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Bartosik K, Debiec K, Czarnecka A, Sochacka E, Leszczynska G. Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach. Molecules 2020; 25:E3344. [PMID: 32717917 PMCID: PMC7436257 DOI: 10.3390/molecules25153344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
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Affiliation(s)
| | | | | | | | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.B.); (K.D.); (A.C.); (E.S.)
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2
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
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Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
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3
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids’ bioconjugation. Part I: An overview of synthetic strategies. Bioorg Chem 2019; 92:103223. [DOI: 10.1016/j.bioorg.2019.103223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/26/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
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4
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Bartosik K, Sochacka E, Leszczynska G. Post-synthetic conversion of 5-pivaloyloxymethyluridine present in a support-bound RNA oligomer into biologically relevant derivatives of 5-methyluridine. Org Biomol Chem 2018; 15:2097-2103. [PMID: 28217770 DOI: 10.1039/c6ob02674e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A post-synthetic reaction of 5-pivaloyloxymethyluridine (present in a support-bound RNA oligomer) with various nucleophilic reagents furnished efficiently the corresponding products bearing one of the tRNA wobble 5-methyluridines (mnm5U, cmnm5U, τm5U, nm5U, inm5U or cnm5U). The syntheses of oligoribonucleotides modified with inm5U and cnm5U are reported for the first time.
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Affiliation(s)
- Karolina Bartosik
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
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5
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Hou X, Wang G, Gaffney BL, Jones RA. Synthesis of guanosine and deoxyguanosine phosphoramidites with cross-linkable thioalkyl tethers for direct incorporation into RNA and DNA. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2009; 28:1076-94. [PMID: 20183575 PMCID: PMC2829721 DOI: 10.1080/15257770903368385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We describe the synthesis of protected phosphoramidites of deoxyriboguanosine and guanosine derivatives containing a thiopropyl tether at the guanine N2 (7a,b) for site-specific crosslinking from the minor groove of either DNA or RNA to a thiol of a protein or another nucleic acid. The thiol is initially protected as a tert-butyl disulfide that is stable during oligonucleotide synthesis. While the completed oligonucleotide is still attached to the support, or after purification, the tert-butyl thiol can readily be removed or replaced by thioethylamine or 5-thio-2-nitrobenzoic acid, which have more favorable crosslinking rates.
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Affiliation(s)
- Xiaorong Hou
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Gang Wang
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Barbara L. Gaffney
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
| | - Roger A. Jones
- Department of Chemistry and Chemical Biology, 610 Taylor Road, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854
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6
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Draper DE, Bukhman YV, Gluick TC. Thermal methods for the analysis of RNA folding pathways. ACTA ACUST UNITED AC 2008; Chapter 11:Unit 11.3. [PMID: 18428829 DOI: 10.1002/0471142700.nc1103s02] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Once a model of the secondary structure of an RNA has been deduced, thermal melting analysis can be used to determine whether the model accounts for all intramolecular interactions of the RNA, or whether noncanonical and tertiary interactions make the structure more stable than predicted, or link parts of the structure in unexpected ways. It is also useful to determine the pH, salt, and temperature ranges under which the RNA adopts a stably folded structure, or to analyze unfolding pathways. This unit discusses sample preparation, instrumentation, and theoretical background. It also provide a sample analysis of tRNA unfolding.
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Affiliation(s)
- D E Draper
- Johns Hopkins University, Baltimore, Maryland, USA
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7
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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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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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Semenyuk A, Földesi A, Johansson T, Estmer-Nilsson C, Blomgren P, Brännvall M, Kirsebom LA, Kwiatkowski M. Synthesis of RNA using 2'-O-DTM protection. J Am Chem Soc 2007; 128:12356-7. [PMID: 16984152 DOI: 10.1021/ja0636587] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
tert-Butyldithiomethyl (DTM), a novel hydroxyl protecting group, cleavable under reductive conditions, was developed and applied for the protection of 2'-OH during solid-phase RNA synthesis. This function is compatible with all standard protecting groups used in oligonucleotide synthesis, and allows for fast and high-yield synthesis of RNA. Oligonucleotides containing the 2'-O-DTM groups can be easily deprotected under the mildest possible aqueous and homogeneous conditions. The preserved 5'-O-DMTr function can be used for high-throughput cartridge RNA purification.
