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Dai Q, Zheng G, Schwartz MH, Clark WC, Pan T. Selective Enzymatic Demethylation of N
2
, N
2
-Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qing Dai
- Department of Chemistry; The University of Chicago; Chicago IL 60637 USA
| | - Guanqun Zheng
- Department of Biochemistry & Molecular Biology; The University of Chicago; Chicago IL 60637 USA
| | - Michael H. Schwartz
- Department of Biochemistry & Molecular Biology; The University of Chicago; Chicago IL 60637 USA
| | - Wesley C. Clark
- Department of Biochemistry & Molecular Biology; The University of Chicago; Chicago IL 60637 USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology; The University of Chicago; Chicago IL 60637 USA
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2
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Dai Q, Zheng G, Schwartz MH, Clark WC, Pan T. Selective Enzymatic Demethylation of N 2 ,N 2 -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing. Angew Chem Int Ed Engl 2017; 56:5017-5020. [PMID: 28371071 DOI: 10.1002/anie.201700537] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/10/2017] [Indexed: 12/17/2022]
Abstract
The abundant Watson-Crick face methylations in biological RNAs such as N1 -methyladenosine (m1 A), N1 -methylguanosine (m1 G), N3 -methylcytosine (m3 C), and N2 ,N2 -dimethylguanosine (m22 G) cause significant obstacles for high-throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild-type E. coli AlkB and its D135S mutant can remove most of m1 A, m1 G, m3 C modifications in transfer RNA (tRNA), but they work poorly on m22 G. Here we report the design and evaluation of a series of AlkB mutants against m22 G-containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m22 G modification to N2 -methylguanosine (m2 G). We also show that this new enzyme improves the efficiency of tRNA sequencing.
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Affiliation(s)
- Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Guanqun Zheng
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael H Schwartz
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Wesley C Clark
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
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3
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Kawashima E, Nakanishi Y, Terui Y, Tomitori H, Kashiwagi K, Ohba Y, Kamaike K. Synthesis and evaluation of pyrrole polyamide-2'-deoxyguanosine 5'-phosphate hybrid. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:196-205. [PMID: 24001193 DOI: 10.1080/15257770.2013.774014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pyrrole polyamide-2'-deoxyguanosine 5'-phosphate hybrid (Hybrid 4) was synthesized and evaluated in terms of the inhibition of mouse mammary carcinoma FM3A cell growth. Hybrid 4 was found to exhibit dose-dependent inhibition of cell growth.
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Affiliation(s)
- Etsuko Kawashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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4
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Maruyama T, Sakakibara N, Tsukamoto I, Isono Y, Takata M, Konishi R, Kato Y. A New Method for Synthesis and Angiogenic Evaluation of Leteprinim Potassium and Its Novel Analogs. HETEROCYCLES 2013. [DOI: 10.3987/com-13-12824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Kawashima E, Ohba Y, Terui Y, Kamaike K. Synthesis and evaluation of oligonucleotide-conjugated pyrrole polyamide-2'-deoxyguanosine hybrids as novel gene expression control compounds. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:850-72. [PMID: 22060551 DOI: 10.1080/15257770.2011.607145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA oligonucleotide-conjugated pyrrole polyamide-2'-deoxyguanosine hybrids were synthesized and examined as novel gene expression control compounds. The T(m) values and circular dichroism spectral analyses showed that the oligonucleotide-conjugated hybrids possess high DNA recognition and a very high binding affinity for DNA that includes the pyrrole polyamide binding sequence.
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Affiliation(s)
- Etsuko Kawashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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6
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Maruyama T, Sakakibara N, Komatsu M, Iwai M, Tsuruta T. A New Method for Synthesis of 2-Alkoxyadenosine Analogs. HETEROCYCLES 2011. [DOI: 10.3987/com-11-12295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Devine SM, Scammells PJ. Synthesis and Utility of 2-Halo-O6-(benzotriazol-1-yl)-Functionalized Purine Nucleosides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001395] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Kawashima E, Kamaike K. [Design, synthesis and evaluation of polyamide-nucleoside hybrids and oligonucleotides conjugated hybrid as a novel gene expression control compound]. YAKUGAKU ZASSHI 2010; 130:355-75. [PMID: 20190521 DOI: 10.1248/yakushi.130.355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
On the basis of reports that a minor groove binder pyrrolepolyamide can interfere with gene expression by the sequence-specific recognition of DNA, we expected that nucleoside bearing a pyrrolepolyamide would be able to regulate gene expression. Therefore, we designed and synthesized the pyrrolepolyamide-adenosine (Hybrid 1) and -2'-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) as lead compounds for gene expression control compounds. The pyrrolepolyamide frame of Hybrid 2 and Hybrid 3 combines at the 2-exocyclic amino group of the 2'-deoxyguanosine by a linker and the 2-exocyclic amino group of guanine exists in the minor groove side of the duplex. Hybrid 2 is the 2'-deoxyguanosine-pyrrolepolyamide hybrid using the 3-aminopropionyl linker, while Hybrid 3 uses the 3-aminopropyl linker. An evaluation of the DNA binding sequence selectivity was performed by analysis of T(m) values and CD spectra, using distamycin A as a contrast. Hybrid 3 has provided more excellent sequence-distinguishable ability than other hybrids and Distamycin A. Moreover, on the basis of these results, we synthesized oligonucleotides conjugated to Hybrid 4, which is stable under conditions of DNA oligonucleotide solid phase synthesis, arranged from Hybrid 3. From T(m) values and CD spectral analysis, it was found that oligonucleotides conjugating Hybrid 4 possess high recognition ability and very high binding ability for the DNA that includes the pyrrolepolyamide binding sequence.
