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Inde T, Masaki Y, Maruyama A, Ito Y, Makio N, Miyatake Y, Tomori T, Sekine M, Seio K. Synthesis of oligonucleotides containing 2-N-heteroarylguanine residues and their effect on duplex/triplex stability. Org Biomol Chem 2018; 15:8371-8383. [PMID: 28937703 DOI: 10.1039/c7ob01875d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To systematically understand the effect of 2-N-heteroarylguanine (GHA) modification on the stability of higher-order DNA structures, nucleoside derivatives and oligodeoxyribonucleotides containing guanine residues modified with four kinds of hereroaryl groups on the 2-amino group were synthesized. The stabilities of the DNA duplex and the parallel-oriented DNA triplex containing these GHAs were studied by measuring their melting temperatures (Tm). Tm experiments and DFT calculations of the modified guanine nucleobases suggested that the base pair formation energy and stability of the two conformations, i.e., the open- and closed-type conformations, are key to determining the stability of the DNA duplex. Finally, the DNA triplex was destabilized when modified guanine residues were introduced into triplex-forming oligonucleotides.
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Affiliation(s)
- Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho Midoriku, Yokohama, Japan.
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2
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Weseliński Ł, Begoyan V, Ferrier A, Tanasova M. Tuning Cross-Coupling Approaches to C3 Modification of 3-Deazapurines. ACS OMEGA 2017; 2:7002-7015. [PMID: 30023537 PMCID: PMC6045343 DOI: 10.1021/acsomega.7b01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/06/2017] [Indexed: 05/04/2023]
Abstract
A general approach to C3 modification of purine scaffold through various types of cross-coupling reactions has been established. Tuning substrate electronics and reaction conditions resulted in the development of highly efficient sp2-sp, sp2-sp2, and sp2-sp3 cross-coupling conditions for modification of 3-deazaadenine to access C3-modified adenine and hypoxanthine scaffolds. The optimized methodologies to access the corresponding 3-deazaadenosine phosphoramidites for solid-phase DNA synthesis have been demonstrated.
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3
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Barros MT, Dey SS, Maycock CD. Metal-Free Synthesis of Secondary Arylamines: An Aliphatic-to-Aromatic Transformation. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Pottiboyina V, Kumar A, Sevilla MD. Formation of N-N cross-links in DNA by reaction of radiation-produced DNA base pair diradicals: a DFT study. J Phys Chem B 2011; 115:15090-7. [PMID: 22050209 PMCID: PMC3240691 DOI: 10.1021/jp207873a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study employs DFT (density functional theory) to investigate the formation of hydrazine-like (N-N) cross-linked structures between DNA base pair diradicals that are likely to result from the interaction of high linear energy transfer (LET) radiation, such as ion-beam radiation, with DNA. In our calculations, we generated the guanine (G), cytosine (C), adenine (A), and thymine (T) radicals by removing one hydrogen atom from an N-H bond involved in the normal base pairing. The radical species formed are those that naturally result from one-electron oxidation of the bases followed by deprotonation. N-N cross-links between G and C or A and T diradicals were studied using the BHandHLYP, B3LYP, M06, and M06-2X density functionals and 6-31G* basis set. From a comparison to several test cases performed with the G3B3 method, which gives thermodynamically reliable values, we found that calculations employing the BHandHLYP/6-31G* method predict the best estimates of bonding energies for hydrazine-like structures. Our study shows that the N-N cross-link formed between guanine radical and a neutral cytosine is endothermic in nature but can form metastable structures. However, the reactions between two DNA base radicals (diradical) to form several N-N cross-linked structures are found to be highly exothermic in nature. The N-N cross-links formed between various G-C, G-G, and C-C diradicals have binding energies in the range of ca. -54 to -68, -41 to -47, and -67 to -75 kcal/mol, respectively, whereas A-T, A-A, and T-T have binding energies of -80, -60, and -98 kcal/mol, respectively. In all purine-pyrimidine N-N cross-linked structures, the highest occupied molecular orbital (HOMO) is found to be localized on the purine moiety and the lowest unoccupied molecular orbital (LUMO) is on the pyrimidine moiety.
