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Madaoui M, Datta D, Wassarman K, Zlatev I, Egli M, Ross BS, Manoharan M. A Chemical Approach to Introduce 2,6-Diaminopurine and 2-Aminoadenine Conjugates into Oligonucleotides without Need for Protecting Groups. Org Lett 2022; 24:6111-6116. [PMID: 35973215 PMCID: PMC9425559 DOI: 10.1021/acs.orglett.2c01848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We report a simple, postsynthetic strategy for synthesis
of oligonucleotides
containing 2,6-diaminopurine nucleotides and 2-aminoadenine conjugates
using 2-fluoro-6-amino-adenosine. The strategy allows introduction
of 2,6-diaminopurine and other 2-amino group-containing ligands. The
strongly electronegative 2-fluoro deactivates 6-NH2 obviating
the need for any protecting group on adenine, and simple aromatic
nucleophilic substitution of fluorine makes reaction with aqueous
NH3 or R-NH2 feasible at the 2-position.
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Affiliation(s)
- Mimouna Madaoui
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Bruce S Ross
- Ross Chemistry Consulting, El Granada, California 94018, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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2
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Chai Y, Kondhare D, Zhang A, Leonard P, Seela F. The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration. Chemistry 2021; 27:2093-2103. [PMID: 33090562 PMCID: PMC7898646 DOI: 10.1002/chem.202004221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 02/05/2023]
Abstract
Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of RespiratoryCritical Care Medicine Targeted Tracer, Research and Development LaboratoryWest China HospitalSichuan610041P. R. China
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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3
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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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4
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Pujari SS, Leonard P, Seela F. Oligonucleotides with "clickable" sugar residues: synthesis, duplex stability, and terminal versus central interstrand cross-linking of 2'-O-propargylated 2-aminoadenosine with a bifunctional azide. J Org Chem 2014; 79:4423-37. [PMID: 24693949 DOI: 10.1021/jo500392j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Duplex DNA with terminal and internal sugar cross-links were synthesized by the CuAAC reaction from oligonucleotides containing 2'-O-propargyl-2-aminoadenosine as a clickable site and a bifunctional azide (4). Stepwise click chemistry was employed to introduce cross-links at internal and terminal positions. Copper turnings were used as catalyst, reducing the copper load of the reaction mixture and avoiding complexing agents. For oligonucleotide building block synthesis, a protecting group strategy was developed for 2'-O-propargyl-2-aminoadenosine owing to the rather different reactivities of the two amino groups. Phosphoramidites were synthesized bearing clickable 2'-O-propargyl residues (14 and 18) as well as a 2'-deoxyribofuranosyl residue (10). Hybridization experiments of non-cross-linked oligonucleotides with 2,6-diaminopurine as nucleobase showed no significant thermal stability changes over those containing adenine. Surprisingly, an isobutyryl group protecting the 2-amino function has no negative impact on the stability of DNA-DNA and DNA-RNA duplexes. Oligonucleotide duplexes with cross-linked 2'-O-propargylated 2-aminoadenosine (1) and 2'-O-propargylated adenosine (3) at terminal positions are significantly stabilized (ΔT(m) = +29 °C). The stability results from a molecularity change from duplex to hairpin melting and is influenced by the ligation position. Terminal ligation led to higher melting duplexes than corresponding hairpins, while duplexes with central ligation sites were less stable.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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5
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Abstract
Protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, prevent irreversible nucleobase modifications that may occur in the presence of alkylating or condensing reagents that are commonly used in nucleoside protection and oligonucleotide synthesis. This unit reviews these protecting groups, and also identifies protecting groups for the exocyclic amino function of cytosine, adenine, and guanine. The unit also explores recent trends in nucleobase protection that permit reliable oligonucleotide synthesis and removal of N-protecting groups under very mild conditions.
