1
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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2
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Rydzik AM, Balk R, Koegler M, Steinle T, Riether D, Gottschling D. Access to 1'-Amino Carbocyclic Phosphoramidite to Enable Postsynthetic Functionalization of Oligonucleotides. Org Lett 2021; 23:6735-6739. [PMID: 34424724 DOI: 10.1021/acs.orglett.1c02302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report a synthesis of a carbocyclic, abasic RNA phosphoramidite decorated with an amino functionality. The building block was efficiently incorporated into an RNA oligonucleotide in a site-specific manner, followed by deprotection to a free amino group. The amino moiety could be further derivatized as exemplified with fluorescein N-hydroxysuccinimide ester. Hence, this convertible building block may provide access to a variety of RNA oligonucleotides via postsynthetic amino group functionalization. In particular, providing a vector toward nucleobase replacements.
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Affiliation(s)
- Anna M Rydzik
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Regina Balk
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | | | - Tobias Steinle
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Dirk Gottschling
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
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3
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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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4
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Decuypere E, Lepikhina A, Halloy F, Hall J. Increased Affinity of 2′‐
O
‐(2‐Methoxyethyl)‐Modified Oligonucleotides to RNA through Conjugation of Spermine at Cytidines. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elodie Decuypere
- ETH ZürichDepartment of Chemistry and Applied Biosciences Vladimir Prelog Weg 1–5 CH-8093 Zürich Switzerland
| | - Anastasia Lepikhina
- ETH ZürichDepartment of Chemistry and Applied Biosciences Vladimir Prelog Weg 1–5 CH-8093 Zürich Switzerland
| | - François Halloy
- ETH ZürichDepartment of Chemistry and Applied Biosciences Vladimir Prelog Weg 1–5 CH-8093 Zürich Switzerland
| | - Jonathan Hall
- ETH ZürichDepartment of Chemistry and Applied Biosciences Vladimir Prelog Weg 1–5 CH-8093 Zürich Switzerland
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5
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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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6
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Lee SJ, Sung RJ, Verdine GL. Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System. RESEARCH (WASHINGTON, D.C.) 2019; 2019:5641746. [PMID: 31549070 PMCID: PMC6750098 DOI: 10.34133/2019/5641746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/26/2019] [Indexed: 11/06/2022]
Abstract
Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.
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Affiliation(s)
- Seung-Joo Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rou-Jia Sung
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory L. Verdine
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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7
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Trifonov L, Nudelman V, Zhenin M, Matsree E, Afri M, Schmerling B, Cohen G, Jozwiak K, Weitman M, Korshin E, Senderowitz H, Shainberg A, Hochhauser E, Gruzman A. Structurally Simple, Readily Available Peptidomimetic 1-Benzyl-5-methyl-4-( n-octylamino)pyrimidin-2(1 H)-one Exhibited Efficient Cardioprotection in a Myocardial Ischemia (MI) Mouse Model. J Med Chem 2018; 61:11309-11326. [PMID: 30507195 DOI: 10.1021/acs.jmedchem.8b01471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
TLR4, a member of the Toll-like receptor (TLR) family, serves as a pattern recognition receptor in the innate immune response to microbial pathogens. TLR4 also regulates the inflammatory reaction to ischemic injury in the heart. The TRIF-related adaptor molecule (TRAM) is an adapter that recruits the Toll/interleukin 1 receptor (TIR) domain, which contains adapter-inducing IFN-β (TRIF), to activate TLR4, following TRIF-dependent cytokine gene transcription. On the basis of a known TRAM-derived decoy peptide, 10 of its peptidomimetics were synthesized. One of them, 1-benzyl-5-methyl-4-( n-octylamino)pyrimidin-2(1 H)-one (21), exhibited high potency and efficacy in vitro. In vitro results and in silico analysis provided evidence for the possible direct interaction of 21 with the TLR4 complex. Administered in mice, 21 was able to block the pathophysiological manifestation of MI, restoring the concomitant tissue damage, with a 100% survival rate. Thus, inhibition of TLR4-mediated inflammation in postischemic myocardium could be used as an approach for developing cardioprotective drugs.
