are entirely
entropic and suggest that major groove cations can stabilize DNA via
enthalpic contributions to the free energy of duplex formation.
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Affiliation(s)
- Marta W Szulik
- Department of Chemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
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3
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Ghude P, Schallenberger MA, Fleming AM, Muller JG, Burrows CJ. Comparison of Transition Metal-Mediated Oxidation Reactions of Guanine in Nucleoside and Single-Stranded Oligodeoxynucleotide Contexts. Inorganica Chim Acta 2011; 369:240-246. [PMID: 21516189 DOI: 10.1016/j.ica.2010.12.063] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As the most readily oxidized of DNA's four natural bases, guanine is a prime target for attack by reactive oxygen species (ROS) and transition metal-mediated oxidants. The oxidation products of a modified guanosine nucleoside and of a single-stranded oligodeoxynucleotide, 5'-d(TTTTTTTGTTTTTTT)-3' have been studied using oxidants that include Co(II), Ni(II), and Ir(IV) compounds as well as photochemically generated oxidants such as sulphate radical, electron-transfer agents (riboflavin) and singlet oxygen. The oxidized lesions formed include spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), imidazolone (Iz), oxazolone (Z) and 5-carboxamido-5-formamido-2-iminohydantion (2-Ih) nucleosides with a high degree of dependence on the exact oxidation system employed. Interestingly, a nickel(II) macrocyclic complex in conjunction with KHSO(5) leads to the recently reported 2-Ih heterocycle as the major product in both the nucleoside and oligonucleotide contexts.
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Affiliation(s)
- Pranjali Ghude
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, UT 84112-0850, USA
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4
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Burns JA, Dreij K, Cartularo L, Scicchitano DA. O6-methylguanine induces altered proteins at the level of transcription in human cells. Nucleic Acids Res 2010; 38:8178-87. [PMID: 20702424 PMCID: PMC3001077 DOI: 10.1093/nar/gkq706] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/20/2010] [Accepted: 07/27/2010] [Indexed: 11/14/2022] Open
Abstract
O(6)-Methylguanine (O(6)-meG), which is produced in DNA following exposure to methylating agents, instructs human RNA polymerase II to mis-insert bases opposite the lesion during transcription. In this study, we examined the effect of O(6)-meG on transcription in human cells and investigated the subsequent effects on protein function following translation of the resulting mRNA. In HEK293 cells, O(6)-meG induced incorporation of uridine or cytidine in nascent RNA opposite the adduct. In cells containing active O(6)-alkylguanine-DNA alkyltransferase (AGT), which repairs O(6)-meG, 3% misincorporation of uridine was observed opposite the lesion. In cells where AGT function was compromised by addition of the AGT inhibitor O(6)-benzylguanine, ∼ 58% of the transcripts contained a uridine misincorporation opposite the lesion. Furthermore, the altered mRNA induced changes to protein function as demonstrated through recovery of functional red fluorescent protein (RFP) from DNA coding for a non-fluorescent variant of RFP. These data show that O(6)-meG is highly mutagenic at the level of transcription in human cells, leading to an altered protein load, especially when AGT is inhibited.
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Affiliation(s)
| | | | | | - David A. Scicchitano
- Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003, USA
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5
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Cai J, Muller JG, Burrows CJ. Reactivity of Bulged Bases in Duplex DNA with Redox-active Nickel and Cobalt Complexes. Supramol Chem 2010. [DOI: 10.1080/10610270290026013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jin Cai
- a Department of Chemistry , University of Utah , 315 S. 1400 East, Salt Lake City , UT , 84112 , USA
| | - James G. Muller
- a Department of Chemistry , University of Utah , 315 S. 1400 East, Salt Lake City , UT , 84112 , USA
| | - Cynthia J. Burrows
- a Department of Chemistry , University of Utah , 315 S. 1400 East, Salt Lake City , UT , 84112 , USA
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6
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Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. Biochemistry 2008; 47:7147-57. [PMID: 18549246 DOI: 10.1021/bi800375m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
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7
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Gold B, Marky LM, Stone MP, Williams LD. A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol 2007; 19:1402-14. [PMID: 17112226 PMCID: PMC2532758 DOI: 10.1021/tx060127n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alkylating agents, including environmental and endogenous carcinogens and DNA targeting antineoplastic agents, that adduct DNA via intermediates with significant cationic charge show a sequence selectively in their covalent bonding to nucleobases. The resulting patterns of alkylation eventually contribute to the agent-dependent distributions and types of mutations. The origin of the regioselective modification of DNA by electrophiles has been attributed to steric and/or electronic factors, but attempts to mechanistically model and predict alkylation patterns have had limited success. In this review, we present data consistent with the role of the intrinsic sequence-dependent electrostatic landscape (SDEL) in DNA that modulates the equilibrium binding of cations and the bonding of reactive charged alkylating agents to atoms that line the floor of the major groove of DNA.