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Affiliation(s)
- R P Iyer
- OriGenix Technologies, Laval, Quebec, Canada
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6
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7
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Chow CS, Mahto SK, Lamichhane TN. Combined Approaches to Site-Specific Modification of RNA. ACS Chem Biol 2008; 3:30-37. [PMID: 18177002 DOI: 10.1021/cb7002225] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Both natural and unnatural modifications in RNA are of interest to biologists and chemists. More than 100 different analogues of the four standard RNA nucleosides have been identified in nature. Unnatural modifications are useful for structure and mechanistic studies of RNA. This Review highlights chemical, enzymatic, and combined (semisynthesis) approaches to generate site specifically modified RNAs. The availability of these methods for site-specific modifications of RNAs of all sizes is important in order to study the relationships between RNA chemical composition, structure, and function.
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Affiliation(s)
- Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Santosh K. Mahto
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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8
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Zatsepin TS, Romanova EA, Oretskaya TS. Synthesis of 2'-O-alkylnucleosides. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc2002v071n06abeh000714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Muraoka M, Takahashi S, Uesugi S. Interaction of (2′ -5′) and (3′ -5′) Linked 2-Aminoadenylyl-3-aminoadenosines with Polyuridylic Acid. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/15257779508009488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Synthesis of novel C4-linked imidazole ribonucleoside phosphoramidites for probing general acid and base catalysis in ribozyme. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.09.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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12
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Okamoto I, Shohda KI, Seio K, Sekine M. A new route to 2'-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives. J Org Chem 2004; 68:9971-82. [PMID: 14682690 DOI: 10.1021/jo035246b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides containing 2-thiouridine (s2U) in place of uridine form stable RNA duplexes with complementary RNAs. Particularly, this modified nucleoside has proved to recognize highly selectively adenosine, the genuine partner, without formation of a mismatched base pair with the guanosine counterpart. In this paper, we describe new methods for the synthesis of 2-thiouridine and various 2'-O-alkyl-2-thiouridine derivatives. Oligoribonucleotides having these modified nucleoside derivatives were synthesized, and their hybridization and structural properties were studied in detail by the 1H NMR analysis of these modified nucleosides and Tm experiments of RNA duplexes with their complementary RNA strands.
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Affiliation(s)
- Itaru Okamoto
- Department of Life Science and Frontier Collaborative Research Center, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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13
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Busca P, Etheve-Quelquejeu M, Valéry JM. Synthesis of 2′-O,3′-O bicyclic adenosine analogues using ring closing metathesis. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.10.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Frieden M, Aviñó A, Eritja R. Convenient synthesis of 8-amino-2'-deoxyadenosine. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:193-202. [PMID: 12744605 DOI: 10.1081/ncn-120019521] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We studied the behaviour of 8-azido-2'-deoxyadenosine and 8-bromo-2'-deoxyadenosine in aqueous solutions of ammonia and primary and secondary amines. Unexpectedly, 8-Azido-2'-deoxyadenosine is converted to 8-amino-2'-deoxyadenosine in excellent yields. The use of this reaction for the preparation of 8-aminoadenine derivatives needed for the preparation of oligonucleotides carrying 8-aminoadenine is discussed.
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Affiliation(s)
- Miriam Frieden
- Instituto de Biologia Molecular de Barcelona, C.S.I.C. Jordi Girona, Barcelona, Spain
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15
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Naval M, Michel T, Vasseur JJ, Debart F. 2-Amino-alpha-2'-deoxyadenosine increased duplex stability of methoxyethylphosphoramidate alpha-oligodeoxynucleotides with RNA target. Bioorg Med Chem Lett 2002; 12:1435-8. [PMID: 12031314 DOI: 10.1016/s0960-894x(02)00215-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A new efficient synthesis of 2-amino-alpha-2'-deoxyadenosine and its incorporation into methoxyethylphosphoramidate alpha-oligodeoxynucleotides (ODNs) via H-phosphonate chemistry were reported. Thermal denaturation experiments demonstrated a significant stabilization of the complexes formed between these analogues and their RNA target (+2 degrees C/NH2A) relative to adenosine-containing phosphoramidate alpha-oligonucleotides. Concerning the binding specificity of these modified ODNs, unlike natural ODNs, discrimination against G pairing is higher and against C pairing is lower.