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Affiliation(s)
- Venkata Pottiboyina
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
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5
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Lukin M, Zaliznyak T, Johnson F, de Los Santos CR. Incorporation of 3-aminobenzanthrone into 2'-deoxyoligonucleotides and its impact on duplex stability. J Nucleic Acids 2011; 2011:521035. [PMID: 22175001 PMCID: PMC3228337 DOI: 10.4061/2011/521035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/03/2011] [Indexed: 12/25/2022] Open
Abstract
3-Nitrobenzanthrone (3NBA), an environmental pollutant and potent mutagen, causes DNA damage via the reaction of its metabolically activated form with the exocyclic amino groups of purines and the C-8 position of guanine. The present work describes a synthetic approach to the preparation of oligomeric 2′-deoxyribonucleotides containing a 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone moiety, one of the major DNA adducts found in tissues of living organisms exposed to 3NBA. The NMR spectra indicate that the damaged oligodeoxyribonucleotide is capable of forming a regular double helical structure with the polyaromatic moiety assuming a single conformation at room temperature; the spectra suggest that the 3ABA moiety resides in the duplex minor groove pointing toward the 5′-end of the modified strand. Thermodynamic studies show that the dG(N2)-3ABA lesion has a stabilizing effect on the damaged duplex, a fact that correlates well with the long persistence of this damage in living organisms.
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Affiliation(s)
- Mark Lukin
- Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
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6
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Thomson PF, Lagisetty P, Balzarini J, De Clercq E, Lakshman MK. Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides. Adv Synth Catal 2010; 352:1728-1735. [PMID: 21818182 PMCID: PMC3148652 DOI: 10.1002/adsc.200900728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Palladium‐catalyzed C—N bond forming reactions of 6‐bromo‐ as well as 6‐chloropurine ribonucleosides and the 2′‐deoxy analogues with arylamines are described. Efficient conversions were observed with palladium(II) acetate/Xantphos/cesium carbonate, in toluene at 100 °C. Reactions of the bromonucleoside derivatives could be conducted at a lowered catalytic loading [5 mol% Pd(OAc)2/7.5 mol% Xantphos], whereas good product yields were obtained with a higher catalyst load [10 mol% Pd(OAc)2/15 mol% Xantphos] when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxy groups appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of arylamines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6‐chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates.
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Affiliation(s)
- Paul F Thomson
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, U.S.A
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7
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Pratap R, Parrish D, Gunda P, Venkataraman D, Lakshman MK. Influence of Biaryl Phosphine Structure on C−N and C−C Bond Formation. J Am Chem Soc 2009; 131:12240-9. [DOI: 10.1021/ja902679b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramendra Pratap
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Damon Parrish
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Padmaja Gunda
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - D. Venkataraman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Mahesh K. Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
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8
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Böge N, Jacobsen MI, Szombati Z, Baerns S, Di Pasquale F, Marx A, Meier C. Synthesis of DNA strands site-specifically damaged by c8-arylamine purine adducts and effects on various DNA polymerases. Chemistry 2009; 14:11194-208. [PMID: 18988239 DOI: 10.1002/chem.200800979] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
C8-Arylamine-dG and C8-arylamine-dA adducts have been prepared using palladium cross-coupling chemistry. These adducts were subsequently converted into the corresponding 5'-O-DMTr-C8-arylamine-3'-O-phosphoramidites and then used for the automated synthesis of different site-specifically modified oligonucleotides. These "damaged" oligonucleotides have been characterized by ESI-MS, UV thermal stability assays, and circular dichroism, and they have been used in EcoRI assays as well as in primer extension studies using various DNA polymerases.