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Affiliation(s)
- Etsuko Kawashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Japan.
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9
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Arico JW, Calhoun AK, Salandria KJ, McLaughlin LW. Tetramethylsuccinimide as a directing/protecting group in purine glycosylations. Org Lett 2010; 12:120-2. [PMID: 19961189 DOI: 10.1021/ol9025028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tetramethylsuccinic anhydride can be used to protect the exocyclic amine of 6-aminopurine derivatives by forming the corresponding tetramethysuccinimide. X-ray crystallography confirms that the imide carbonyl and the methyl groups are positioned to sterically block the N7 nitrogen so that glycosylations occur with very high regiochemical control at N9. This approach is particularly effective for 3-substituted purines where the substituent tends to block access to N9 and inhibit glycosylation at that site.
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Affiliation(s)
- Joseph W Arico
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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10
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Kawashima E, Ohba Y, Terui Y, Kamaike K. Design, Synthesis, and Analysis of Minor Groove Binder Pyrrolepolyamide- 2′-Deoxyguanosine Hybrids. J Nucleic Acids 2010; 2010. [PMID: 20700414 PMCID: PMC2911594 DOI: 10.4061/2010/235240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 09/19/2009] [Accepted: 11/09/2009] [Indexed: 11/23/2022] Open
Abstract
Pyrrolepolyamide-2′-deoxyguanosine hybrids (Hybrid 2 and Hybrid 3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis of previously reported results of a pyrrolepolyamide-adenosine hybrid (Hybrid 1). Evaluation of the DNA binding sequence selectivity of pyrrolepolyamide-2′-deoxyguanosine hybrids was performed by CD spectral and Tm analyses. It was shown that Hybrid 3 possessed greater binding specificity than distamycin A, Hybrid 1 and Hybrid 2.
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Affiliation(s)
- Etsuko Kawashima
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yusuke Ohba
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yusuke Terui
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025, Japan
| | - Kazuo Kamaike
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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11
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Lakshman MK, Frank J. A simple method for C-6 modification of guanine nucleosides. Org Biomol Chem 2009; 7:2933-40. [PMID: 19582304 DOI: 10.1039/b905298d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A facile method for the introduction of various substituents at the C-6 position of guanosine and 2'-deoxyguanosine is reported. In a simple, 1-step transformation, tert-butyldimethylsilyl protected guanosine and 2'-deoxyguanosine were converted to the O(6)-(benzotriazol-1-yl) derivatives via reaction with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and 1,8-diazabicyclo[5.4.0]undec-7ene (DBU). The easily isolated, stable and storable, O(6)-(benzotriazol-1-yl) guanosine derivatives upon exposure to a range of nucleophiles, under appropriate conditions, led to the C-6 modified 2-amino purine nucleoside analogues in good yields.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031-9198, USA.
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12
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Swamy KCK, Kumar NNB, Balaraman E, Kumar KVPP. Mitsunobu and Related Reactions: Advances and Applications. Chem Rev 2009; 109:2551-651. [PMID: 19382806 DOI: 10.1021/cr800278z] [Citation(s) in RCA: 852] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. C. Kumara Swamy
- School of Chemistry, University of Hyderabad, Hyderabad − 500046, A. P., India
| | - N. N. Bhuvan Kumar
- School of Chemistry, University of Hyderabad, Hyderabad − 500046, A. P., India
| | - E. Balaraman
- School of Chemistry, University of Hyderabad, Hyderabad − 500046, A. P., India
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Kamaike K, Kayama Y, Mitsuhisa I, Etsuko K. Efficient synthesis of [2-15N]guanosine and 2'-deoxy[2'-15N]guanosine derivatives using N-(tert-butyldimethylsilyl)[15N]phthalimide as a 15N-labeling reagent. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:29-35. [PMID: 16440983 DOI: 10.1080/15257770500377771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nucleophilic aromatic substitution of 9-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-6-chloro-2-fluoro-9H-purine with N-(tert-butyldimethylsilyl) [15N]phthalimide in the presence of a catalytic amount of CsF at room temperature in DMF efficiently afforded the 6-chloro-2-[15N]phthalimidopurine derivative, which was subsequently converted to the [2-15N]guanosine derivative. The 2'-deoxy[2'-15N]guanosine derivative was also efficiently synthesized through a similar procedure.