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Affiliation(s)
- Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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8
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Ru Hwu J, Tsai FY, Tsay SC, Hsien Chuang S, Su TR, Lin SB, Lin WC, Hsieh CL, Kan LS. Interaction Between 3-(p-Tolylamino)-1,5-azulenequinone and the Deoxyguanosine Residue in Various Oligonucleotides upon Photolysis¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0740686ibptaa2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Matkar SS, Wrischnik LA, Jones PR, Hellmann-Blumberg U. Two closely related nickel complexes have different effects on DNA damage and cell viability. Biochem Biophys Res Commun 2006; 343:754-61. [PMID: 16563351 DOI: 10.1016/j.bbrc.2006.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 03/03/2006] [Indexed: 11/22/2022]
Abstract
Nickel is considered a weak carcinogen. It is known to interact with DNA and DNA-binding proteins. The ability of certain nickel compounds to cleave DNA has been exploited mainly for research purposes and less for developing new anticancer drugs. Here we compare the interactions of two closely related nickel complexes, [NiCR]2+ and [Ni(CR-2H)]2+, with DNA. CR stands for 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene. [NiCR]2+ has been used in the past as a structure-specific probe for RNA and DNA oligonucleotides in the presence of oxidizing agent but little is known about the biological effects of either complex. Our results show that [Ni(CR-2H)]2+ can damage DNA in vivo and in vitro in the absence of an added oxidizing agent and has an IC50 of 70 microM in human breast cancer cells whereas [NiCR]2+ and NiCl2 do not exhibit significant cytotoxicity. However, both [NiCR]2+ and [Ni(CR-2H)]2+ bind to the minor groove of double-stranded DNA.
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Affiliation(s)
- Smita S Matkar
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
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10
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Abstract
DNA is normally considered to be a stiff rod-like molecule, but proteins and small molecules, which either equilibrium bind to, or covalent bond with, DNA, can overcome the barrier(s) to non-linearity by changing the local hydrophobic and electrostatic environment at specific DNA sequences. The deformation of DNA by proteins has been shown to be a critical event in transcriptional regulation. In this review, we have focused on how the introduction of cationic charge, and its location, can affect DNA structure. To study the effect of charge, we have used DNA modified with 3-aminopropyl substitutions at the 5-position of deoxyuracil that mimic basic lysine-like sidechains, and which place the cationic charge in the major groove. Previous gel mobility studies with these sidechains have shown that they bend DNA. The location of the cationic sidechains and how they bend DNA is discussed.
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Affiliation(s)
- Barry Gold
- Eppley Institute for Research in Cancer and Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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11
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Spassky A, Angelov D. Temperature-dependence of UV laser one-electron oxidative guanine modifications as a probe of local stacking fluctuations and conformational transitions. J Mol Biol 2002; 323:9-15. [PMID: 12368094 DOI: 10.1016/s0022-2836(02)00878-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
By monitoring R(pip)/R(Fpg), i.e. the relative sensitivity to hot piperidine and to formamidopyrimidine DNA glycosylase (Fpg protein) of the guanine lesions induced in DNA exposed to UV laser irradiation, we have previously observed that the formation of the two major types of one-electron oxidative guanine modifications, oxazolone and 7,8-dihydro-8-oxoguanine (8-oxodG), depends on DNA conformational features. While oxazolone is largely predominant at each site of single-stranded DNA (R(pip)>R(Fpg)), 8-oxodG is the major lesion at most of the sites of double-stranded DNA (R(pip)<R(Fpg)). In the present study, we investigated the temperature dependence of R(pip) and R(Fpg) at individual sites of a DNA sequence during the transition between the double-stranded and the melted random coiled states. The striking result is that the transition curves of the ratio R(pip)/R(Fpg) display a shape similar to the helix-coil melting profile of the DNA fragment determined from UV absorbance measurements with, at individual sites, subtle differences in the slope of the curves and in the temperature at the mid-point of the transitions. At a few guanine residues of the DNA duplex, R(pip)>R(Fpg) at 20 degrees C and the ratio R(pip)/R(Fpg) does not vary significantly during the melting process. Interestingly, these guanine residues display a high sensitivity to dimethyl sulfoxide methylation while the opposite cytosine residues are unsensitive, suggesting that the prevalence of R(pip) over R(Fpg) is related not to base-pairing disruption but rather to the local helical alteration of the B-DNA stacking geometry. This leads us to propose that the slight variations in the ratios R(pip)/R(Fpg) observed, at individual sites, at temperatures below the helix-coil transition reflect local small-scale breathing motions, unstacking single dinucleotide steps prior to opening. Our results thus support the view that the temperature dependence of the ratio of R(pip)/R(Fpg) at sites of B-DNA provides a sensitive probe of the DNA internal local thermal stability and are discussed in relation with the mechanisms proposed for the intramolecular rearrangement of the guanyl radical.