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Affiliation(s)
- Nicolas Böge
- Organic Chemistry, Department of Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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9
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Takamura-Enya T, Enomoto S, Wakabayashi K. Palladium-catalyzed direct N-arylation of nucleosides, nucleotides, and oligonucleotides for efficient preparation of dG-N2 adducts with carcinogenic amino-/nitroarenes. J Org Chem 2007; 71:5599-606. [PMID: 16839139 DOI: 10.1021/jo0605243] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for direct palladium-catalyzed N-arylation reaction of nucleobases was developed for the convenient synthesis of DNA adducts with carcinogenic compounds. Using xantphos as the phosphine ligand and tetraethylammonium fluoride as the base in DMSO, several o-iodonitroarenes could be efficiently coupled with 2'-deoxyguanosine, 2'-deoxyadenosine, and 2'-deoxycytidine. The presence of a 3'-phosphate group in the deoxyribose moiety was found to be compatible with this N-arylation reaction; further, oligonucleotides could serve as substrates. The facile nitroreduction of the coupling compounds (12) yielded 2'-deoxyguanosin-N2-ylarylamine adducts, which are known to be biologically important. Compound 12 was easily converted to phosphoramidite derivatives, allowing the preparation of site-specific modified oligonucleotides with arylamine after the nitroreduction.
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Affiliation(s)
- Takeji Takamura-Enya
- Cancer Prevention Basic Research Project, National Cancer Centre Research Institute, Tokyo 104-0045, Japan.
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10
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Böge N, Gräsl S, Meier C. Synthesis and properties of oligonucleotides containing C8-deoxyguanosine arylamine adducts of borderline carcinogens. J Org Chem 2007; 71:9728-38. [PMID: 17168591 DOI: 10.1021/jo061803t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C8-Arylamine-dG adducts of borderline carcinogens and the bladder and breast carcinogen 4-aminobiphenyl were prepared using cross-coupling chemistry. These adducts were converted into the corresponding C8-arylamine-5'-O-DMTr-2'-deoxyguanosine phosphoramidites and then used as building blocks for automated synthesis of site-specifically modified oligonucleotides. The oligonucleotides were characterized by UV melting temperature analysis, enzymatic digestion, and circular dichroism.
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Affiliation(s)
- Nicolas Böge
- Institute of Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Martin-Luther-King-Platz 6, D-20149 Hamburg, Germany
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11
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Nagatsugi F, Ogata Y, Imoto S, Sasaki S. Efficient Synthesis of 6-Substituted Purine Derivatives Using Pd-Catalyzed Cross-Coupling Reactions with 2’-Deoxyguanosine O6-Tosylate. HETEROCYCLES 2007. [DOI: 10.3987/com-07-s(u)24] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Abstract
[structure: see text] After bioactivation, the potent dietary mutagen 2-amino-3-methylimidazo[4,5-f]-quinoline (IQ) reacts with DNA to give two regioisomeric adducts of deoxyguanosine. The synthesis of the minor N2-adduct has been achieved utilizing the Buchwald-Hartwig palladium-catalyzed N-arylation reaction as the key step.
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Affiliation(s)
- James S Stover
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, Tennessee 37235-1822, USA
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13
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Pottabathini N, Bae S, Pradhan P, Hahn HG, Mah H, Lakshman MK. Synthesis and Reactions of 2-Chloro- and 2-Tosyloxy-2‘-deoxyinosine Derivatives. J Org Chem 2005; 70:7188-95. [PMID: 16122237 DOI: 10.1021/jo050847j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Convenient syntheses of 2-chloro- and 2-tosyloxy-2'-deoxyinosine as their tert-butyldimethylsilyl ethers are described. Both compounds can be synthesized via a common route and rely on commercially available 2'-deoxyguanosine. The present method leading to the chloro nucleoside is operationally simpler compared to previously reported glycosylation techniques where isomeric products were obtained. Both electrophilic nucleosides can be used for the preparation of N-substituted 2'-deoxyguanosine analogues via displacement of the leaving groups, and a comparison of their reactivities shows the chloro analogue to be superior. Interestingly, a Pd catalyst-mediated, two-step, one-pot conversion of an allyl-protected chloro nucleoside intermediate to the final modified 2'-deoxyguanosine derivatives is also feasible. On the basis of these observations, initial assessments of Pd-catalyzed aryl amination as well as a C-C cross-coupling have also been performed with the chloro and tosyloxy nucleoside substrates. Results indicate a potentially high synthetic utility of 2-chloro-2'-deoxyinosine and in many instances this derivative can supplant the bromo and fluoro analogues that are more cumbersome to prepare or are not readily available.
