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Shahsavari S, Eriyagama DNAM, Chen J, Halami B, Yin Y, Chillar K, Fang S. Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups. J Org Chem 2019; 84:13374-13383. [PMID: 31536351 PMCID: PMC6825528 DOI: 10.1021/acs.joc.9b01527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In traditional oligodeoxynucleotide (ODN) synthesis, phosphate groups are protected with the 2-cyanoethyl group, and amino groups are protected with acyl groups. At the end of ODN synthesis, deprotection is achieved with strong bases and nucleophiles. Therefore, traditional technologies are not suitable for the synthesis of ODNs containing sensitive functionalities. To address the problem, we report the use of Dim and Dmoc groups, which are based on the 1,3-dithian-2-yl-methyl function, for phosphate and amine protection for the solid phase ODN synthesis. Using the new Dim-Dmoc protection, deprotection was achieved under mild oxidative conditions without using any strong bases and nucleophiles. As a result, the new technology is suitable for the synthesis of ODNs containing sensitive functions. To demonstrate feasibility, seven 20-mer ODNs including four that contain sensitive ester and alkyl chloride groups were synthesized, purified with RP HPLC, and characterized with MALDI-TOF MS and enzyme digestion essays. High purity ODNs were obtained.
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Affiliation(s)
- Shahien Shahsavari
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Dhananjani N A M Eriyagama
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Jinsen Chen
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Bhaskar Halami
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Yipeng Yin
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Komal Chillar
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
| | - Shiyue Fang
- Department of Chemistry , Michigan Technological University , 1400 Townsend Drive , Houghton , Michigan 49931 , United States
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Shahsavari S, Eriyagama DNAM, Halami B, Begoyan V, Tanasova M, Chen J, Fang S. Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection. Beilstein J Org Chem 2019; 15:1116-1128. [PMID: 31164948 PMCID: PMC6541367 DOI: 10.3762/bjoc.15.108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023] Open
Abstract
Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.
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Affiliation(s)
- Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Dhananjani N A M Eriyagama
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Vagarshak Begoyan
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
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Aviñó A, Güimil García R, Díaz A, Albericio F, Eritja R. A COMPARATIVE STUDY OF SUPPORTS FOR THE SYNTHESIS OF OLIGONUCLEOTIDES WITHOUT USING AMMONIA. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002739] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Eritja R, Adam V, AviñTó A, Díaz AR, Fàbrega C, Ferrer E, GrøStli M, García RG, Hofmann M, Márquez VE, Wiersma M. Preparation of Oligonucleotides Containing Non-Natural Base Analogs. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ramon Eritja
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Viviane Adam
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Anna AviñTó
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Antonio R. Díaz
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Carme Fàbrega
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Elisenda Ferrer
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Morten GrøStli
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Ramón Güimil García
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Mechtild Hofmann
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Víctor E. Márquez
- b National Cancer Institute, N.I.H. , Bethesda , Maryland , 20892 , USA
| | - Marten Wiersma
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
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Güimil García R, Brank AS, Christman JK, Marquez VE, Eritja R. Synthesis of oligonucleotide inhibitors of DNA (Cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:369-78. [PMID: 11838638 DOI: 10.1089/108729001753411335] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The incorporation of 5-azacytosine residues into DNA causes potent inhibition of DNA (Cytosine-C5) methyltransferases. The synthesis of oligodeoxyribonucleotides incorporating single or multiple 5-aza-2'-deoxycytidine residues at precise sites was undertaken to generate an array of sequences containing the reactive 5-azacytosine base as specific target sites for enzymatic methylation. Preparation of these modified oligonucleotides requires the use of 2-(p-nitrophenyl)ethyloxycarbonyl (NPEOC) groups for the protection of exocyclic amino functions. These groups are removed under mild conditions, thus avoiding conventional protocols that are detrimental to the integrity of the 5-azacytosine ring.