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Affiliation(s)
- Magali Naval
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM II, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Cedex 05, France
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16
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Prakash TP, Kawasaki AM, Fraser AS, Vasquez G, Manoharan M. Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides. J Org Chem 2002; 67:357-69. [PMID: 11798305 DOI: 10.1021/jo0103975] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., 2292 Faraday Avenue, Carlsbad, California 92008, USA
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17
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Bailly C, Waring MJ. Use of DNA molecules substituted with unnatural nucleotides to probe specific drug-DNA interactions. Methods Enzymol 2001; 340:485-502. [PMID: 11494865 DOI: 10.1016/s0076-6879(01)40438-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- C Bailly
- INSERM U-524, and Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret IRCL, 59045 Lille, France
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18
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Seela F, Becher G. Pyrazolo[3,4-d]pyrimidine nucleic acids: adjustment of dA-dT to dG-dC base pair stability. Nucleic Acids Res 2001; 29:2069-78. [PMID: 11353076 PMCID: PMC55453 DOI: 10.1093/nar/29.10.2069] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2001] [Revised: 03/19/2001] [Accepted: 03/19/2001] [Indexed: 11/12/2022] Open
Abstract
Oligonucleotides incorporating 8-aza-7-deazapurin-2,6-diamine (pyrazolo[3,4-d]pyrimidin-4,6-diamine) nucleoside 2a or its 7-bromo derivative 2b show enhanced duplex stability compared to those containing dA. While incorporation of 2a opposite dT increases the T(m) value only slightly, the 7-bromo compound 2b forms a very stable base pair which is as strong as the dG-dC pair. Compound 2b shows a similar base discrimination in duplex DNA as dA. The base-modified nucleosides 2a,b have a significantly more stable N-glycosylic bond than the rather labile purin-2,6-diamine 2'-deoxyribonucleoside 1. Base protection with acyl groups, with which we had difficulties in the case of purine nucleoside 1, was effective with pyrazolo[3,4-d]-pyrimidine nucleosides 2a,b. Oligonucleotides containing 2a,b were obtained by solid phase synthesis employing phosphoramidite chemistry. Compound 2b harmonizes the stability of DNA duplexes. Their stability is no longer dependent on the base pair composition while they still maintain their sequence specificity. Thus, they have the potential to reduce the number of mispairs when hybridized in solution or immobilized on arrays.
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Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany.
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19
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Herdewijn P. Heterocyclic modifications of oligonucleotides and antisense technology. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:297-310. [PMID: 10984123 DOI: 10.1089/108729000421475] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Modification of the heterocyclic moiety of oligonucleotides has led to the discovery of potent antisense compounds. This review describes the physicochemical factors that are responsible for duplex stabilization through base modification. A summary is given of the different heterocyclic modifications that can be used to beneficially influence this duplex stability. The biologic activity of base-modified oligonucleotides is described, and the different factors that are important for obtaining in vivo antisense activity with heterocyclic-modified oligonucleotides are summarized.
