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Ingale SA, Leonard P, Tran QN, Seela F. Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability. J Org Chem 2015; 80:3124-38. [PMID: 25742047 DOI: 10.1021/acs.joc.5b00040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.
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Affiliation(s)
- Sachin A Ingale
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Quang Nhat Tran
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,‡Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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2
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Tang W, Zhu L, Smith LM. Controlling DNA Fragmentation in MALDI-MS by Chemical Modification. Anal Chem 2012; 69:302-12. [PMID: 21639184 DOI: 10.1021/ac960865o] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragmentation has proven to be a major factor limiting accessible mass range, sensitivity, and mass resolution in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Previous work has shown that this DNA fragmentation is strongly dependent on both the MALDI matrix and the nucleic acid sequence employed. Fragmentation is initiated by nucleobase protonation, leading to cleavage of the N-glycosidic bond with base loss, followed by cleavage of the phosphodiester backbone. In this study, asymmetric oligonucleotides incorporating cytidine and cytidine analogs such as 5-methyl-2'-deoxycytidine, 5-bromo-2'-deoxycytidine, aracytidine, and 2'-fluorodeoxycytidine nucleosides were used to systematically investigate the influence of the structural changes on the stability of the N-glycosidic bond. Modifications of the deoxyribose sugar ring by replacing the 2'-hydrogen with more electron-withdrawing groups such as the hydroxyl or fluoro group stabilize the N-glycosidic bond to a greater extent than the C5 nucleobase modifications. 2'-Hydroxyl and 2'-fluoro groups respectively are shown to partially or completely block fragmentation at the modified nucleosides. Mixtures of oligonucleotides incorporating such modifications demonstrate remarkably extended accessible mass range, as well as increased sensitivity and mass resolution. The stabilization provided by these chemical modifications also expands the range of matrices useful for nucleic acid analysis, yielding in some cases greatly improved performance.
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Affiliation(s)
- W Tang
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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Dai Q, Sengupta R, Deb SK, Piccirilli JA. Synthesis of 2′- N-Methylamino-2′-deoxyguanosine and 2′- N, N-Dimethylamino-2′-deoxyguanosine and Their Incorporation into RNA by Phosphoramidite Chemistry. J Org Chem 2011; 76:8718-25. [DOI: 10.1021/jo201364x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qing Dai
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Raghuvir Sengupta
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Shirshendu K. Deb
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
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4
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Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry 2008; 47:6883-94. [PMID: 18517225 DOI: 10.1021/bi800519a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many enzymes use metal ions within their active sites to achieve enormous rate acceleration. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). The three-dimensional arrangement determined by X-ray crystallography provides a powerful starting point for identifying ground state interactions, but only functional studies can establish and interrogate transition state interactions. The Tetrahymena group I ribozyme is a paradigm for the study of RNA catalysis, and previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified catalytic metal ions making five contacts with the substrate atoms. Here, we have combined atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to establish transition state ligands on the ribozyme for one of the catalytic metal ions, referred to as M A. We identified the pro-S P oxygen atoms at nucleotides C208, A304, and A306 as ground state ligands for M A, verifying interactions suggested by the Azoarcus crystal structures. We further established that these interactions are present in the chemical transition state, a conclusion that requires functional studies, such as those carried out herein. Elucidating these active site connections is a crucial step toward an in-depth understanding of how specific structural features of the group I intron lead to catalysis.
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Affiliation(s)
- Marcello Forconi
- Department of Biochemistry and Chemistry, Stanford University, Stanford, California 94305, USA
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5
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Cohen SB, Cech TR. Engineering disulfide cross-links in RNA using thiol-disulfide interchange chemistry. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.1. [PMID: 18428857 DOI: 10.1002/0471142700.nc0501s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protocols for postsynthetic modification of 2-amino-containing oligoribonucleotides with either an alkyl-phenyl disulfide or an alkyl thiol group are described. These groups react under mild conditions to form disulfide cross-links by thiol-disulfide interchange. These reactants do not form a disulfide bond when incorporated on opposite faces of a short continuous RNA helix, but do form disulfide bonds rapidly when they are placed in proximity. In addition, by incorporating these groups at various positions on large RNAs by semisynthesis, the dynamics of thermal motions can be detected. Such motions are believed to be linked to biological function, and the protocols presented in this unit are among the few simple ways to assess such dynamics.