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Affiliation(s)
| | - Vadim Nudelman
- Cardiac Research Laboratory, Felsenstein Research Center, Rabin Medical Center, Sackler Faculty of Medicine , Tel Aviv University , Jabotinsky Street , Petach Tikva 49100 , Israel
| | | | - Erez Matsree
- Cardiac Research Laboratory, Felsenstein Research Center, Rabin Medical Center, Sackler Faculty of Medicine , Tel Aviv University , Jabotinsky Street , Petach Tikva 49100 , Israel
| | | | | | - Guy Cohen
- The Skin Research Institute , The Dead-Sea & Arava Science Center , Masada 86910 , Israel
| | - Krzysztof Jozwiak
- Department of Biopharmacy , Medical University of Lublin , W. Chodzki 4a , Lublin 20-093 , Poland
| | | | | | | | | | - Edith Hochhauser
- Cardiac Research Laboratory, Felsenstein Research Center, Rabin Medical Center, Sackler Faculty of Medicine , Tel Aviv University , Jabotinsky Street , Petach Tikva 49100 , Israel
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8
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Frouws TD, Barth PD, Richmond TJ. Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability. J Mol Biol 2017; 430:45-57. [PMID: 29113904 PMCID: PMC5757783 DOI: 10.1016/j.jmb.2017.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/04/2022]
Abstract
We engineered nucleosome core particles (NCPs) with two site-specific cysteine crosslinks that increase the stability of the particle. The first disulfide was introduced between the two copies of H2A via an H2A-N38C point mutation, effectively crosslinking the two H2A/H2B heterodimers together to stabilize the histone octamer against H2A/H2B dimer dissociation. The second crosslink was engineered between an R40C point mutation on the N-terminal tail of H3 and the NCP DNA ends by the introduction of a convertible nucleotide. This crosslink maintains the nucleosome DNA in a fixed translational setting relative to the histone octamer and prevents dilution-driven dissociation. The X-ray crystal structures of NCPs containing the disulfides in isolation and in combination were determined. Both disulfides stabilize the structure of the NCP without disturbing the overall structure. Nucleosomes containing these modifications will be advantageous for biochemical and structural studies as a consequence of their greater resistance to dissociation during high dilution in purification, elevated salt for crystallization and vitrification for cryogenic electron microscopy. Crosslinked nucleosome core particles have increased stability against H2A/H2B dimer loss and DNA dissociation. A site-specific disulfide crosslink was introduced between the two copies of H2A in the histone octamer to stabilize its quaternary structure. Site-specific disulfide crosslinks were introduced between histone H3 and DNA within the nucleosome core particle. Three X-ray crystal structures of crosslinked nucleosome core particles were determined at high resolution.
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Affiliation(s)
- Timothy D Frouws
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Philip D Barth
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Timothy J Richmond
- ETH Zürich, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.
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9
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Grewal CS, Kent OA, MacMillan AM. Radical probing of spliceosome assembly. Methods 2017; 125:16-24. [PMID: 28669867 DOI: 10.1016/j.ymeth.2017.06.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 10/19/2022] Open
Abstract
Here we describe the synthesis and use of a directed hydroxyl radical probe, tethered to a pre-mRNA substrate, to map the structure of this substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly. This methodology may be adapted to the synthesis of a wide variety of modified RNAs for use as probes of RNA structure and RNA-protein interaction.
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Affiliation(s)
- Charnpal S Grewal
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Oliver A Kent
- Princess Margaret Cancer Centre, 101 College St., University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andrew M MacMillan
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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10
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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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11
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Avirah RR, Schuster GB. Fluorescence Quenching by Intercalation of a Pyrene Group Tethered to anN4-modified Cytosine in Duplex DNA. Photochem Photobiol 2012; 89:332-5. [DOI: 10.1111/j.1751-1097.2012.01243.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/11/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Rekha R. Avirah
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
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12
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Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J Biol Chem 2012; 287:24916-28. [PMID: 22511791 PMCID: PMC3408145 DOI: 10.1074/jbc.m111.316497] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A poorly understood aspect of DNA repair proteins is their ability to identify exceedingly rare sites of damage embedded in a large excess of nearly identical undamaged DNA, while catalyzing repair only at the damaged sites. Progress toward understanding this problem has been made by comparing the structures and biochemical behavior of these enzymes when they are presented with either a target lesion or a corresponding undamaged nucleobase. Trapping and analyzing such DNA-protein complexes is particularly difficult in the case of base extrusion DNA repair proteins because of the complexity of the repair reaction, which involves extrusion of the target base from DNA followed by its insertion into the active site where glycosidic bond cleavage is catalyzed. Here we report the structure of a human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, in which a normal guanine from DNA has been forcibly inserted into the enzyme active site. Although the interactions of the nucleobase with the active site are only subtly different for G versus oxoG, hOGG1 fails to catalyze excision of the normal nucleobase. This study demonstrates that even if hOGG1 mistakenly inserts a normal base into its active site, the enzyme can still reject it on the basis of catalytic incompatibility.