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Affiliation(s)
- P Herdewijn
- Rega Institute for Medical Research, K.U. Leuven, Laboratory for Medicinal Chemistry, Belgium
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20
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Affiliation(s)
- S T Crooke
- ISIS Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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21
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Manfredini S, Baraldi PG, Durini E, Vertuani S, Balzarini J, De Clercq E, Karlsson A, Buzzoni V, Thelander L. 5'-Phosphoramidates and 5'-diphosphates of 2'-O-allyl-beta-D-arabinofuranosyluracil, -cytosine, and -adenine: inhibition of ribonucleotide reductase. J Med Chem 1999; 42:3243-50. [PMID: 10464011 DOI: 10.1021/jm9807095] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Continuing our studies on ribonucleotide reductase (RNR) mechanism-based inhibitors, we have now prepared the diphosphates (DP) of 2'-O-allyl-1-beta-D-arabinofuranosyl-uracil and -cytosine and 2'-O-allyl-9-beta-D-arabinofuranosyl-adenine and evaluated their inhibitory activity against recombinant murine RNR. 2'-O-Allyl-araUDP proved to be inhibitory to RNR at an IC(50) of 100 microM, whereas 2'-O-allyl-araCDP was only marginally active (IC(50) 1 mM) and 2'-O-allyl-araADP was completely inactive. The susceptibility of the parent nucleosides to phosphorylation by thymidine kinase and 2'-deoxycytidine kinase was also investigated, and all nucleosides proved to be poor substrates for the above-cited kinases. Moreover, prodrugs of 2'-O-allyl-araU and -araC monophosphates, namely 2'-O-allyl-5'-(phenylethoxy-L-alanyl phosphate)-araU and -araC, were prepared and tested against tumor cell proliferation but proved to be inactive. A molecular modeling study has been conducted in order to explain our results. The data confirm that for both the natural and analogue nucleoside diphosphates, the principal determinant interaction with the active site of RNR is with the diphosphate group, which forms strong hydrogen bonds with Glu623, Thr624, Ser625, and Thr209. Our findings indicate that the poor phosphorylation may represent an explanation for the lack of marked in vitro cytostatic activity of the test compounds.
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Affiliation(s)
- S Manfredini
- Department of Pharmaceutical Sciences, Ferrara University, Italy
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22
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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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23
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24
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Groebke K, Hunziker J, Fraser W, Peng L, Diederichsen U, Zimmermann K, Holzner A, Leumann C, Eschenmoser A. Warum Pentose- und nicht Hexose-Nucleins�uren?? Teil V. (Purin-Purin)-Basenpaarung in der homo-DNS-Reihe: Guanin, Isoguanin, 2,6-Diaminopurin und Xanthin. Helv Chim Acta 1998. [DOI: 10.1002/hlca.19980810302] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Hosono K, Gozu H, Hosaka H, Sakamoto K, Yokoyama S, Takai K, Takaku H. Cleavage effect of oligoribonucleotides substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1354:211-8. [PMID: 9427530 DOI: 10.1016/s0167-4781(97)00099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The precursor of an RNA molecule from T4-infected E. coli cells (p2Spl RNA) has the capacity to cleave itself at specific positions [UpA (139-140) and CpA (170-171)], within a putative loop and stem structure. This sequence-specific cleavage requires at least a monovalent cation and non-ionic detergents. In order to determine the influence of the pyrimidine and purine bases on these sequence-specific cleavage reactions, we studied the cleavage reactions of hairpin loop RNAs substituted at the cleavage sites with modified pyrimidine- and purine-nucleosides. The cleavage was affected by the 2'-hydroxyl groups and the bases of the pyrimidines, and the 6-amino group of the purine.
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Affiliation(s)
- K Hosono
- Department of Industrial Chemistry, Chiba Institute of Technology, Narashino, Japan
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26
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Paalman SR, Noll DM, Clarke ND. Formation of a covalent complex between methylguanine methyltransferase and DNA via disulfide bond formation between the active site cysteine and a thiol-containing analog of guanine. Nucleic Acids Res 1997; 25:1795-801. [PMID: 9108163 PMCID: PMC146672 DOI: 10.1093/nar/25.9.1795] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
DNA repair methyltransferases (MTases) remove methyl or other alkyl groups from the O6 position of guanine or the O4 position of thymine by transfering the group to an active site cysteine. In order to trap an MTase-DNA complex via a disulfide bond, 2'-deoxy-6-(cystamine)-2-aminopurine (d6Cys2AP) was synthesized and incorporated into oligonucleotides. d6Cys2AP has a disulfide bond within an alkyl chain linked to the 6 position of 2,6-diaminopurine, which disulfide can be reduced to form a free thiol. Addition of human MTase to reduced oligonucleotide resulted in a protein-DNA complex that was insensitive to denaturation by SDS and high salt, but which readily dissociated in the presence of dithiothreitol. Formation of this complex was prevented by methylation of the active site cysteine. Evidence that the active site cysteine is directly involved in disulfide bond formation was obtained by N-terminal sequencing of peptides that remained associated with DNA after proteolysis of the complex.