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Affiliation(s)
- Annick Spassky
- UMR 8532-CNRS, Institut Gustave Roussy, Villejuif, 94805, France.
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12
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Hwu JR, Tsai FY, Tsay SC, Chuang SH, Su TR, Lin SB, Lin WC, Hsieh CL, Kan LS. Interaction between 3-(p-tolylamino)-1,5-azulenequinone and the deoxyguanosine residue in various oligonucleotides upon photolysis. Photochem Photobiol 2001; 74:686-93. [PMID: 11723796 DOI: 10.1562/0031-8655(2001)074<0686:ibptaa>2.0.co;2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Eight single-stranded oligodeoxyribonucleotides 32P-labeled at the 5'-end were synthesized; they were annealed with the complementary oligodeoxyribonucleotides to form the corresponding double-stranded helices. These duplexes possessed standard Watson-Crick base pairs, locally perturbed sites of a base mismatch, or a bulge. Further, 5'-32P-labeled oligodeoxyribonucleotides with a hairpin loop were also synthesized. Cleavage of these single- and double-stranded oligodexyribonucleotides selectively at the deoxyguanosine residue was accomplished by use of 3-(p-tolylamino)-1,5-azulenequinone 1 upon irradiation with 350 nm UV light. The single strands were cleaved more efficiently than the double-helices. For the helices containing a deoxyguanosine residue at a bulge, at a hairpin loop or toward the end, the cleaving efficiency was increased. Computation results indicate that two possibilities exist for agent 1 to form two "Watson-Crick type" hydrogen bonds with guanine in single-stranded oligodeoxyribonucleotides; yet, only one possibility exists in duplexes.
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Affiliation(s)
- J R Hwu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC.
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13
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Grimm C, Wenzel A, Behrens A, Hafezi F, Wagner EF, Remé CE. AP-1 mediated retinal photoreceptor apoptosis is independent of N-terminal phosphorylation of c-Jun. Cell Death Differ 2001; 8:859-67. [PMID: 11526439 DOI: 10.1038/sj.cdd.4400871] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2000] [Revised: 02/27/2001] [Accepted: 03/06/2001] [Indexed: 01/27/2023] Open
Abstract
Apoptosis is essential for retinal development but it is also a major mode of cell loss in many human retinal dystrophies. High levels of visible light induce retinal apoptosis in mice and rats. This process is dependent on the induction of the transcription factor AP-1, a dimeric complex composed of c-Fos and c-Jun/JunD phosphoproteins. While c-Fos is essential, JunD is dispensable for light-induced photoreceptor apoptosis. Here we show that N-terminal phosphorylation of c-Jun, the other main partner of c-Fos in induced AP-1 complexes is not required for programmed cell death during retinal development in vivo and is also dispensable for photoreceptor apoptosis induced by the exogenous stimuli "excessive light" and N-nitroso-N-methylurea (MNU). Mice expressing a mutant c-Jun protein (JunAA) that cannot be phosphorylated at its N-terminus are apoptosis competent and their retina is not distinguishable from wild-type mice. Accordingly, Jun kinase, responsible for phosphorylation of wild-type c-Jun protein is at best only marginally induced by the apoptotic stimuli "light" and MNU. Complex composition of light-induced AP-1 complexes is similar in wild-type and JunAA mice. This shows that the mutant c-Jun protein can be part of the DNA binding complex AP-1 and demonstrates that induction of the DNA binding activity of AP-1 after light insult does not depend on N-terminal phosphorylation of c-Jun. Our results suggest that transactivation of target genes by phosphorylated c-jun/AP-1 is not required for MNU- or light-induced apoptosis of photoreceptor cells.