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McDougall MG, Sun L, Livshin I, Hosta LP, McArdle BF, Samols SB, Fuller CW, Kumar S. Analogs of guanine nucleoside triphosphates for sequencing applications. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:501-6. [PMID: 11563066 DOI: 10.1081/ncn-100002325] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have synthesized more than 30 different deoxyribonucleosides and triphosphates with modifications either in the base or the phosphate moiety as analogs of 2'-dGTP for DNA sequencing applications. All the modified nucleoside triphosphates were tested as substrates for DNA polymerases, including Sequenase T7 DNA polymerase or Thermo Sequenase DNA polymerase. Two of the analogs, 7-ethyl-7-deaza-dGTP and 7-hydroxymethyl-7-deaza-dGTP meet our requirements as better sequencing reagents.
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Affiliation(s)
- M G McDougall
- Amersham Pharmacia Biotech, 800 Centennial Ave., Piscataway, New Jersey 08855, USA
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Kim HY, Nechev L, Zhou L, Tamura P, Harris CM, Harris TM. Synthesis and adduction of fully deprotected oligodeoxynucleotides containing 6-chloropurine. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01462-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Fàbrega C, Güimil García R, Díaz AR, Eritja R. Studies on the synthesis of oligonucleotides containing photoreactive nucleosides: 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine. Biol Chem 1998; 379:527-33. [PMID: 9628347 DOI: 10.1515/bchm.1998.379.4-5.527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Oligonucleotides containing the photoreactive nucleosides 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine have been prepared using protected 2-fluoro-2'-deoxyinosine and 8-bromo-2'-deoxyadenosine phosphoramidites. After the assembly of the oligonucleotides, the nucleoside derivatives are converted to the corresponding azido derivatives by treatment with lithium azide in dry DMF. Deprotection of oligonucleotides carrying these azidonucleosides is performed with concentrated ammonia at room temperature.
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Affiliation(s)
- C Fàbrega
- European Molecular Biology Laboratory, Heidelberg, Germany
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Diaz AR, Eritja R, Garcia RG. Synthesis of Oligodeoxynucleotides Containing 2-Substituted Guanine Derivatives Using 2-Fluoro-2′-Deoxyinosine as Common Nucleoside Precursor. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002554] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Eritja R, Marquez VE, García RG. Synthesis and Properties of Oligonucleotides Containing 5-Aza-2′-deoxycytidine. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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DeCorte BL, Tsarouhtsis D, Kuchimanchi S, Cooper MD, Horton P, Harris CM, Harris TM. Improved strategies for postoligomerization synthesis of oligodeoxynucleotides bearing structurally defined adducts at the N2 position of deoxyguanosine. Chem Res Toxicol 1996; 9:630-7. [PMID: 8728509 DOI: 10.1021/tx9501795] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Improved methodology has been developed for preparation of oligodeoxynucleotides bearing adducts on the N2 position of guanine in which the adduction reaction is carried out in homogeneous solution rather than while the oligonucleotide is immobilized on a solid matrix. The methodology utilizes a new synthon, 2-fluoro-O6-(trimethylsilylethyl)-2'-deoxyinosine (3). Nucleoside 3 is stable to the conditions of oligonucleotide synthesis, but the O6 protection is eliminated under very mild conditions following displacement of the 2-fluoro group by amine nucleophiles. Oligonucleotides containing 3 could be removed from the solid support by treatment with 0.1 M NaOH (8 h, rt) without disruption of 3. Reaction of the crude, partially deprotected oligonucleotide with (R)-2-amino-2-phenylethanol in homogeneous solution, followed by removal of the remaining protective groups with NH4OH (60 degrees C, 8 h) and then 0.1% acetic acid, gave the adducted oligonucleotide in good purity and yield. Alternatively, fully deprotected oligonucleotide containing 3 could be prepared by use of labile phenoxyacetyl-type protecting groups on the exocyclic amino groups.
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Affiliation(s)
- B L DeCorte
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37235, USA
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