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Affiliation(s)
- S R Paalman
- Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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27
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Manfredini S, Baraldi PG, Bazzanini R, Simoni D, Balzarini J, De Clercq E. Synthesis and antiproliferative activity of 2′-O-allyl-1-β-D-arabinofuranosyl-uracil, -cytosine and -adenine. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00044-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Crooke ST. Advances in understanding the pharmacological properties of antisense oligonucleotides. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1997; 40:1-49. [PMID: 9217922 DOI: 10.1016/s1054-3589(08)60136-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- S T Crooke
- Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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30
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Abstract
This review is aimed at biochemists and molecular biologists, and covers the chemistry and key features involved in the solid-phase synthesis of a variety of the better known DNA and RNA analogues by the phosphoramidite and H-phosphonate methods. A wide spectrum of biological applications such as inhibition of gene expression, translation arrest, RNA processing, affinity purification of RNA-protein complexes, in situ hybridization, and synthetic ribozymes are then discussed in some detail, enabling the molecular biologist to get an idea of what is possible using the current technology.
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Brownlee GG, Fodor E, Pritlove DC, Gould KG, Dalluge JJ. Solid phase synthesis of 5'-diphosphorylated oligoribonucleotides and their conversion to capped m7Gppp-oligoribonucleotides for use as primers for influenza A virus RNA polymerase in vitro. Nucleic Acids Res 1995; 23:2641-7. [PMID: 7544461 PMCID: PMC307087 DOI: 10.1093/nar/23.14.2641] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have synthesized four different 5'-diphosphorylated oligoribonucleotides, varying in length from 11 to 13 nucleotides by a new solid phase method. After deprotection and partial purification the 5'-diphosphorylated oligoribonucleotides could be converted to capped (m7Gppp) oligoribonucleotides using guanylyl transferase. Radiolabelled capped oligoribonucleotides acted as primers for the influenza A virus RNA polymerase in vitro. The solid phase method described here should also allow the addition of 5'-diphosphates to synthetic oligodeoxyribonucleotides and be capable automation.
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Affiliation(s)
- G G Brownlee
- Chemical Pathology Unit, Sir William Dunn School of Pathology, University of Oxford, UK
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33
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Martin P. Ein neuer Zugang zu 2?-O-Alkylribonucleosiden und Eigenschaften deren Oligonucleotide. Helv Chim Acta 1995. [DOI: 10.1002/hlca.19950780219] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Leydier C, Bellon L, Barascut JL, Morvan F, Rayner B, Imbach JL. 4'-Thio-RNA: synthesis of mixed base 4'-thio-oligoribonucleotides, nuclease resistance, and base pairing properties with complementary single and double strand. ANTISENSE RESEARCH AND DEVELOPMENT 1995; 5:167-74. [PMID: 8785472 DOI: 10.1089/ard.1995.5.167] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
4'-Thio-beta-D-oligoribonucleotides (12 mer and 16 mer) containing a mixed base sequence were synthesized via the phosphoramidite solid support approach. These RNA analogs showed very good nuclease resistance as compared with wild-type RNA. Furthermore, 4'-thio-beta-D-oligoribonucleotides were shown to hybridize with a complementary DNA or RNA strand to form a duplex or with a DNA hairpin to form a triple helix. 4'-Thio-RNA binds more tightly to its complementary RNA strand than to its complementary DNA strand. A 4'-thio-RNA:RNA duplex is as stable as a 2'-O-methyl-RNA:RNA duplex. 4'-Thio-RNA, however, forms a 4'-thio-RNA:DNA:DNA triplex with a stability similar to the corresponding triplex with all wild-type DNA.