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Affiliation(s)
- S B Cohen
- University of Colorado, Boulder, USA
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6
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Antsypovitch SI, Oretskaya TS. Double-helical nucleic acids with cross-linked strands: synthesis and applications in molecular biology. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1998v067n03abeh000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Dai Q, Deb SK, Hougland JL, Piccirilli JA. Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite. Bioorg Med Chem 2005; 14:705-13. [PMID: 16202607 DOI: 10.1016/j.bmc.2005.08.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 08/25/2005] [Accepted: 08/26/2005] [Indexed: 10/25/2022]
Abstract
2'-Amino-2'-deoxynucleosides and oligonucleotides containing them have proven highly effective for an array of biochemical applications. The guanosine analogue and its phosphoramidite derivatives have been accessed previously from 2'-amino-2'-deoxyuridine by transglycosylation, but with limited overall efficiency and convenience. Using simple modifications of known reaction types, we have developed useful protocols to obtain 2'-amino-2'-deoxyguanosine and two of its phosphoramidite derivatives with greater convenience, fewer steps, and higher yields than reported previously. These phosphoramidites provide effective synthons for the incorporation of 2'-amino-2'-deoxyguanosine into oligonucleotides.
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Affiliation(s)
- Qing Dai
- Howard Hughes Medical Institute, The University of Chicago, MC 1028, Chicago, IL 60637, USA
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8
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Jin S, Miduturu CV, McKinney DC, Silverman SK. Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA. J Org Chem 2005; 70:4284-99. [PMID: 15903302 DOI: 10.1021/jo050061l] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For studies of RNA structure, folding, and catalysis, site-specific modifications are typically introduced by solid-phase synthesis of RNA oligonucleotides using nucleoside phosphoramidites. Here, we report the preparation of two complete series of RNA nucleoside phosphoramidites; each has an appropriately protected amine or thiol functional group. The first series includes each of the four common RNA nucleotides, U, C, A, and G, with a 2'-(2-aminoethoxy)-2'-deoxy substitution (i.e., a primary amino group tethered to the 2'-oxygen by a two-carbon linker). The second series encompasses the four common RNA nucleotides, each with the analogous 2'-(2-mercaptoethoxy)-2'-deoxy substitution (i.e., a tethered 2'-thiol). The amines are useful for acylation and reductive amination reactions, and the thiols participate in displacement and oxidative cross-linking reactions, among other likely applications. The new phosphoramidites will be particularly valuable for enabling site-specific introduction of biophysical probes and constraints into RNA.
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Affiliation(s)
- Shengxi Jin
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Ross BS, Springer RH, Sprankle KG, Vasquez G. An Efficient and Scalable Synthesis of Arabinosylguanine and 2′-Deoxy-2′-Fluoro-guanosine. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006246] [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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10
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McGee DPC, Vaughn-Settle A, Vargeese C, Zhai Y. 2'-Amino-2'-deoxyuridine via an Intramolecular Cyclization of a Trichloroacetimidate. J Org Chem 1996; 61:781-785. [PMID: 11667006 DOI: 10.1021/jo9510548] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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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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12
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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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13
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Heidenreich O, Benseler F, Fahrenholz A, Eckstein F. High activity and stability of hammerhead ribozymes containing 2'-modified pyrimidine nucleosides and phosphorothioates. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42145-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Beaucage SL, Iyer RP. The synthesis of specific ribonucleotides and unrelated phosphorylated biomolecules by the phosphoramidite method. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)81543-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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An indexed bibliography of antisense literature, 1992. ANTISENSE RESEARCH AND DEVELOPMENT 1993; 3:95-153. [PMID: 8495109 DOI: 10.1089/ard.1993.3.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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