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Kuzuya A, Machida K, Shi Y, Tanaka K, Komiyama M. Site-Selective RNA Activation by Acridine-Modified Oligodeoxynucleotides in Metal-Ion Catalyzed Hydrolysis: A Comprehensive Study. ACS OMEGA 2017; 2:5370-5377. [PMID: 31457805 PMCID: PMC6644747 DOI: 10.1021/acsomega.7b00966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/21/2017] [Indexed: 06/10/2023]
Abstract
Various types of acridine were conjugated to DNA and used for site-selective RNA scission together with another unmodified DNA and a Lu(III) ion. The target phosphodiester linkage in the substrate RNA was selectively and efficiently activated, and was hydrolyzed by the free Lu(III) ion. Among the investigated 14 conjugates, the conjugate bearing 9-amino-2-isopropoxy-6-nitroacridine was the best RNA-activator. Systematic evaluation of the RNA-activating ability of the acridines showed that (1) the acridines act as an acid catalyst within the RNA activation, (2) the amino-group at the 9-position of acridine is essential to modulate the acidity of acridine, (3) the electron-withdrawing group at the 3-position further enhances the acid catalysis, and (4) the substituent at the 2-position sterically modulates the orientation of acridine-intercalation favorably for the catalysis. Moreover, it is revealed that the opposite base of acridine does not inhibit direct interaction of acridine with the target phosphodiester linkage.
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Affiliation(s)
- Akinori Kuzuya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
| | - Kenzo Machida
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Yun Shi
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Keita Tanaka
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- International
Center for Materials Nanoarchitechtonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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2
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Satheeshkumar R, Sayin K, Kaminsky W, Rajendra Prasad KJ. Synthesis, spectral analysis and quantum chemical studies on molecular geometry, chemical reactivity of 7-chloro-9-(2′-chlorophenyl)-2,3-dihydroacridin-4(1H)-one and 7-chloro-9-(2′-fluorophenyl)-2,3-dihydroacridin-4(1H)-one. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Theoretical and experimental investigations on molecular structure of 7-Chloro-9-phenyl-2,3-dihydroacridin-4(1H)-one with cytotoxic studies. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Li C, Zhang F. Single step incorporation of isatin to enaminone: a recyclable catalyst towards assembly of diverse four ring fused pyrrolo[2,3,4-kl]acridin-1-ones. RSC Adv 2016. [DOI: 10.1039/c6ra18048e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single step synthesis of four ring fused pyrrolo[2,3,4-kl]acridin-1-ones using recoverable sulfonated carbonaceous material as heterogeneous catalyst.
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Affiliation(s)
- Chunmei Li
- School of Chemistry and Chemical Engineering
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing
- China
| | - Furen Zhang
- School of Chemistry and Chemical Engineering
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing
- China
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5
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Wan Y, Zhang XX, Wang C, Zhao LL, Chen LF, Liu GX, Huang SY, Yue SN, Zhang WL, Wu H. The first example of glucose-containing Brønsted acid synthesis and catalysis: efficient synthesis of tetrahydrobenzo[α]xanthens and tetrahydrobenzo[α]acridines in water. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Patel S, Rana J, Roy J, Huang H. Cleavage of pyrene-stabilized RNA bulge loops by trans-(±)-cyclohexane-1,2-diamine. Chem Cent J 2012; 6:3. [PMID: 22244351 PMCID: PMC3319420 DOI: 10.1186/1752-153x-6-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/13/2012] [Indexed: 11/10/2022] Open
Abstract
Chemical agents that cleave HIV genome can be potentially used for anti-HIV therapy. In this report, the cleavage of the upper stem-loop region of HIV-1 TAR RNA was studied in a variety of buffers containing organic catalysts. trans-(±)-Cyclohexane-1,2-diamine was found to cleave the RNA with the highest activity (31%, 37°C, 18 h). Cleavage of the RNA in trans-(±)-cyclohexane-1,2-diamine buffer was also studied when the RNA was hybridized with complementary DNAs. A pyrene-modified C3 spacer was incorporated to the DNA strand to facilitate the formation of a RNA bulge loop in the RNA/DNA duplex. In contrast, unmodified DNAs cannot efficiently generate RNA bulge loops, regardless of the DNA sequences. The results showed that the pyrene-stablized RNA bulge loops were efficiently and site-specifically cleaved by trans-(±)-cyclohexane-1,2-diamine.
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Affiliation(s)
- Sejal Patel
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, 323 Martin L, King Blvd, Newark, NJ, 07102, USA.