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Affiliation(s)
- C Leydier
- Laboratoire de Chimie Bio-Organique, URA 488, CNRS, Université de Montpellier II, France
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35
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Grasby JA, Pritchard CE, Gait MJ. Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function. J CHEM SCI 1994. [DOI: 10.1007/bf02841914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Grunder-Klotz E, Just G. Synthesis of Deoxycytidine (dC) Building Blocks for Amide-Linked Dimers or Oligomers: Example of a Deoxycytidine-amide-thymidine Dimer. ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408010666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Beijer B, Gr⊘tli M, Douglas ME, Sproat BS. Simplified and Cost Effective Syntheses of Fully Protected Phosphoramidite Monomers Suitable for the Assembly of Oligo(2′-O-allylribonucleotides). ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408010672] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Canol A, Goodman MF, Eritja R. Synthesis of Oligodeoxyribonucleotides Containing 2,6-Diaminopurine. ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408013258] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Pantopoulos K, Johansson HE, Hentze MW. The role of the 5' untranslated region of eukaryotic messenger RNAs in translation and its investigation using antisense technologies. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 48:181-238. [PMID: 7938549 PMCID: PMC7133200 DOI: 10.1016/s0079-6603(08)60856-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter discusses the recent advances in the field of translational control and the possibility of applying the powerful antisense technology to investigate some of the unanswered questions, especially those pertaining to the role of the 5’untranslated region ( UTR) on translation initiation. Translational regulation is predominantly exerted during the initiation phase that is considered to be the rate-limiting step. Two types of translational regulation can be distinguished: global, in which the initiation rate of (nearly) all cellular messenger RNA (mRNA) is controlled and selective, in which the translation rate of specific mRNAs varies in response to the biological stimuli. In most cases of global regulation, control is exerted via the phosphorylation state of certain initiation factors, whereas only a few examples of selective regulation have been characterized well enough to define the underlying molecular events. Interestingly, cis-acting regulatory sequences, affecting translation initiation, have been found not only in the 5’UTRs of selectively regulated mRNAs, but also in the 3’UTRs. Thus, in addition to the protein encoding open reading frames, both the 5’ and 3’UTRs of mRNAs must be considered for their effect on translation.
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Key Words
- alas, 5-aminolevulinate synthase
- bfgf, basic fibroblast growth factor
- bip, immunoglobulin-binding protein
- cat, chloramphenicol acetyltransferase
- dai, double-stranded rna-activated inhibitor
- ealas, erythroid-specific form of alas
- frp, ferritin repressor protein
- gcd, general control derepressible
- gcn, general control nonderepressible
- gef, guanine-nucleotide exchange factor
- grp, glucose-regulated protein
- hgh, human growth hormone
- icam, intracellular adhesion molecule
- ire, iron-responsive element
- ire-bp, iron-responsive element-binding protein
- ires, internal ribosomal entry site
- irf, iron regulatory factor
- irp, iron regulatory protein
- la, lupus erythematosus antigen
- lap, liver-enriched activating protein
- lip, liver-enriched inhibitory protein
- mep, methyl phosphonate
- pa, phosphoramidate
- pdgf, platelet-derived growth factor
- pest, phosphotriester
- pll, poly(1-lysine)
- po, phosphodiester
- ps, phosphorothioate
- ps2, phosphorodithioate
- ssl, suppressor of stem-loop
- tce, translational control element
- tgf, transforming growth factor
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Affiliation(s)
- K Pantopoulos
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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40
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Grasby JA, Gait MJ. Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function analysis. Biochimie 1994; 76:1223-34. [PMID: 7538326 DOI: 10.1016/0300-9084(94)90053-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Synthetic oligoribonucleotides have become increasingly valuable in studies of RNA structure and function. A range of nucleotide analogues is available which carry modifications in the base, sugar or phosphate moieties. Such analogues have been incorporated into synthetic RNA structures to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparisons of the properties of the modified RNAs with unmodified RNA models allow conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. These methods have been applied to studies of RNA interactions with proteins, RNA catalysis and RNA structure.