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Affiliation(s)
- Kazuo Kamaike
- School of Pharmarcy, Tokyo University of Pharmarcy and Life Sciences, Hachioji, Tokyo, Japan.
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14
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Shankar S, Zalutsky MR, Vaidyanathan G. O6-3-[125I]iodobenzyl-2'-deoxyguanosine ([125I]IBdG): synthesis and evaluation of its usefulness as an agent for quantification of alkylguanine-DNA alkyltransferase (AGT). Bioorg Med Chem 2005; 13:3889-98. [PMID: 15911305 DOI: 10.1016/j.bmc.2005.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 04/07/2005] [Indexed: 11/21/2022]
Abstract
The development of O(6)-(3-[(125)I]iodobenzyl)-2'-deoxyguanosine ([(125)I]IBdG), the glycosylated analogue of the O(6)-3-iodobenzylguanine (IBG), as an agent for the in vivo mapping of the DNA repair protein alkylguanine-DNA alkyltransferase (AGT) is described. Synthesis of its tin precursor, O(6)-3-trimethylstannylbenzyl-2'-deoxyguanosine (TBdG) was achieved in four steps from deoxyguanosine. Radioiodination of TBdG in a single step gave [(125)I]IBdG in 70-85% isolated radiochemical yield. [(125)I]IBdG bound specifically to pure AGT with an IC(50) of 7.1 microM. From paired-label assays, [(125)I]IBdG showed a 2- to 3-fold higher cellular uptake than [(131)I]IBG in DAOY medulloblastoma, TE-671 rhabdomyosarcoma, SK-Mel-28 melanoma, and HT-29 colon carcinoma human cell lines. Uptake of both labeled compounds in these cell lines decreased with increasing concentrations of unlabeled O(6)-benzylguanine (BG) when BG was present in the medium during incubation with the labeled compounds. Compared to BG, unlabeled IBdG diminished the uptake of [(125)I]IBdG and [(131)I]IBG in DAOY cells more efficiently (IC(50)<1 microM vs >10 microM for BG). There was no significant change in cell-bound activity of [(125)I]IBdG and [(131)I]IBG when BG was removed from the incubation medium before incubating cells with the tracers, suggesting that only a very small portion of radioactivity taken up by the cells is AGT bound. This was corroborated by gel-electrophoresis performed on extracts from cells treated with varying amounts of BG and then incubated with [(125)I]IBdG in the presence of BG. No radiolabeled AGT band was discernable by phosphor-imaging, signifying low cellular AGT binding of the radiotracer. In contrast, when cell extracts were prepared from BG pre-treated cells and aliquots were incubated with [(125)I]IBdG subsequently, the intensity of radiolabeled AGT band decreased linearly as a function of BG concentration. This suggests that the low level of [(125)I]IBdG that binds to AGT does so in a concentration dependent manner. These data suggest that IBdG is transported across the cell membrane to a higher degree than IBG. However, to be a practical tracer for quantifying cellular AGT, considerable localization of such derivatives need to occur within the cell nucleus where AGT is present predominantly.
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Affiliation(s)
- Sriram Shankar
- Department of Radiology, Duke University Medical Center, Box 3808, Durham, NC 27710, USA
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Janeba Z, Francom P, Robins MJ. Efficient syntheses of 2-chloro-2'-deoxyadenosine (cladribine) from 2'-deoxyguanosine(1). J Org Chem 2003; 68:989-92. [PMID: 12558425 DOI: 10.1021/jo020644k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report efficient syntheses of the clinical agent cladribine (2-chloro-2'-deoxyadenosine, CldAdo), which is the drug of choice against hairy-cell leukemia and other neoplasms, from 2'-deoxyguanosine. Treatment of 3',5'-di-O-acetyl- or benzoyl-2'-deoxyguanosine (1) with 2,4,6-triisopropyl- or 4-methylbenzenesulfonyl chloride gave high yields of the 6-O-arylsulfonyl derivatives 2 or 2'b. Deoxychlorination at C6 of 1 also proceeded to give the 2-amino-6-chloropurine derivative 5 in excellent yields. The nonaqueous diazotization/chloro dediazoniation (acetyl chloride/benzyltriethylammonium nitrite) of 2, 2'b, and 5 gave the 2-chloropurine derivatives 3, 3'b, and 6, respectively. The selective ammonolysis at C6 (arylsulfonate with 3 or chloride with 6) and accompanying deprotection of the sugar moiety gave CldAdo (64-75% overall yield from 1).
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Affiliation(s)
- Zlatko Janeba
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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