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7
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Jiang B, Wang X, Li MY, Wu Q, Ye Q, Xu HW, Tu SJ. A domino synthetic strategy leading to two-carbon-tethered fused acridine/indole pairs and fused acridine derivatives. Org Biomol Chem 2012; 10:8533-8. [DOI: 10.1039/c2ob26315g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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8
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Kuzuya A, Tanaka K, Komiyama M. Photoswitching of site-selective RNA scission by sequential incorporation of azobenzene and acridine residues in a DNA oligomer. J Nucleic Acids 2011; 2011:162452. [PMID: 21941627 PMCID: PMC3177363 DOI: 10.4061/2011/162452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/06/2011] [Indexed: 11/20/2022] Open
Abstract
Photoresponsive systems for site-selective RNA scission have been prepared by combining Lu(III) ions with acridine/azobenzene dual-modified DNA. The modified DNA forms a heteroduplex with substrate RNA, and the target phosphodiester linkages in front of the acridine residue is selectively activated so that Lu(III) ion rapidly cleaves the linkage. Azobenzene residue introduced adjacent to the acridine residue acts as a photoresponsive switch, which triggers the site-selective scission upon UV irradiation. A trans isomer of azobenzene efficiently suppresses the scission, whereas the cis isomer formed by UV irradiation hardly affects the scission. As a result, 1.7-2.4-fold acceleration of the cleavage was achieved simply by irradiating UV for 3 min to the mixture prior to the reaction. Considering the yield of photoisomerization, the intrinsic activity of a cis isomer is up to 14.5-fold higher than that of the trans isomer.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Kamiyamate-cho, Suita, Osaka 564-8680, Japan
| | - Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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9
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Murtola M, Wenska M, Strömberg R. PNAzymes that are artificial RNA restriction enzymes. J Am Chem Soc 2010; 132:8984-90. [PMID: 20545354 DOI: 10.1021/ja1008739] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
DNA-cleaving restriction enzymes are well-known tools in biomedical and biotechnological research. There are, however, no corresponding enzymes known for RNA cleavage. There has been an ongoing development of artificial ribonucleases, including some attempts at sequence selectivity. However, so far these systems have displayed modest rates of cleavage, and in most cases, the cleaver has been used in excess or in stoichiometric amounts. In the current work, we present PNA-based systems (PNAzymes) that carry a Cu(II)-2,9-dimethylphenanthroline group and that act as site and sequence specific RNases. The general basis for the systems is that the target is cleaved at a nonbase paired region (RNA bulge) which is formed in the substrate upon binding of the PNAzyme. With this copper based system, cleavage takes place at virtually only one site and with a half-life of down to 30 min under stoichiometric conditions. Efficient turnover of RNA-substrate is shown with a 100-fold excess of substrate, thus, demonstrating true enzyme behavior. In addition, alteration of the sequence in the RNA bulge or a mismatch in the base-pairing region leads to substantial decreases in rate showing both kinetic resolution and binding discrimination in the substrate selectivity. The selectivity is further demonstrated by the substrates, with two potential cleavage sites differing in only one base, are cleaved only at the site that either does not have a mismatch or is kinetically preferred. We suggest that these systems can serve as a basis for construction of RNA restriction enzymes for in vitro manipulations.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, S-14183, Huddinge, Sweden
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Huang X, Zhang T. Cascade nucleophilic addition-cyclic Michael addition of arynes and phenols/anilines bearing ortho alpha,beta-unsaturated groups: facile synthesis of 9-functionalized xanthenes/acridines. J Org Chem 2010; 75:506-9. [PMID: 20020766 DOI: 10.1021/jo902311a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile synthesis of xanthenes and acridines based on a cascade nucleophilic addition-cyclic Michael addition process of arynes and phenols/anilines substituted with alpha,beta-unsaturated groups at the ortho positions is described. The reaction has also been successfully extended to the synthesis of 9-spiro-xanthene and acridine derivatives with potential biochemical interest.
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Affiliation(s)
- Xian Huang
- Department of Chemistry, Zhejiang University (Xixi Campus), Hangzhou 310028, People's Republic of China.