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Affiliation(s)
- J A Grasby
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
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41
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Keller TH, Häner R. Synthesis and hybridization properties of oligonucleotides containing 2'-O-modified ribonucleotides. Nucleic Acids Res 1993; 21:4499-505. [PMID: 8233783 PMCID: PMC311181 DOI: 10.1093/nar/21.19.4499] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A versatile, general way is described for the introduction of different functional groups into oligonucleotides by means of a simple linker at the 2'-position of the sugar. Nucleotide building blocks carrying lipophilic, intercalating or tertiary amino groups can be placed deliberately at any desired position of oligonucleotides by standard automated oligonucleotide synthesis. Thermal denaturation studies with these oligonucleotides reveal the following general trends: i) Modification with lipophilic n-octyl groups has little if any effect on duplex stability; a destabilizing (lipophilic) substituent is better tolerated at or near the ends than in the middle of the oligo. ii) An intercalating substituent (2-aminoanthraquinone) substantially increases duplex stability. iii) N,N-Dimethyl amino residues also increase duplex stability though to a smaller extent than intercalating residues. iv) Modifications at the 5'-end have a more pronounced influence on the TM than the corresponding 3'-modifications. v) Oligonucleotides modified in such a way show little or no loss in sequence specificity.
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42
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Beaucage SL, Iyer RP. The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87958-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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43
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Blencowe BJ, Carmo-Fonseca M, Behrens SE, Lührmann R, Lamond AI. Interaction of the human autoantigen p150 with splicing snRNPs. J Cell Sci 1993; 105 ( Pt 3):685-97. [PMID: 8408296 DOI: 10.1242/jcs.105.3.685] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An important goal of studies on pre-mRNA splicing is to identify factors that mediate the snRNP-snRNP and snRNP-pre-mRNA interactions that take place in the spliceosome. The U4/U6 snRNP is one of the four snRNPs that are subunits of spliceosomes. A rare patient autoimmune serum (MaS serum) has recently been identified that specifically immunoprecipitates U4/U6 snRNP from HeLa cell extracts through recognition of a 150 kDa autoantigen (p150) (Okano and Medsger, Journal of Immunology, 146, 535–542, 1991). Here we show that in addition to U4/U6 snRNP, p150 can also be detected associated with 20 S U5, U4/U6.U5 and 17 S U2 snRNPs, but not with U1 snRNP. In each particle p150 is present in sub-stoichiometric levels relative to the major snRNP proteins. We show that MaS serum selectively immunoprecipitates a sub-population of U4/U6 snRNPs in which the m3G-cap structure is masked and that p150 is preferentially associated with U6 snRNA in the U4/U6 particle. Anti-p150 antibodies show widespread nucleoplasmic staining, excluding nucleoli, with an elevated concentration in coiled bodies. This changes to a discrete punctate pattern when cells are treated with alpha-amanitin. Both the cytological and biochemical data indicate that the p150 autoantigen is a snRNP-associated factor in vivo. We also present biochemical evidence confirming that assembly of U4/U6 and U5 snRNPs into a U4/U6.U5 tri-snRNP particle is an integral step in the spliceosome assembly pathway. Addition of the purified U4/U6.U5 tri-snRNP restores splicing activity to inactivated HeLa nuclear extracts in which splicing had been inhibited by specific depletion of either the U4/U6 or U5 snRNPs.
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Affiliation(s)
- B J Blencowe
- European Molecular Biology Laboratory, Heidelberg, Germany
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44
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Lamond AI, Sproat BS. Antisense oligonucleotides made of 2'-O-alkylRNA: their properties and applications in RNA biochemistry. FEBS Lett 1993; 325:123-7. [PMID: 7685712 DOI: 10.1016/0014-5793(93)81427-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Oligo(2'-O-alkylribonucleotides) have been developed recently as novel oligonucleotide analogues with properties that enhance their use as antisense probes. They possess high chemical stability and are resistant to hydrolysis by DNA- or RNA-specific nucleases. Many forms of oligo(2'-O-alkylribonucleotides) hybridise specifically and efficiently to complementary RNA sequences, forming stable duplexes that are not substrates for cleavage by RNAse H. In combination with prosthetic reporter groups, such as biotin, DNP or fluorophores, oligo(2'-O-alkylribonucleotides) have important applications in a wide range of biochemical studies on RNA function and structure.