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Affiliation(s)
- Charisse M. Crenshaw
- From the Departments of Molecular and Cellular Biology, ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Kwangho Nam
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Peter S. Kutchukian
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Brian R. Bowman
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Martin Karplus
- Chemical and Chemical Biology, and ,the L'Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Gregory L. Verdine
- Chemical and Chemical Biology, and ,Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, ,the Program in Cancer Chemical Biology and Chemical Biology Initiative, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, and , To whom correspondence should be addressed. 12 Oxford St., Cambridge, MA 02138. Fax: 617-495-8755; E-mail:
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13
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Abstract
Stille Coupling is a versatile C-C bond forming reaction with high functional group tolerance under mild conditions. Our on column synthesis concept for RNA modification is based on the incorporation of iodo substituted nucleotide precursors to RNA during automated standard solid phase synthesis via TBDMS-, TC-, and ACE- protecting group strategies. Subsequently, the RNA, still bound on solid support, is ready for orthogonal postsynthetic functionalization via Stille cross-couplings utilizing the advantages of solid phase synthesis. Several monomer test reactions were employed with 2-iodo adenosine and 5-iodo uridine and organostannanes as coupling partners under different conditions, changing the catalyst/ligand system, temperature, and reaction time as well as conventional heating and microwave irradiation. Finally, Stille cross-couplings under optimized conditions were transferred to fully protected 5-mer and 12-mer RNA oligonucleotides on-column. Deprotection and cleavage from solid support resulted in site-specifically labeled oligonucleotides. Derivatizations via Stille cross-couplings were performed initially with vinyltributylstannane as well as later with 2-furanyl-, 2-thiophene-, and benzothiophene-2-tributylstannanes yielding fluorescently functionalized RNA.
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Affiliation(s)
- Lena Wicke
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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14
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Song CX, He C. Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. Acc Chem Res 2011; 44:709-17. [PMID: 21539303 DOI: 10.1021/ar2000502] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA is not merely a combination of four genetic codes, namely A, T, C, and G. It also contains minor modifications that play crucial roles throughout biology. For example, the fifth DNA base, 5-methylcytosine (5-mC), which accounts for ∼1% of all the nucleotides in mammalian genomic DNA, is a vital epigenetic mark. It impacts a broad range of biological functions, from development to cancer. Recently, an oxidized form of 5-methylcytosine, 5-hydroxymethylcytosine (5-hmC), was found to constitute the sixth base in the mammalian genome; it was believed to be another crucial epigenetic mark. Unfortunately, further study of this newly discovered DNA base modification has been hampered by inadequate detection and sequencing methods, because current techniques fail to differentiate 5-hmC from 5-mC. The immediate challenge, therefore, is to develop robust methods for ascertaining the positions of 5-hmC within the mammalian genome. In this Account, we describe our development of the first bioorthogonal, selective labeling of 5-hmC to specifically address this challenge. We utilize β-glucosyltransferase (βGT) to transfer an azide-modified glucose onto 5-hmC in genomic DNA. The azide moiety enables further bioorthogonal click chemistry to install a biotin group, which allows for detection, affinity enrichment, and, most importantly, deep sequencing of the 5-hmC-containing DNA. With this highly effective and selective method, we revealed the first genome-wide distribution of 5-hmC in the mouse genome and began to shed further light on the biology of 5-hmC. The strategy lays the foundation for developing high-throughput, single-base-resolution sequencing methods for 5-hmC in mammalian genomes in the future. DNA and RNA are not static inside cells. They interact with protein and other DNA and RNA in fundamental biological processes such as replication, transcription, translation, and DNA and RNA modification and repair. The ability to investigate these interactions will also be enhanced by developing and utilizing bioorthogonal probes. We have chosen the photoreactive diazirine photophore as a bioorthogonal moiety to develop nucleic acid probes. The small size and unique photo-cross-linking activity of diazirine enabled us to develop a series of novel cross-linking probes to streamline the study of protein-nucleic acid and nucleic acid-nucleic acid interactions. In the second half of this Account, we highlight a few examples of these probes.
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Affiliation(s)
- Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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15
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Hou X, Wang G, Gaffney BL, Jones RA. Preparation of DNA and RNA fragments containing guanine N(2)-thioalkyl tethers. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2010; Chapter 5:Unit-5.8. [PMID: 20517990 PMCID: PMC2967349 DOI: 10.1002/0471142700.nc0508s41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This unit describes procedures for preparation of deoxyguanosine and guanosine derivatives in which the guanine N(2) contains a thiopropyl tether, protected as a tert-butyl disulfide. After incorporation into a DNA or RNA fragment, this tether allows site-specific cross-linking to a thiol of a protein or another nucleic acid.
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Affiliation(s)
- Xiaorong Hou
- Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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16
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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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17
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Abstract
The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.