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Affiliation(s)
- Narender Pottabathini
- Department of Chemistry, City College and City University of New York, 138th Street at Convent Avenue, New York, New York 10031-9198, USA
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Glaser R, Wu H, Lewis M. Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation. J Am Chem Soc 2005; 127:7346-58. [PMID: 15898783 DOI: 10.1021/ja0501159] [Citation(s) in RCA: 22] [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
Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).
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Affiliation(s)
- Rainer Glaser
- Department of Chemistry, University of Missouri-Columbia, 65211, USA.
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15
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Qian M, Glaser R. Demonstration of an alternative mechanism for G-to-G cross-link formation. J Am Chem Soc 2005; 127:880-7. [PMID: 15656626 DOI: 10.1021/ja045108j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cross-link dG-to-dG is an important product of DNA nitrosation. Its formation has commonly been attributed to nucleophilic substitution of N2 in a guaninediazonium ion by guanine, while recent studies suggest guanine addition to a cyanoamine derivative formed after dediazoniation, deprotonation, and pyrimidine ring-opening. The chemical viability of the latter mechanism is supported here by the experimental demonstration of rG-to-aG formation via rG addition to a synthetic cyanoamine derivative. Thus, all known products of nitrosative guanine deamination are consistent with the postulate of pyrimidine ring-opening. This postulated mechanism not only explains what is already known but also suggests that other products and other cross-links also might be formed in DNA deamination. The study suggests one possible new product: the structure isomer aG(N1)-to-rG(C2) of the classical G(N2)-to-G(C2) cross-link. While the formation of aG(N2)-to-rG(C2) has been established by chemical synthesis, the structure isomer aG(N1)-to-rG(C2) has been assigned tentatively based on its MS/MS spectrum and because this assignment is reasonable from a mechanistic perspective. Density functional calculations show preferences for the amide-iminol tautomer of the classical cross-link G(N2)-to-G(C2) and the amide-amide tautomer of G(N1)-to-G(C2). Moreover, the results suggest that both cross-links are of comparable thermodynamic stability, and that there are no a priori energetic or structural reasons that would prevent the formation of the structure isomer in the model reaction or in DNA.
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Affiliation(s)
- Ming Qian
- Department of Chemistry, University of Missouri-Columbia, 605 South College Avenue, Columbia, Missouri 65211, USA
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16
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Elmquist CE, Stover JS, Wang Z, Rizzo CJ. Site-specific synthesis and properties of oligonucleotides containing C8-deoxyguanosine adducts of the dietary mutagen IQ. J Am Chem Soc 2005; 126:11189-201. [PMID: 15355100 DOI: 10.1021/ja0487022] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The site-specific synthesis of oligonucleotides containing the C8-deoxyguanosine adduct of the highly mutagenic heterocyclic amine 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) has been achieved, and the oligonucleotides were characterized by UV melting temperature analysis, circular dichroism, and UV absorption spectroscopy. Examination of these data indicated that the IQ-adduct is accommodated in dramatically different environments. This sequence-dependent conformational preference is likely to play a key role in the mutagenicity and repair of IQ-modified oligonucleotides.
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Affiliation(s)
- C Eric Elmquist
- Department of Chemistry and Center in Molecular Toxicology, Vanderbilt University, VU Station B 351822, Nashville, Tennessee 37235-1822, USA
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17
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200590025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/anie.200590025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2004; 43:6372-7. [PMID: 15558680 DOI: 10.1002/anie.200460782] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Padmaja Gunda
- Department of Chemistry, The City College and The City University of New York, 138th Street at Convent Avenue, New York, NY 10031, USA
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20
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460782] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Janeba Z, Lin X, Robins MJ. Functionalization of guanosine and 2'-deoxyguanosine at C6: a modified Appel process and S(N)Ar displacement of imidazole. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 23:137-47. [PMID: 15043142 DOI: 10.1081/ncn-120027823] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Treatment of sugar-protected 2-N-trityl derivatives of guanosine and 2'-deoxyguanosine with imidazole/triphenylphosphine/iodine/ethyldiisopropylamine gives the corresponding 6-(imidazol-1-yl)-2-(tritylamino)purine nucleosides. S(N)Ar displacement of the imidazole moiety with nucleophiles provides 2-amino-6-substituted-purine nucleosides and 2'-deoxynucleosides.