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Affiliation(s)
- C Grimm
- Department of Ophthalmology, University Hospital, Frauenklinikstrasse 24, 8091 Zurich, Switzerland.
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14
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Cloutier JF, Castonguay A, O'Connor TR, Drouin R. Alkylating agent and chromatin structure determine sequence context-dependent formation of alkylpurines. J Mol Biol 2001; 306:169-88. [PMID: 11237592 DOI: 10.1006/jmbi.2000.4371] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We determined the adduct maps of S(N)1 and S(N)2 alkylating agents in cultured human cells (in vivo) and in vitro to probe DNA-protein interactions along sequences of the promoter and exon 1 of the Fragile-X mental retardation 1 (FMR1) gene. Using ligation-mediated polymerase chain reaction (LMPCR), we compared the piperidine-sensitive alkylpurines sites generated by treating cultured cells (in vivo) and naked DNA (in vitro) with S(N)1 (N-methyl-N-nitrosourea, N-nitroso(acetoxymethyl)methylamine and 1-methyl-3-nitro-1-nitrosoguanidine) and S(N)2 alkylating agents (dimethyl sulfate (DMS), methane sulfonic acid methyl ester, iodo methane, diethyl sulfate, methane sulfonic acid ethyl ester and iodo ethane). The FMR1 promoter has four sites where DNA-protein interactions are observed. In these regions, the S(N)1 methylating agent reactions produced only hypo-reactive sites. In contrast, iodoalkane S(N)2 alkylating agents (MeI and EtI) reactions generated only hyper-reactive sites. Although there are hyper-reactive sites for the other S(N)2 reagents, the hyper-reactive site at +14 on the FMR1 map is more pronounced for the sulfate and sulfonate-derived alkylating agents than for the iodoalkanes. However, DMS modification in the presence of methyl sulfone, a compound that does not alkylate DNA, eliminates the hyper-reactive site observed at +14. This suggests that the electron-rich oxygen atoms of the sulfate and sulfonate-derived S(N)2 alkylating agent structure position the alkylating moiety to the neighboring N-7-guanine position to favor alkyl transfer to the guanine. Using KMnO(4) to probe for single-strand DNA, an unpaired cytosine base was detected at the 5'-side of the hyper- reactive guanine base at position +14, consistent with the formation of a local DNA single-strand bulge. In conclusion, we show that the sequence context-dependent formation of alkylpurines is determined by the chemical nature of the alkylating agent, the DNA sequence context, chromatin structure, and the presence of other non-reactive molecules that can inhibit alkylation.
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Affiliation(s)
- J F Cloutier
- Laboratory of Cancer Etiology and Chemoprevention, Faculty of Pharmacy, Laval University, Quebec City, G1K 7P4, Canada
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15
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Burrows CJ, Muller JG. Oxidative Nucleobase Modifications Leading to Strand Scission. Chem Rev 1998; 98:1109-1152. [PMID: 11848927 DOI: 10.1021/cr960421s] [Citation(s) in RCA: 1395] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850
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16
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Laayoun A, Smith SS. Methylation of slipped duplexes, snapbacks and cruciforms by human DNA(cytosine-5)methyltransferase. Nucleic Acids Res 1995; 23:1584-9. [PMID: 7784214 PMCID: PMC306901 DOI: 10.1093/nar/23.9.1584] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
When human DNA(cytosine-5)methyltransferase was used to methylate a series of snapback oligodeoxy-nucleotides of differing stem lengths, each containing a centrally located CG dinucleotide recognition site, the enzyme required a minimum of 22 base pairs in the stem for maximum activity. Extrahelical cytosines in slipped duplexes that were 30 base pairs in length acted as effective methyl acceptors and were more rapidly methylated than cytosines that were Watson-Crick paired. Duplexes containing hairpins of CCG repeats in cruciform structures in which the enzyme recognition sequence was disrupted by a C.C mispair were also more rapidly methylated than control Watson-Crick-paired duplexes. Since enzymes have higher affinities for their transition states than for their substrates, the results with extrahelical and mispaired cytosines suggest that these structures can be viewed as analogs of the transition state intermediates produced during catalysis by methyltransferases.
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Affiliation(s)
- A Laayoun
- Department of Cell and Tumor Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
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