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Affiliation(s)
- K A Malecka
- The Wistar Institute, Philadelphia, PA 19104, USA
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18
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Culf AS, Cuperlović-Culf M, Laflamme M, Tardiff BJ, Ouellette RJ. Fast deprotection of synthetic oligodeoxyribonucleotides using standard reagents under microwave irradiation. Oligonucleotides 2008; 18:81-92. [PMID: 18321165 DOI: 10.1089/oli.2007.0072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fast methods for the removal of permanent amide exo-cyclic protective groups widely used in phosphoramidite-method DNA synthesis are desirable for many genomics and proteomics applications. In this communication, we present a method for the deprotection of a range of N-acyl deoxyribonucleosides (T, dA Bz, dC Bz, dC Ac, dG ibu, dG PAC) and synthetic oligodeoxyribonucleotides, ranging in length from 5-mer to 50-mer. Oligodeoxyribonucleotides were synthesized using standard amide protecting groups (dA Bz, dC Bz, dG ibu) and phosphoramidite chemistry on cis-diol solid phase support. This deprotection method utilizes 29% aqueous ammonia solution at 170 degrees C for 5 minutes under monomode microwave irradiation at a 20-nmole reaction scale. Reaction products were analyzed by TLC, RP-HPLC, CE, ESI-MS, real-time PCR, agarose gel electrophoresis, and by DNA uracil glycosylase (UDG) and phosphodiesterase I (PDE) enzymatic digestions.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.
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19
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Abstract
This unit begins with a discussion of the advantages and disadvantages of oligonucleotide synthesis using solid supports. The physical and chemical properties of solid-phase supports are discussed in terms of their suitability for oligonucleotide synthesis. In addition, the unit outlines the properties of linkers used for transient or permanent attachment of properly protected nucleosides to the derivatized support, as well as strategies for coupling nucleosides to linkers and conditions for the release of synthetic oligonucleotides from specific supports.
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Affiliation(s)
- R T Pon
- University of Calgary, Calgary, Alberta, Canada
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20
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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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21
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Shigdel U, Zhang J, He C. Diazirine-Based DNA Photo-Cross-Linking Probes for the Study of Protein–DNA Interactions. Angew Chem Int Ed Engl 2008; 47:90-3. [DOI: 10.1002/anie.200703625] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Delaney JC, Essigmann JM. Biological properties of single chemical-DNA adducts: a twenty year perspective. Chem Res Toxicol 2008; 21:232-52. [PMID: 18072751 PMCID: PMC2821157 DOI: 10.1021/tx700292a] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The genome and its nucleotide precursor pool are under sustained attack by radiation, reactive oxygen and nitrogen species, chemical carcinogens, hydrolytic reactions, and certain drugs. As a result, a large and heterogeneous population of damaged nucleotides forms in all cells. Some of the lesions are repaired, but for those that remain, there can be serious biological consequences. For example, lesions that form in DNA can lead to altered gene expression, mutation, and death. This perspective examines systems developed over the past 20 years to study the biological properties of single DNA lesions.
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Affiliation(s)
- James C. Delaney
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - John M. Essigmann
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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23
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Shigdel U, Zhang J, He C. Diazirine-Based DNA Photo-Cross-Linking Probes for the Study of Protein–DNA Interactions. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200703625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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24
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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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25
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Corn JE, Berger JM. FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies. Structure 2007; 15:773-80. [PMID: 17637338 PMCID: PMC2041450 DOI: 10.1016/j.str.2007.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 05/11/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Structural studies of macromolecular complexes have produced extraordinary insights into a wide variety of biological processes. Unfortunately, as structural biologists pursue larger and more challenging assemblies, weakly stable and/or nonspecific interactions can become significant roadblocks to structure determination. We have developed a rapid and effective pool-based screen, termed FASTDXL (focused array screening technique for disulfide X-linking), to produce and identify disulfide-stabilized protein-nucleic acid assemblies. A significant strength of FASTDXL is that it can take advantage of prior structural knowledge about molecular interactions, but does not necessarily rely upon it. A detailed application of the approach to the difficult problem of trapping a bacterial primase-ssDNA complex is described, validating the method as a route toward obtaining diffracting crystals suitable for structure determination.
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Affiliation(s)
- Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, 327B Hildebrand Hall, Berkeley, CA 94720, USA
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26
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Abstract
In order to expand the repertoire of DNA sequences specifically interacting with transition metals, we report here the first examples of DNA sequences carrying mono- and bidentate phosphane ligands as well as P,N-ligands. Aminoalkyl-modified oligonucleotides have been reacted at predetermined internal sites with carboxylate derivatives of pyrphos, BINAP and phosphinooxazoline (PHOX) 2 b-d. Carbodiimide coupling in the presence of N-hydroxysuccinimide provided the DNA-ligand conjugates in 38-78 % yield. Phosphane-containing oligonucleotides and their phosphane sulfide analogues were characterized by mass spectrometry (MALDI-TOF and FT-ICR-ESI) and their stability after purification and isolation was systematically investigated. While DNA-appended pyrphos ligand was quickly oxidized, BINAP and PHOX conjugates showed high stabilities, making them useful precursors for incorporation of transition metals into DNA.