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Affiliation(s)
- Zlatko Janeba
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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22
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Terrazas M, Ariza X, Farràs J, Guisado-Yang JM, Vilarrasa J. A direct, efficient method for the preparation of n6-protected 15n-labeled adenosines. J Org Chem 2004; 69:5473-5. [PMID: 15287800 DOI: 10.1021/jo049490u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
N6-Protected adenosines have been prepared from inosines by activation of the C6 position and Pd-catalyzed coupling with amides. An efficient route to [6-15NH2]-N6-benzoyladenosine and [1-15N,6-15NH2]-N6-benzoyladenosine has been achieved.
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Affiliation(s)
- Montserrat Terrazas
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
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23
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Chakraborti D, Colis L, Schneider R, Basu AK. Synthesis of N2 2'-deoxyguanosine adducts formed by 1-nitropyrene. Org Lett 2003; 5:2861-4. [PMID: 12889893 DOI: 10.1021/ol034904b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[reaction: see text] Synthesis of N(2) 2'-deoxyguanosine adducts formed by the ubiquitous carcinogen, 1-nitropyrene, is reported. Various conditions of Buchwald-Hartwig palladium-catalyzed amination are examined. The most convenient synthetic approach involved a straightforward coupling between protected 2'-deoxyguanosine and bromonitropyrenes, which, upon reductive deprotection, provided excellent yield of the two 1-nitropyrene adducts.
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Affiliation(s)
- Debasis Chakraborti
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA
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Hooper MW, Hartwig JF. Understanding the Coupling of Heteroaromatic Substrates: Synthesis, Structures, and Reductive Eliminations of Heteroarylpalladium Amido Complexes. Organometallics 2003. [DOI: 10.1021/om030257g] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mark W. Hooper
- Department of Chemistry, P.O. Box 208107, Yale University, New Haven, Connecticut 06520-8107
| | - John F. Hartwig
- Department of Chemistry, P.O. Box 208107, Yale University, New Haven, Connecticut 06520-8107
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25
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Enguehard C, Allouchi H, Gueiffier A, Buchwald SL. Easy access to novel substituted 6-aminoimidazo[1,2-a]pyridines using palladium- and copper-catalyzed aminations. J Org Chem 2003; 68:4367-70. [PMID: 12762738 DOI: 10.1021/jo0341463] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Convenient and efficient methods for the preparation of novel 6-aminoimidazo[1,2-a]pyridine derivatives are reported that utilized palladium- or copper-catalyzed methodology. The crystal structure for 6-N-methylanilinoimidazo[1,2-a]pyridine 10 is also described.
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Affiliation(s)
- Cécile Enguehard
- EA 3247, Laboratoire de Chimie Thérapeutique, Laboratoire de Chimie Physique, UFR des Sciences Pharmaceutiques, 31 Avenue Monge, 37200 Tours, France
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26
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Affiliation(s)
- Luigi A Agrofoglio
- Institut de Chimie Organique et Analytique, UMR CNRS 6005, Université d'Orléans, BP 6759-Rue de Chartres, 45067 Orléans, France
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27
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Lakshman MK, Gunda P. Palladium-catalyzed synthesis of carcinogenic polycyclic aromatic hydrocarbon epoxide-nucleoside adducts: the first amination of a chloro nucleoside. Org Lett 2003; 5:39-42. [PMID: 12509885 DOI: 10.1021/ol027084w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pd-catalyzed coupling of the axially constrained, less reactive benzo[a]pyrene bay-region amino benzoates, derived from the tetrahydro and diol epoxides, with C-6 and C-2 halopurine deoxynucleosides offers an efficient approach to the synthesis of the corresponding nucleoside-epoxide adducts. Also reported are the first examples involving the coupling of a 6-chloropurine deoxynucleoside with these amines, a reaction that is difficult by direct halide displacement. Certain mechanistic aspects of this metal-catalyzed C-N bond formation are also discussed. [reaction--see text]
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry, City College of CUNY, 138th Street at Convent Avenue, New York, NY 10031-9198, USA.