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Affiliation(s)
- Andrey Semenyuk
- Department of Genetics and Pathology, Uppsala University, Sweden
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10
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Li NS, Piccirilli JA. Synthesis of 2‘-C-α-(Hydroxyalkyl) and 2‘-C-α-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA. J Org Chem 2007; 72:1198-210. [PMID: 17288373 DOI: 10.1021/jo062002t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleoside analogues bearing 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkyl substitutes have numerous applications in RNA chemistry and biology. In particular, they provide a strategy to probe the interaction between the 2'-hydroxyl group of RNA and water. To incorporate these nucleoside analogues into oligonucleotides for studies of the group II intron (Gordon, P. M.; Fong, R.; Deb, S.; Li, N.-S.; Schwans, J. P.; Ye, J.-D.; Piccirilli, J. A. Chem. Biol. 2004, 11, 237), we synthesized six new phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-(hydroxyalkyl)cytidine (36: R = -(CH2)2OH; 38: R = -(CH2)3OH; 40: R = -(CH2)4OH) and 2'-deoxy-2'-C-alpha-alkylcytidine (37: R = -CH2CH3; 39: R = -(CH2)2CH3; 41: R = -(CH2)3CH3) from cytidine or uridine via 2'-C-alpha-allylation, followed by alkene and alcohol transformations. Phosphoramidites 36 and 37 were prepared from cytidine in overall yields of 14% (10 steps) and 7% (11 steps), respectively. Phosphoramidites 38 and 39 were prepared from uridine in overall yields of 30% (10 steps) and 13% (11 steps), respectively. Phosphoramidites 40 and 41 were synthesized from uridine in overall yields of 21% (13 steps) and 25% (14 steps), respectively.
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Affiliation(s)
- Nan-Sheng Li
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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11
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Sharma PK, Mikkelsen BH, Christensen MS, Nielsen KE, Kirchhoff C, Pedersen SL, Sørensen AM, Ostergaard K, Petersen M, Nielsen P. A cyclic dinucleotide with a four-carbon 5'-C-to-5'-C connection; synthesis by RCM, NMR-examination and incorporation into secondary nucleic acid structures. Org Biomol Chem 2006; 4:2433-45. [PMID: 16763689 DOI: 10.1039/b603830a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 5'-C-allylthymidine derivative was prepared from thymidine by the application of a stereoselective allylation procedure and its 5'(S)-configuration was confirmed. From this nucleoside derivative, appropriately protected building blocks were prepared and coupled using standard phosphoramidite chemistry to afford a dinucleotide with two 5'-C-allylgroups. This molecule was used as a substrate for a ring-closing metathesis (RCM) reaction and after deprotection, a 1 : 1 mixture of E- and Z-isomers of a cyclic dinucleotide with an unsaturated 5'-C-to-5'-C connection was obtained. Alternatively, a hydrogenation of the double bond and deprotection afforded a saturated cyclic dinucleotide. An advanced NMR-examination confirmed the constitution of this molecule and indicated a restriction in its overall conformational freedom. After variation of the protecting group strategy, a phosphoramidite building block of the saturated cyclic dinucleotide with the 5'-O-position protected as a pixyl ether and the phosphate protected as a methyl phosphotriester was obtained. This building block was used in the preparation of two 14-mer oligonucleotides with a central artificial bend due to the cyclic dinucleotide moiety. These were found to destabilise duplexes, slightly destabilise bulged duplexes but, to some extent, stabilise a three-way junction in high Mg(2+)-concentrations.
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Affiliation(s)
- Pawan K Sharma
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark
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12
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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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13
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Børsting P, Nielsen KE, Nielsen P. Stabilisation of a nucleic acid three-way junction by an oligonucleotide containing a single 2'-C to 3'-O-phosphate butylene linkage prepared by a tandem RCM-hydrogenation method. Org Biomol Chem 2005; 3:2183-90. [PMID: 15917908 DOI: 10.1039/b502720a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cyclic dinucleotide with a butylene linker between the upper 2'-C position and the 3'-O-phosphate linkage was synthesised from simple nucleoside building blocks via a tandem ring-closing metathesis and hydrogenation procedure. The major of two phosphorus epimers was incorporated into an oligodeoxynucleotide, as well as into an LNA-DNA mixmer oligonucleotide. These were evaluated as parts in three different secondary structures, a duplex, a bulged duplex and a three-way junction, with both DNA and RNA complements. In the DNA:RNA hybrid molecule, the oligodeoxynucleotide containing this single 2'-C to 3'-O-phosphate butylene linkage was found to stabilise a three-way junction.