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Affiliation(s)
- Mihaela Caprioara
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls University Heidelberg, 69120 Heidelberg, Germany
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27
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Grimau MG, Aviñó A, Gargallo R, Eritja R. Synthesis and triplex-forming properties of cyclic oligonucleotides with (G,A)-antiparallel strands. Chem Biodivers 2007; 2:275-85. [PMID: 17191980 DOI: 10.1002/cbdv.200590010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cyclic oligonucleotides carrying an oligopurine Watson-Crick sequence linked to the corresponding (G,A)- and (G,T)-antiparallel strands were prepared by nonenzymatic template-assisted cyclization of phosphorylated precursors. Cyclization was attempted using 3'-phosphate and 5'-phosphate linear precursors with carbodiimide or BrCN activation. The best results were obtained with the 5'-phosphorylated precursors and carbodiimide activation. Cyclic oligonucleotides bind polypyrimidine target sequence by formation of antiparallel triplexes. We have used UV and circular dichroism (CD) spectroscopy to analyze triplexes formed by cyclic oligonucleotides carrying G and A in the reverse-Hoogsteen strand. The relative stability of the triplexes formed by cyclic and linear oligonucleotides with a common polypyrimidine target was determined by melting experiments. The most-stable triplexes were formed by the cyclic oligonucleotide, followed by the unphosphorylated and phosphorylated oligonucleotide precursors, and, finally, the corresponding hairpin. Although the differences in binding affinity between cyclic oligonucleotides and their corresponding linear precursors are small, the use of cyclic oligonucleotides offers a clear advantage over conventional duplex recognition.
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Affiliation(s)
- Marta G Grimau
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona, C.S.I.C., Jordi Girona 18-26, E-08034 Barcelona
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29
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Radom CT, Banerjee A, Verdine GL. Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations. J Biol Chem 2006; 282:9182-94. [PMID: 17114185 DOI: 10.1074/jbc.m608989200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5' to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is "hardwired." Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F(*149)) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F(*292)) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.
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Affiliation(s)
- Christopher T Radom
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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30
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Banerjee A, Verdine GL. A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex. Proc Natl Acad Sci U S A 2006; 103:15020-5. [PMID: 17015827 PMCID: PMC1622772 DOI: 10.1073/pnas.0603644103] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Indexed: 12/20/2022] Open
Abstract
How DNA glycosylases search through millions of base pairs and discriminate between rare sites of damage and otherwise undamaged bases is poorly understood. Even less understood are the details of the structural states arising from DNA glycosylases interacting with undamaged DNA. Recognizing the mutagenic lesion 7,8-dihydro-8-oxoguanine (8-oxoguanine, oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G), and buried in the structure of naked B-form DNA, oxoG and G are practically indistinguishable from each other. We have used disulfide cross-linking technology to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1) sampling an undamaged G:C base pair located adjacent to an oxoG:C base pair in DNA. The x-ray structure of the trapped complex reveals that the presence of the 8-oxoG drastically changes the local conformation of the extruded G. The extruded but intrahelical state of the G in this structure offers a view of an early intermediate in the base-extrusion pathway.
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Affiliation(s)
| | - Gregory L. Verdine
- Departments of *Chemistry and Chemical Biology and
- Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
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31
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Eritja R, Adam V, AviñTó A, Díaz AR, Fàbrega C, Ferrer E, GrøStli M, García RG, Hofmann M, Márquez VE, Wiersma M. Preparation of Oligonucleotides Containing Non-Natural Base Analogs. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ramon Eritja
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Viviane Adam
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Anna AviñTó
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Antonio R. Díaz
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Carme Fàbrega
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Elisenda Ferrer
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Morten GrøStli
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Ramón Güimil García
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Mechtild Hofmann
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
| | - Víctor E. Márquez
- b National Cancer Institute, N.I.H. , Bethesda , Maryland , 20892 , USA
| | - Marten Wiersma
- a European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69 1 17, Heidelberg , Germany
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32
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Kojima N, Sugino M, Mikami A, Ohtsuka E, Komatsu Y. Generation of an abasic site in an oligonucleotide by using acid-labile 1-deaza-2'-deoxyguanosine and its application to postsynthetic modification. Org Lett 2006; 7:709-12. [PMID: 15704931 DOI: 10.1021/ol0474498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed a new convenient method for generation of an abasic site at the 3'-terminus of an oligonucleotide. This method uses a 1-deaza-2'-deoxyguanosine residue, which easily undergoes depurination under acidic conditions. The abasic site of the oligonucleotide can be further modified with external functional groups. We report herein the chemical stability of 1-deaza-2'-deoxyguanosine in the oligodeoxynucleotide and the application to the postsynthetic modification of an oligonucleotide by utilizing the chemical property of 1-deaza-2'-deoxyguanosine. [Structure: see text]
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Affiliation(s)
- Naoshi Kojima
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science & Technology (AIST Hokkaido), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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33
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Ali MM, Nagatsugi F, Sasaki S, Nakahara R, Maeda M. Application of 2-amino-6-vinylpurine as an efficient agent for conjugation of oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:159-69. [PMID: 16541959 DOI: 10.1080/15257770500446873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Attempts have been made to conjugate a variety of molecules with oligonucleotides to achieve useful functions. In this study, we have established a new efficient method for post-synthetic conjugation of oligonucleotides with the use of the 2-amino-6-vinylpurine nucleoside. Amino nucleophiles form the corresponding conjugates under acidic conditions, whereas thiol nucleophiles reacted efficiently under alkaline conditions. Thus, glutathione and HS-Cys-(Arg)8 without protecting groups were efficiently conjugated to the 2-amino-6-vinylpurine-bearing ODN under alkaline conditions. The use of 2-amino-6-vinylpurine as an agent for conjugation is advantageous in that it is stable during the reaction and may be applied to conjugation of ODNs with multiple functional molecules.