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28
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Lakshman MK. Palladium-catalyzed C–N and C–C cross-couplings as versatile, new avenues for modifications of purine 2′-deoxynucleosides. J Organomet Chem 2002. [DOI: 10.1016/s0022-328x(02)01267-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Lakshman MK, Thomson PF, Nuqui MA, Hilmer JH, Sevova N, Boggess B. Facile Pd-catalyzed cross-coupling of 2'-deoxyguanosine O6-arylsulfonates with arylboronic acids. Org Lett 2002; 4:1479-82. [PMID: 11975608 DOI: 10.1021/ol025673w] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text]. The O6-(2-mesitylenesulfonyl) derivative of 2'-deoxyguanosine undergoes a facile palladium-mediated C-C cross-coupling with arylboronic acids. Demonstrating the general applicability of this method, the synthesis of a previously undescribed class of 2-amino-6-arylpurine 2'-deoxynucleosides has been accomplished. The study also describes an evaluation of the O6-(2,4,6-triisopropylphenylsulfonyl) and the O6-(4-toluenesulfonyl) derivatives for the cross-coupling.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry, City College of CUNY, 138th Street at Convent Avenue, New York, New York 10031-9198, USA.
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30
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31
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Hocek M, Stará IG, Starý I, Dvořáková H. Covalent Analogues of DNA Base-Pairs and Triplets IV. Synthesis of Trisubstituted Benzenes Bearing Purine and/or Pyrimidine Rings by Cyclotrimerization of 6-Ethynylpurines and/or 5-Ethynyl-1,3-dimethyluracil. ACTA ACUST UNITED AC 2002. [DOI: 10.1135/cccc20021223] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ni-Catalyzed cyclotrimerizations of 6-ethynylpurines 3 or 5-ethynyl-1,3-dimethyluracil (4) afforded the 1,2,4-tris(purin-6-yl)benzenes 7 or 1,2,4-tris(1,3-dimetyhyluracil-5-yl)benzene (9), respectively. The symmetrical 1,3,5-tris(purin-6-yl)benzenes 8 were also formed as minor products in very low yields. Co-cyclotrimerization of 9-benzyl-6-ethynylpurine (3a) with 4 afforded the tris(purinyl)benzene 7a as a major product along with 1,2-bis(9-benzylpurin-6-yl)-4-(1,3-dimethyluracil-5-yl)benzene (10) and a complex mixture of other derivatives and isomers. Compounds 7-10 are analogues of Hoogsteen base-triplets.
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32
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Lakshman MK, Hilmer JH, Martin JQ, Keeler JC, Dinh YQ, Ngassa FN, Russon LM. Palladium catalysis for the synthesis of hydrophobic C-6 and C-2 aryl 2'-deoxynucleosides. Comparison of C-C versus C-N bond formation as well as C-6 versus C-2 reactivity. J Am Chem Soc 2001; 123:7779-87. [PMID: 11493051 DOI: 10.1021/ja0107172] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Suzuki-Miyaura cross-coupling of haloaromatic compounds with arylboronic acids provides a simple entry to biaryl systems. Despite its ease, to date, there are no detailed investigations of this procedure for deoxynucleoside modification. As shown in this study, a wide variety of C-6 arylpurine 2'-deoxyriboside (C-6 aryl 2'-deoxynebularine analogues) and C-2 aryl 2'-deoxyinosine analogues can be conveniently prepared via the Pd-mediated cross-coupling of arylboronic acids with the C-6 halonucleosides, 6-bromo- or 6-chloro-9[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-beta-D-erythro-pentofuranosyl]purine (1 and 2), and the C-2 halonucleoside, 2-bromo-O(6)-benzyl-3',5'-bis-O-(tert-butyldimethylsilyl)-2'-deoxyinosine (3). Although bromonucleoside 1 proved to be a good substrate for the Pd-catalyzed Suzuki-Miyaura cross-couplings, we have noted that for several C-6 arylations, the chloronucleoside 2 provides superior coupling yields. Also described in this study is a detailed evaluation of catalytic systems that led to optimal product recoveries. Finally, a comparison of the C-C and C-N bond-forming reactions of deoxynucleosides is also reported. On the basis of this comparison, we provide evidence that C-N bond formation at the C-6 position, leading to N-aryl 2'-deoxyadenosine analogues, is more sensitive to the ligand used, whereas C-C bond-forming reactions at the same position are not. In contrast to the ligand dependency exhibited in C-N bond formation at the C-6 position, comparable reactions at the C-2 position of purine deoxynucleosides proceed with less sensitivity to the ligand used.