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Affiliation(s)
- Philip Børsting
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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14
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Tona R, Haner R. Crosslinking of diene-modified DNA with bis-maleimides. MOLECULAR BIOSYSTEMS 2005; 1:93-8. [PMID: 16880969 DOI: 10.1039/b418502a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chemical crosslinking of modified nucleic acids via the Diels-Alder reaction is reported. For this purpose, 1,3-butadiene derived building blocks were incorporated into complementary oligodeoxynucleotides. Treatment of the obtained duplex with difunctional dienophiles results in the clean crosslinking of the two strands. Non-crosslinked adducts arising from a single Diels-Alder reaction of a maleimide to only one strand were not observed, indicating that the first reaction is the rate determining step of the overall process. Based on their thermal denaturation profiles, the crosslinked hybrids behave like two separate, hairpin-like structures, rather than like a single, continuous duplex.
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Affiliation(s)
- Rolf Tona
- Department of Chemistry, University of Bern, CH-3012 Bern, Switzerland
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15
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Fujimoto K, Yoshimura Y, Ikemoto T, Nakazawa A, Hayashi M, Saito I. Photoinduced DNA end capping viaN3-methyl-5-cyanovinyl-2′-deoxyuridine. Chem Commun (Camb) 2005:3177-9. [PMID: 15968363 DOI: 10.1039/b504162g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A modified oligodeoxynucleotide (ODN) containing N(3)-methyl-5-cyanovinyl-2'-deoxyuridine reacts by photoirradiation at 366 nm with an adenine residue of a complementary template ODN to yield an end-capped ODN in 87% yield.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa.
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16
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Guérineau V, Matus SKA, Halgand F, Laprévote O, Clivio P. Studies on the chemical synthesis of oligodeoxynucleotides containing the s 5T(6-4)T photoproduct: side reactions derived from the methylsulfenyl thiol protection elucidated by MALDI mass spectrometry. Org Biomol Chem 2004; 2:899-907. [PMID: 15007420 DOI: 10.1039/b314831a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attempts to incorporate the phosphoramidite of the thymine-thymine (6-4) photoproduct C5 thiol analogue (s(5)T(6-4)T PP), whose sulfur atom was protected with the methylsulfenyl group, into oligodeoxynucleotides (ODNs), are reported. Using matrix-assisted laser desorption-ionisation mass spectrometry (MALDI-MS) coupled to enzymatic digestion, accurate mass measurements and tandem mass spectrometry experiments, we demonstrated that ODNs containing the (2-cyanoethylthio)(5)T(6-4)T PP were obtained. Supported by model reactions, these results were explained 1) by the incorporation, during oligonucleotide synthesis, of the sulfur deprotected phosphoramidite that arose from a Michaelis-Arbusov-type rearrangement, and 2) the Michael addition to the thiol of acrylonitrile released upon the cyanoethyl phosphotriester deprotection. To avoid the formation of the cyanoethyl adduct, the phosphotriester deprotection was carried out in the presence of a thiol in excess. This afforded the ODN containing the h(5)T(6-4)T PP.
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Affiliation(s)
- Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS, avenue de la Terrasse, F-91 198 Gif-sur-Yvette cedex, France
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17
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Zhu XF, Williams HJ, Ian Scott A. Aqueous Trichloroacetic Acid: Another Useful Reagent for Highly Selective 5′-Desilylation of Multisilylated Nucleosides. SYNTHETIC COMMUN 2003. [DOI: 10.1081/scc-120021027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Zhu XF, Williams HJ, Ian Scott A. An Improved Transient Method for the Synthesis ofN-Benzoylated Nucleosides. SYNTHETIC COMMUN 2003. [DOI: 10.1081/scc-120017200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Chambert S, Décout JL. RECENT DEVELOPMENTS IN THE SYNTHESIS, CHEMICAL MODIFICATIONS AND BIOLOGICAL APPLICATIONS OF SULFUR MODIFIED NUCLEOSIDES, NUCLEOTIDES AND OLIGONUCLEOTIDES. ORG PREP PROCED INT 2002. [DOI: 10.1080/00304940209355745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Maglott EJ, Glick GD. Engineering disulfide cross-links in RNA via air oxidation. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2001; Chapter 5:Unit 5.4. [PMID: 18428860 DOI: 10.1002/0471142700.nc0504s00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This unit presents protocols for the synthesis of alkylthiol-modified ribonucleosides, their incorporation into synthetic RNA, and the formation of intramolecular disulfide bonds in RNA by air oxidation. The disulfide bonds can be formed in quantitative yields between thiols positioned in close proximity by virtue of either the secondary or tertiary structure of the RNA. Disulfide cross-links are useful tools to probe solution structures of RNA, to monitor dynamic motion, to stabilize folded RNAs, and to study the process of tertiary structure folding.