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Affiliation(s)
- Md Monsur Ali
- Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
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34
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Abstract
The p53 tumor suppressor protein binds to DNA as a dimer of dimers to regulate transcription of genes that mediate responses to cellular stress. We have prepared a cross-linked trapped p53 core domain dimer bound to decamer DNA and have determined its structure by x-ray crystallography to 2.3A resolution. The p53 core domain subunits bind nearly symmetrically to opposite faces of the DNA in a head-to-head fashion with a loophelix motif making sequence-specific DNA contacts and bending the DNA by about 20 degrees at the site of protein dimerization. Protein subunit interactions occur over the central DNA minor groove and involve residues from a zinc-binding region. Analysis of tumor derived p53 mutations reveals that the dimerization interface represents a third hot spot for mutation that also includes residues associated with DNA contact and protein stability. Residues associated with p53 dimer formation on DNA are poorly conserved in the p63 and p73 paralogs, possibly contributing to their functional differences. We have used the dimeric protein-DNA complex to model a dimer of p53 dimers bound to icosamer DNA that is consistent with solution bending data and suggests that p53 core domain dimer-dimer contacts are less frequently mutated in human cancer than intra-dimer contacts.
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35
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Duguid EM, Rice PA, He C. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol 2005; 350:657-66. [PMID: 15964013 DOI: 10.1016/j.jmb.2005.05.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 05/04/2005] [Accepted: 05/14/2005] [Indexed: 11/23/2022]
Abstract
O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents. We present an X-ray crystal structure of the wild-type human protein (hAGT) bound to double-stranded DNA with a chemically modified cytosine base. The protein binds at two different sites: one at the modified base, and the other across a sticky-ended DNA junction. The protein molecule that binds the modified cytosine base flips the base and recognizes it in its active site. The one that binds ends of neighboring DNA molecules partially flips an overhanging thymine base. This base is not inserted into the active-site pocket of the protein. These two different hAGT/DNA interactions observed in the structure suggest that hAGT may not detect DNA lesions by searching for the adduct itself, but rather for weakened and/or distorted base-pairs caused by base damage in the duplex DNA. We propose that hAGT imposes a strain on the DNA duplex and searches for DNA regions where the native structure is destabilized. The structure provides implications for pyrimidine recognition, improved inhibitor design, and a possible protein/protein interaction patch on hAGT.
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Affiliation(s)
- Erica M Duguid
- Department of Chemistry, 5735 South Ellis Avenue, The University of Chicago, Chicago, IL 60637, USA
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36
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Aviñó A, García RG, Eritja R. Synthesis of oligoribonucleotides containing 4-thiouridine using the convertible nucleoside approach and the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl group. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1767-77. [PMID: 15598077 DOI: 10.1081/ncn-200034044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Oligoribonucleotides containing 4-thiouridine were prepared using the Fpmp group for protection of the 2'-OH. Two uridine derivatives with the 1,2,4-triazolyl and the 2-nitrophenyl groups at position 4 were used to obtain 4-thiouridine by postsynthetic substitution with sodium hydrogen sulfide. Both uridine derivatives allow the preparation of the desired oligonucleotides in good yields.
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Affiliation(s)
- Anna Aviñó
- Instituto de Biología Molecular de Barcelona, Barcelona, Spain
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37
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Banerjee A, Yang W, Karplus M, Verdine GL. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 2005; 434:612-8. [PMID: 15800616 DOI: 10.1038/nature03458] [Citation(s) in RCA: 287] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 02/14/2005] [Indexed: 01/22/2023]
Abstract
How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.