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Affiliation(s)
- M K Lakshman
- Department of Chemistry, City College of CUNY, 138th Street at Convent Avenue, New York, New York 10031-9198, USA.
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Abstract
Aryl iodides are coupled with amines to give the corresponding arylamines in high yield in the presence of palladium, a suitable ligand, and NaOt-Bu. Functionalized aryl iodides give good yields of the corresponding arylamines when Cs(2)CO(3) is substituted as the base.
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Affiliation(s)
- M H Ali
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Abstract
[structure: see text] The C8-2'-deoxyguanosine adduct of the food mutagen 2-amino-3-methylimadazo[4,5-f]-quinoline (IQ) has been synthesized. The key step is a palladium-catalyzed N-arylation of a suitably protected 8-bromo-2'-deoxyguanosine derivative.
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Affiliation(s)
- Z Wang
- Department of Chemistry, Vanderbilt University, VU Station B 351822, Nashville, Tennessee 37235-1822, USA
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Hocek M, Stará IG, Starý I, Dvořáková H. Cyclotrimerization of 6-ethynylpurines. Synthesis of 1,2,4- and 1,3,5-tris(purin-6-yl)benzenes as novel Hoogsteen-triplet analogues. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(00)01989-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Lin X, Robins MJ. Mild and efficient functionalization at C6 of purine 2'-deoxynucleosides and ribonucleosides. Org Lett 2000; 2:3497-9. [PMID: 11082018 DOI: 10.1021/ol000255h] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[reaction: see text] Treatment of sugar-protected inosine and 2'-deoxyinosine derivatives with a cyclic secondary amine or imidazole and I(2)/Ph(3)P/EtN(i-Pr)(2)/(CH(2)Cl(2) or toluene) gave quantitative conversions into 6-N-(substituted)purine nucleosides. S(N)Ar reactions with 6-(imidazol-1-yl) derivatives gave 6-(N, O, or S)-substituted products. The 6-(benzylsulfonyl) group underwent S(N)Ar displacement with an arylamine at ambient temperature.
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Affiliation(s)
- X Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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Harwood EA, Hopkins PB, Sigurdsson ST. Chemical synthesis of cross-link lesions found in nitrous acid treated DNA: a general method for the preparation of N2-substituted 2'-deoxyguanosines. J Org Chem 2000; 65:2959-64. [PMID: 10814184 DOI: 10.1021/jo991501+] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Treatment of DNA with nitrous acid results in the formation of DNA-DNA cross-links. Two cross-link lesions have previously been isolated and their structures assigned based on spectroscopic data. The major lesion has been proposed to consist of two deoxyguanosine (dG) nucleosides sharing a common N2 atom (1), while the structure of the minor lesion has been proposed to consist of a common nitrogen atom linking C2 of a dG nucleoside to C6 of deoxyadenosine (2). The chemical synthesis of 1 and 2, utilizing a palladium-catalyzed coupling, is described herein. It is demonstrated that the spectroscopic properties of synthetic 1 are identical to that of lesion 1 obtained from nitrous acid cross-linked DNA, thus providing a proof of its structure. Comparison of the limited spectroscopic data available for lesion 2 originating from nitrous acid cross-linked DNA to synthetic 2 supports its structural assignment. The synthetic approach used for synthesis of 1 and 2 is shown to be a general method for the preparation of a variety of N2-substituted dG nucleosides in good yields.
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Affiliation(s)
- E A Harwood
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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