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21
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Pinard R, Lambert D, Heckman JE, Esteban JA, Gundlach CW, Hampel KJ, Glick GD, Walter NG, Major F, Burke JM. The hairpin ribozyme substrate binding-domain: a highly constrained D-shaped conformation. J Mol Biol 2001; 307:51-65. [PMID: 11243803 DOI: 10.1006/jmbi.2000.4472] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The two domains of the hairpin ribozyme-substrate complex, usually depicted as straight structural elements, must interact with one another in order to form an active conformation. Little is known about the internal geometry of the individual domains in an active docked complex. Using various crosslinking and structural approaches in conjunction with molecular modeling (constraint-satisfaction program MC-SYM), we have investigated the conformation of the substrate-binding domain in the context of the active docked ribozyme-substrate complex. The model generated by MC-SYM showed that the domain is not straight but adopts a bent conformation (D-shaped) in the docked state of the ribozyme, indicating that the two helices bounding the internal loop are closer than was previously assumed. This arrangement rationalizes the observed ability of hairpin ribozymes with a circularized substrate-binding strand to cleave a circular substrate, and provides essential information concerning the organization of the substrate in the active conformation. The internal geometry of the substrate-binding strand places G8 of the substrate-binding strand near the cleavage site, which has allowed us to predict the crucial role played by this nucleotide in the reaction chemistry.
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Affiliation(s)
- R Pinard
- Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington, VT 05405, USA
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22
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Luchansky SJ, Nolan SJ, Baranger AM. Contribution of RNA Conformation to the Stability of a High-Affinity RNA−Protein Complex. J Am Chem Soc 2000. [DOI: 10.1021/ja000837u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah J. Luchansky
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
| | - Scott J. Nolan
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
| | - Anne M. Baranger
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
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Abstract
In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids.
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Affiliation(s)
- G D Glick
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA.
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24
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Alefelder S, Sigurdsson ST. Interstrand disulfide cross-linking of internal sugar residues in duplex RNA. Bioorg Med Chem 2000; 8:269-73. [PMID: 10968286 DOI: 10.1016/s0968-0896(99)00280-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Disulfide cross-linking is being used increasingly more to study the structure and dynamics of nucleic acids. We have previously developed a procedure for the formation of disulfide cross-links through the sugar-phosphate backbone of nucleic acids. Here we report the preparation and characterization of an RNA duplex containing a disulfide interstrand cross-link. A self-complementary oligoribonucleotide duplex containing an interstrand cross-link was prepared from the corresponding 2'-amino modified oligomer. Selective modification of the 2'-amino group with an aliphatic isocyanate, containing a protected disulfide, gave the corresponding 2'-urea derivative in excellent yield. An RNA duplex containing an intrahelical, interstrand disulfide cross-link was subsequently prepared by a thiol disulfide exchange reaction in nearly quantitative yield as judged by denaturing polyacrylamide gel electrophoresis (DPAGE). The cross-linked RNA was further characterized by enzymatic digestion and the Structure of the cross-link lesion was verified by comparison to an authentic sample, prepared by chemical synthesis. The effect of the chemical modifications on duplex stability was determined by UV thermal denaturation experiments. The intrahelical cross-link stabilized the duplex considerably: the disulfide cross-linked oligomer had a melting temperature that was ca. 40 degrees C higher than that of the noncross-linked oligomer.
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Affiliation(s)
- S Alefelder
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
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25
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Wu X, Pitsch S. Functionalization of the sugar moiety of oligoribonucleotides on solid support. Bioconjug Chem 1999; 10:921-4. [PMID: 10563759 DOI: 10.1021/bc9900901] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A solid-phase method for the introduction of a variety of different side chains into oligoribonucleotides is presented. It is based on a beta-D-allofuranosyl phosphoramidite with a bromopentyl-substituent tethered to the 6'-O position. After its incorporation into fully protected, immobilized RNA sequences, the bromine was substituted with a variety of soft nucleophiles which, in some cases, allowed further transformations. After deprotection and detachment, the corresponding functionalized oligoribonucleotides were purified and characterized. Incorporation of such side chains led to a slight lowering of transition temperatures, but some of them led to a significant enthalpic stabilization of an A-type RNA duplex.