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Affiliation(s)
- A I Lamond
- European Molecular Biology Laboratory, Heidelberg, Germany
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45
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Gopalakrishnan V, Kumar V, Ganesh KN. Regioselective 2′/3′-O-Allylation of Pyrimidine Ribonucleosides Using Phase Transfer Catalysis. ACTA ACUST UNITED AC 1992. [DOI: 10.1080/07328319208018341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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46
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Kumar V, Gopalakrishnan V, Ganesh KN. Regioselective Allylations of Pyrimidine Ribonucleosides Using Pd(0) Catalyst. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1992. [DOI: 10.1246/bcsj.65.1665] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Carmo-Fonseca M, Pepperkok R, Carvalho MT, Lamond AI. Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies. J Cell Biol 1992; 117:1-14. [PMID: 1532583 PMCID: PMC2289407 DOI: 10.1083/jcb.117.1.1] [Citation(s) in RCA: 332] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have recently shown that discrete foci are present in the nuclei of mammalian cells in which each of the U1, U2, U4/U6, and U5 snRNPs involved in pre-mRNA splicing, and the non-snRNP-splicing factor U2AF, are concentrated (Carmo-Fonseca, M., D. Tollervey, R. Pepperkok, S. Barabino, A. Merdes, C. Brunner, P. D. Zamore, M. R. Green, E. Hurt, and A. I. Lamond. 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:195-206; Carmo-Fonseca, M., R. Pepperkok, B. S. Sproat, W. Ansorge, M. S. Swanson, and A. I. Lamond. 1991 EMBO (Eur. Mol. Biol. Organ.) J. 10:1863-1873). Here, we identify these snRNP-rich organelles as coiled bodies. snRNPs no longer concentrate in coiled bodies after cells are treated with the transcription inhibitors alpha-amanitin or actinomycin D. snRNP association with coiled bodies is also disrupted by heat shock. This indicates that the association of snRNPs with coiled bodies may be connected with the metabolism of nascent transcripts. A novel labeling method is described which shows both the RNA and protein components of individual snRNPs colocalizing in situ. Using this procedure all spliceosomal snRNPs are seen distributed in a nonhomogeneous pattern throughout the nucleoplasm, excluding nucleoli. They are most concentrated in coiled bodies, but in addition are present in "speckled" structures which are distinct from coiled bodies and which contain the non-snRNP splicing factor SC-35. U1 snRNP shows a more widespread nucleoplasmic staining, outside of coiled bodies and "speckled" structures, relative to the other snRNPs. The association of snRNPs with "speckles" is disrupted by heat shock but enhanced when cells are treated with alpha-amanitin.
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48
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49
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Xu YZ, Zheng Q, Swann PF. Synthesis by post-synthetic substitution of oligomers containing guanine modified at the 6-position with S-, N-, O-derivatives. Tetrahedron 1992. [DOI: 10.1016/s0040-4020(01)88731-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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50
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Wagner E, Oberhauser B, Holzner A, Brunar H, Issakides G, Schaffner G, Cotten M, Knollmüller M, Noe CR. A simple procedure for the preparation of protected 2'-O-methyl or 2'-O-ethyl ribonucleoside-3'-O-phosphoramidites. Nucleic Acids Res 1991; 19:5965-71. [PMID: 1945882 PMCID: PMC329054 DOI: 10.1093/nar/19.21.5965] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protected 2'-O-methyl and 2'-O-ethyl ribonucleoside-3'-O-phosphoramidites were prepared via alkylation of the ribonucleosides at an early stage in the synthesis. Utilizing a strategy of minimal protection, the alkylation was performed with unprotected cytidine and adenosine, or with O6-protected guanosine and N3,5'-O-protected uridine using methyl or ethyl iodide and sodium hydride. In subsequent steps, the introduction of standard protective groups for oligonucleotide synthesis and the concomitant separation from 3'-O-alkylated isomers was accomplished. A modification of the phosphitylation procedure permitted facile isolation of the desired phosphoramidites which show high coupling efficiencies in oligomer assembly.
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Affiliation(s)
- E Wagner
- Institute for Molecular Pathology, Vienna, Austria
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