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Affiliation(s)
- Anirban Banerjee
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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38
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Takeda S, Tsukiji S, Nagamune T. A cysteine-appended deoxyuridine for the postsynthetic DNA modification using native chemical ligation. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Santangelo TJ, Roberts JW. Formation of long DNA templates containing site-specific alkane-disulfide DNA interstrand cross-links for use in transcription reactions. Methods Enzymol 2004; 371:120-32. [PMID: 14712695 DOI: 10.1016/s0076-6879(03)71008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Thomas J Santangelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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40
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Neeley WL, Henderson PT, Essigmann JM. Efficient Synthesis of DNA Containing the Guanine Oxidation-Nitration Product 5-Guanidino-4-nitroimidazole: Generation by a Postsynthetic Substitution Reaction. Org Lett 2004; 6:245-8. [PMID: 14723539 DOI: 10.1021/ol036188j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A convertible nucleoside was synthesized and used to prepare the 2'-deoxynucleoside of 5-guanidino-4-nitroimidazole, a putative in vivo product of the reaction of peroxynitrite with guanine. The convertible nucleoside was incorporated into an oligodeoxynucleotide by the phosphoramidite method and converted postsynthetically to yield an oligodeoxynucleotide containing 5-guanidino-4-nitroimidazole at a specific site. The oligodeoxynucleotide was inserted into a viral genome. Melting temperature analysis revealed that duplexes containing 5-guanidino-4-nitroimidazole were greatly destabilized relative to unmodified duplexes.
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Affiliation(s)
- William L Neeley
- Department of Chemistry and Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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41
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Abstract
High-resolution structural studies of protein-DNA complexes have proven to be an invaluable means of understanding the diverse functions of proteins that manage the genome. Most of the structures determined to date represent proteins bound noncovalently to various DNA sequences or structures. Although noncovalent complexation is often adequate to study the structures of proteins that have robust, specific interactions with DNA, it is poorly suited to the study of transient intermediates in enzyme-catalyzed DNA processing reactions or of complexes that exist in multiple equilibrating forms. In recent years, strategies developed for the covalent trapping of protein-DNA complexes have begun to show promise as a window into an otherwise inaccessible world of structure.
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Affiliation(s)
- Gregory L Verdine
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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42
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Duguid EM, Mishina Y, He C. How Do DNA Repair Proteins Locate Potential Base Lesions? A Chemical Crosslinking Method to Investigate O6-Alkylguanine-DNA Alkyltransferases. ACTA ACUST UNITED AC 2003; 10:827-35. [PMID: 14522053 DOI: 10.1016/j.chembiol.2003.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O(6)-alkylguanine-DNA alkyltransferases directly reverse the alkylation on the O(6) position of guanine in DNA. This group of proteins has been proposed to repair the damaged base in an extrahelical manner; however, the detailed mechanism is not understood. Here we applied a chemical disulfide crosslinking method to probe the damage-searching mechanism of two O(6)-alkylguanine-DNA alkyltransferases, the Escherichia coli C-Ada and the human AGT. Crosslinking reactions with different efficiency occur between the reactive Cys residues of both proteins and a modified cytosine bearing a thiol tether in various DNA probes. Our results indicate that it is not necessary for these proteins to actively flip out every base to find damage. Instead they can locate potential lesions by simply capturing a lesioned base that is transiently extrahelical or sensing the unstable nature of a damaged base pair.
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Affiliation(s)
- Erica M Duguid
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
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43
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Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Münch U, Chen L, Bayly SF, Torrence PF. Probing the activation site of ribonuclease L with new N6-substituted 2',5'-adenylate trimers. Bioorg Med Chem 2003; 11:2041-9. [PMID: 12670655 DOI: 10.1016/s0968-0896(03)00060-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
2-5A trimer [5'-monophosphoryladenylyl(2'-5')adenylyl(2'-5')adenosine] activates RNase L. While the 5'-terminal and 2'-terminal adenosine N(6)-amino groups play a key role in binding to and activation of RNase L, the exocyclic amino function of the second adenylate (from the 5'-terminus) plays a relatively minor role in 2-5A's biological activity. To probe the available space proximal to the amino function of the central adenylate of 2-5A trimer during binding to RNase L, a variety of substituents were placed at that position. To accomplish this, the convertible building block 5'-O-dimethoxytrityl-3'-O-(tert-butyldimethylsilyl)-6-(2,4-dinitrophenyl)thioinosine 2'-(2-cyanoethylN,N-diisopropylphosphoramidite) was prepared as a synthon to introduce 6-(2,4-dinitrophenyl)thioinosine into the middle position of the 2-5A trimer during automated synthesis. Post-synthetic treatment with aqueous amines transformed the (2,4-dinitrophenyl)thioinosine into N(6)-substituted adenosines. Assays of these modified trimers for their ability to bind and activate RNase L showed that activation activity could be retained, albeit with some sacrifice compared to unmodified p5'A2'p5'A2'p5'A. Thus, the spatial domain about this N(6)-amino function could be available for modifications to enhance the biological potency of 2-5A analogues and to ligate 2-5A to targeting vehicles such as antisense molecules.