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Affiliation(s)
- X Wu
- Organisch-chemisches Laboratorium der Eidgenössischen Technischen Hochschule, Universitätstrasse 16, CH-8092 Zürich, Switzerland
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26
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Maglott EJ, Goodwin JT, Glick GD. Probing the Structure of an RNA Tertiary Unfolding Transition State. J Am Chem Soc 1999. [DOI: 10.1021/ja9913075] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emily J. Maglott
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48105-1055
| | - Jay T. Goodwin
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48105-1055
| | - Gary D. Glick
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48105-1055
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27
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Abstract
RNA performs multiple functions in cellular environments, such as transferring genetic information, catalyzing chemical reactions, and providing an integral component of ribonucleoprotein complexes involved in mRNA processing and translation. Many of these functions are poorly understood, mainly due to the lack of structural information. Because limited information has been obtained by physical and biophysical techniques, chemical and biochemical methods have been extensively used for studying RNA structure. This article outlines one such method which relies on site-specific incorporation of thiols into RNA. A brief overview of the methods for incorporation of thiols into RNA is followed by a detailed description of a procedure which utilizes postsynthetic modification of 2'-amino-containing RNA for incorporation of thiols. The use of thiol-containing RNA to form disulfide cross-links for the study of the structure and dynamics of ribozymes is subsequently described.
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Affiliation(s)
- S T Sigurdsson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
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Maglott EJ, Deo SS, Przykorska A, Glick GD. Conformational transitions of an unmodified tRNA: implications for RNA folding. Biochemistry 1998; 37:16349-59. [PMID: 9819227 DOI: 10.1021/bi981722u] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unmodified tRNAs are powerful systems to study the effects of posttranscriptional modifications and site-directed mutations on both the structure and function of these ribonucleic acids. To define the general limitations of synthetic constructs as models for native tRNAs, it is necessary to elucidate the conformational states of unmodified tRNAs as a function of solution conditions. Here we report the conformational properties of unmodified yeast tRNAPhe as a function of ionic strength, [Mg2+], and temperature using a combination of spectroscopic measurements along with chemical and enzymatic probes. We find that in low [Na+] buffer at low temperature, native yeast tRNAPhe adopts tertiary structure in the absence of Mg2+. By contrast, tertiary folding of unmodified yeast tRNAPhe has an absolute requirement for Mg2+. Below the melting temperature of the cloverleaf, unmodified yeast tRNAPhe exists in a Mg2+-dependent equilibrium between secondary and tertiary structure. Taken together, our findings suggest that although the tertiary structures of tRNAs are broadly comparable, the intrinsic stability of the tertiary fold, the conformational properties of intermediate states, and the stability of intermediate states can differ significantly between tRNA sequences. Thus, the use of unmodified tRNAs as models for native constructs can have significant limitations. Broad conclusions regarding "tRNA folding" as a whole must be viewed cautiously, particularly in cases where structural changes occur, such as during protein synthesis.
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Affiliation(s)
- E J Maglott
- Department of Chemistry, University of Michigan, Ann Arbor 48109-1055, USA
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29
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Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
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Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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30
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Chen XY, Link TM, Schramm VL. Ricin A-chain: kinetics, mechanism, and RNA stem-loop inhibitors. Biochemistry 1998; 37:11605-13. [PMID: 9708998 DOI: 10.1021/bi980990p] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ricin A-chain (RTA) catalyzes the depurination of a single adenine at position 4324 of 28S rRNA in a N-ribohydrolase reaction. The mechanism and specificity for RTA are examined using RNA stem-loop structures of 10-18 nucleotides which contain the required substrate motif, a GAGA tetraloop. At the optimal pH near 4.0, the preferred substrate is a 14-base stem-loop RNA which is hydrolyzed at 219 min-1 with a kcat/Km of 4.5 x 10(5) M-1 s-1 under conditions of steady-state catalysis. Smaller or larger stem-loop RNAs have lower kcat values, but all have Km values of approximately 5 microM. Both the 10- and 18-base substrates have kcat/Km near 10(4) M-1 s-1. Covalent cross-linking of the stem has a small effect on the kinetic parameters. Stem-loop DNA (10 bases) of the same sequence is also a substrate with a kcat/Km of 0.1 that for RNA. Chemical mechanisms for enzymatic RNA depurination reactions include leaving group activation, stabilization of a ribooxocarbenium transition state, a covalent enzyme-ribosyl intermediate, and ionization of the 2'-hydroxyl. A stem-loop RNA with p-nitrophenyl O-riboside at the depurination site is not a substrate, but binds tightly to the enzyme (Ki = 0.34 microM), consistent with a catalytic mechanism of leaving group activation. The substrate activity of stem-loop DNA eliminates ionization of the 2'-hydroxyl as a mechanism. Incorporation of the C-riboside formycin A at the depurination site provides an increased pKa of the adenine analogue at N7. Binding of this analogue (Ki = 9.4 microM) is weaker than substrate which indicates that the altered pKa at this position is not an important feature of transition state recognition. Stem-loop RNA with phenyliminoribitol at the depurination site increases the affinity substantially (Ki = 0.18 microM). The results are consistent with catalysis occurring by leaving group protonation at ring position(s) other than N7 leading to a ribooxocarbenium ion transition state. Small stem-loop RNAs have been identified with substrate activity within an order of magnitude of that reported for intact ribosomes.
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Affiliation(s)
- X Y Chen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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31
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Earnshaw DJ, Masquida B, Müller S, Sigurdsson ST, Eckstein F, Westhof E, Gait MJ. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J Mol Biol 1997; 274:197-212. [PMID: 9398527 DOI: 10.1006/jmbi.1997.1405] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The hairpin ribozyme is a small catalytic RNA composed of two helical domains containing a small and a large internal loop and, thus, constitutes a valuable paradigm for the study of RNA structure and catalysis. We have carried out molecular modelling of the hairpin ribozyme to learn how the two domains (A and B) might fold and approach each other. To help distinguish alternative inter-domain orientations, we have chemically synthesized hairpin ribozymes containing 2'-2' disulphide linkages of known spacing (12 or 16 A) between defined ribose residues in the internal loop regions of each domain. The abilities of cross-linked ribozymes to carry out RNA cleavage under single turnover conditions were compared to the corresponding disulphide-reduced, untethered ribozymes. Ribozymes were classed in three categories according to whether their cleavage rates were marginally, moderately, or strongly affected by cross-linking. This rank order of activity guided the docking of the two domains in the molecular modelling process. The proposed three-dimensional model of the hairpin ribozyme incorporates three different crystallographically determined structural motifs: in domain A, the 5'-GAR-3'-motif of the hammerhead ribozyme, in domain B, the J4/5 motif of group I ribozymes, and connecting the two domains, a "ribose zipper", another group I ribozyme feature, formed between the hydroxyl groups of residues A10, G11 of domain A and C25, A24 of domain B. This latter feature might be key to the selection and precise orientation of the inter-domain docking necessary for the specific phosphodiester cleavage. The model provides an important basis for further studies of hairpin ribozyme structure and function.
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Affiliation(s)
- D J Earnshaw
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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33
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Allerson CR, Chen SL, Verdine GL. A Chemical Method for Site-Specific Modification of RNA: The Convertible Nucleoside Approach. J Am Chem Soc 1997. [DOI: 10.1021/ja962858n] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Cohen SB, Cech TR. Dynamics of Thermal Motions within a Large Catalytic RNA Investigated by Cross-linking with Thiol−Disulfide Interchange. J Am Chem Soc 1997. [DOI: 10.1021/ja9707421] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Gundlach C, Ryder TR, Glick GD. Synthesis of guanosine analogs bearing pendant alkylthiol tethers. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00868-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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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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38
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Osborne SE, Ellington AD. Nucleic Acid Selection and the Challenge of Combinatorial Chemistry. Chem Rev 1997; 97:349-370. [PMID: 11848874 DOI: 10.1021/cr960009c] [Citation(s) in RCA: 425] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Scott E. Osborne
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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39
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Osborne SE, Cain RJ, Glick GD. Structure and Dynamics of Disulfide Cross-Linked DNA Triple Helices. J Am Chem Soc 1997. [DOI: 10.1021/ja963285h] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Scott E. Osborne
- Contribution from the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Robert J. Cain
- Contribution from the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Gary D. Glick
- Contribution from the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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40
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Affiliation(s)
- Cathy L. Dantzman
- Contribution from the Department of Chemistry, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Laura L. Kiessling
- Contribution from the Department of Chemistry, University of WisconsinMadison, Madison, Wisconsin 53706
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41
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Osborne SE, Ellington AD. Incorporating disulfide cross-links at the terminus of oligonucleotides via solid-phase nucleic acid synthesis. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00431-3] [Citation(s) in RCA: 6] [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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