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Affiliation(s)
- Ursula Münch
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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He C, Verdine GL. Trapping distinct structural states of a protein/DNA interaction through disulfide crosslinking. CHEMISTRY & BIOLOGY 2002; 9:1297-303. [PMID: 12498882 DOI: 10.1016/s1074-5521(02)00283-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The N-terminal domain of the Escherichia coli Ada protein (N-Ada) repairs methyl phosphotriesters in DNA through a zinc-mediated transfer to Cys38 of the protein. Methylation of Cys38 enhances the sequence-specific DNA affinity of N-Ada by approximately 1000-fold, thereby enabling the protein to activate the genes of a methylation-resistance regulon. It is of interest to understand the structural basis for metalloactivated methyl transfer and methylation-dependent enhancement of DNA binding activity. Although recent progress has been made on the structural front, efforts to develop a complete picture of N-Ada structure/function have been hampered by the inability to prepare homogeneous protein/DNA complexes representing different states of the unmethylated protein. Here, we describe the development of an approach to trap both sequence-specific and nonsequence-specific DNA recognition complexes of N-Ada through formation of an intermolecular disulfide crosslink between the protein and DNA.
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Affiliation(s)
- Chuan He
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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Klostermeier D, Millar DP. Time-resolved fluorescence resonance energy transfer: a versatile tool for the analysis of nucleic acids. Biopolymers 2002; 61:159-79. [PMID: 11987179 DOI: 10.1002/bip.10146] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The biological functions of nucleic acids in processes of DNA replication, transcription, homologous recombination, mRNA translation, and ribozyme catalysis are intimately linked to their three-dimensional structures and to conformational changes induced by proteins, metal ions and other ligands. Fluorescence spectroscopy is a powerful technique for probing the structure and conformational dynamics of biological macromolecules under a wide range of solution conditions. Fluorescence resonance energy transfer (FRET) provides long-range distance information from 10 to 100 A, a range that is useful for probing the global structure of nucleic acids. While steady-state measurements of FRET provide the average distance between donor and acceptor, much more information is available from the analysis of the nanosecond emission decay of the donor in time-resolved FRET (trFRET) experiments. Analysis of the decay in terms of donor-acceptor distance distributions can resolve different conformers in a heterogeneous mixture, providing information on the global structure and flexibility of each species as well as their equilibrium populations. In this review, we outline the principles of trFRET and the methods used to incorporate fluorescent probes into DNA and RNA. Examples of specific applications are presented to illustrate the versatility of trFRET as a tool to define global structures, to identify conformational heterogeneity and flexibility, to investigate the energetics of tertiary structure formation and to probe structural rearrangements of nucleic acids.
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Affiliation(s)
- D Klostermeier
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Civitello ER, Leniek RG, Hossler KA, Haebe K, Stearns DM. Synthesis of peptide-oligonucleotide conjugates for chromium coordination. Bioconjug Chem 2001; 12:459-63. [PMID: 11459447 DOI: 10.1021/bc0100105] [Citation(s) in RCA: 9] [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
The synthesis of the first peptide-oligonucleotide conjugate designed to coordinate chromium(III) is reported. The overall goal of this work is to synthesize di-deoxynucleotides tethered with chromium(III)-coordinating appendages to model chromium-DNA-protein cross-links, which are a type of DNA lesion that may be involved in chromium-induced cancers. The conjugate dGp(NHCH(2)CH(2)S-Ac-Gly-Ser-Gly-OH)G was made by coupling the peptide, ClAc-Gly-Ser-Gly-OH, and dinucleotide, dGp(NHCH(2)CH(2)SH)G, through a thioether moiety. The conjugate was characterized by HPLC and mass spectrometry. Previously reported methods for small-scale solid-phase synthesis of peptides and dinucleotide were unsuitable; therefore, gram-scale solution-phase methods were developed. We also report the gram-scale syntheses of two other serine-containing peptides, ClAc-betaAla-Ser-Gly-OH and ClAc-Ser-Gly-OH, and three histidine-containing peptides, ClAc-Gly-His-Gly-OH, ClAc-betaAla-His-Gly-OH, and ClAc-His-Gly-OH. The synthesis and characterization of chromium-containing peptide-oligonucleotide conjugates will ultimately help us to understand chromium-DNA interactions at a molecular level, which is necessary before we can determine how chromium causes cancer.
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Affiliation(s)
- E R Civitello
- Department of Chemistry, Northern Arizona University, P.O. Box 5698, Flagstaff, Arizona 86011-5698, USA
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Affiliation(s)
- H Gadgil
- Department of Biochemistry, University of Tennessee, 858 Madison Avenue, Memphis, Tennessee 38163, USA
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Robles J, Grandas A, Pedroso E. Synthesis of modified oligonucleotides containing 4-guanidino-2-pyrimidinone nucleobases. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)00991-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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