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11
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Kuzuya A, Shi Y, Tanaka K, Machida K, Komiyama M. Efficient Site-selective RNA Activation and Scission Achieved by Geometry Control of Acridine Intercalation in RNA/DNA Heteroduplex. CHEM LETT 2009. [DOI: 10.1246/cl.2009.432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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13
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Dijk EW, Feringa BL, Roelfes G. DNA in Metal Catalysis. TOP ORGANOMETAL CHEM 2008. [DOI: 10.1007/3418_2008_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Yamayoshi A, Kato K, Suga S, Ichinoe A, Arima T, Matsuda T, Kato H, Murakami A, Wake N. Specific apoptosis induction in human papillomavirus-positive cervical carcinoma cells by photodynamic antisense regulation. Oligonucleotides 2007; 17:66-79. [PMID: 17461764 DOI: 10.1089/oli.2006.0047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human papillomavirus type 18 (HPV18) is frequently detected in cervical cancer cells. The viral proteins E6 and E7 are expressed consistently and have oncogenic activities. The E7 protein binds to a tumor suppressor, the retinoblastoma gene product (pRB), however, leading to the stabilization of tumor suppressor, p53 protein. On the other hand, another viral product, E6, forms complexes with p53 and abrogates its function, resulting in tumor progression. These facts imply that the E6 oncogene is one of the ideal targets for directed gene therapy in HPV-positive cervical cancer. In this study, we tried photodynamic antisense regulation of the antiapoptotic E6 expression using a photocross-linking reagent, 4,5',8-trimethylpsoralen, conjugated oligo(nucleoside phosphorothioate) (Ps-S-Oligo). This photodynamic antisense strategy effectively elicited the apoptotic death of HPV18-positive cervical cancer cells through the selective repression of E6 mRNA and consequent stabilization of p53 protein. E7-mediated signals potentially activated the p53 function and mobilized the p53 pathway to deliver pro-apoptotic signals to the cancer cells, leading to the suppression of in vivo tumorigenesis. An extremely low concentration of cisplatin in addition to Ps-S-Oligos further up-regulated p53 activity, provoking massive apoptotic induction. These results suggest that the photodynamic antisense strategy has the great therapeutic potential in HPV-positive cervical cancers.
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Affiliation(s)
- Asako Yamayoshi
- Department of Molecular Genetics, Division of Molecular and Cell Therapeutics, Kyushu University, Maidashi, Fukuoka 812-8582, Japan
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15
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Sasayama T, Kato M, Aburatani H, Kuzuya A, Komiyama M. Simultaneous genotyping of indels and SNPs by mass spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:3-8. [PMID: 16338145 DOI: 10.1016/j.jasms.2005.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/20/2005] [Accepted: 08/26/2005] [Indexed: 05/05/2023]
Abstract
Nucleotide insertion/deletion polymorphisms (indels) in ApoE gene were precisely genotyped using artificial ribonucleases and MALDI-TOF MS. The RNA fragments for MS analysis were prepared by treating RNA specimens with our artificial ribonucleases, which consist of LuCl(3) (molecular scissors) and oligonucleotides bearing two acridine groups (RNA-activator for site-selective scission). RNA scission by Lu(III) ion always occurred at the phosphodiester linkages in front of the two acridines, even when the RNA specimens involved consecutive cytidine sequences of different lengths. Thus, even complicated mixtures of these indel specimens were completely genotyped by using only one acridine-bearing oligonucleotide and by subjecting the reaction mixture to single MS measurement. Moreover, single nucleotide polymorphism (SNP) in the consecutive sequences could be genotyped simultaneously with the indels.
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Affiliation(s)
- Takuro Sasayama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Mayu Kato
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
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16
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Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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17
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Shi Y, Machida K, Kuzuya A, Komiyama M. Design of phosphoramidite monomer for optimal incorporation of functional intercalator to main chain of oligonucleotide. Bioconjug Chem 2005; 16:306-11. [PMID: 15769083 DOI: 10.1021/bc049698m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chirally pure phosphoramidite monomers bearing 9-amino-6-chloro-2-methoxyacridine were synthesized from D- or L-threoninol and omega-aminocarboxylic acid, and incorporated into oligonucleotides. These acridine-DNA conjugates formed stable duplexes with complementary RNA because of intercalation of the acridine to DNA/RNA heteroduplexes. The stability of duplexes was not very dependent on either the chirality of the central carbon bearing the acridine or the length of the side chain. However, the ability for site-selective activation of the phosphodiester linkage in front of the acridine, which induced Lu(III)-promoted RNA scission, was strongly dependent on these two factors. The largest activation was achieved when the monomer unit was prepared from L-threoninol and 4-aminobutyric acid and the acridine was bound to the amino group. By attaching the more acidic 9-amino-2-methoxy-6-nitroacridine to this optimized scaffold, a quite effective acridine-DNA conjugate for site-selective RNA scission was obtained.
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Affiliation(s)
- Yun Shi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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18
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Kuzuya A, Shi Y, Sasayama T, Komiyama M. Cooperation of metal-ion fixation and target-site activation for efficient site-selective RNA scission. J Biol Inorg Chem 2005; 10:270-4. [PMID: 15772817 DOI: 10.1007/s00775-005-0638-4] [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] [Received: 01/14/2005] [Accepted: 02/21/2005] [Indexed: 10/25/2022]
Abstract
Iminodiacetate-DNA conjugates and acridine-DNA conjugates were synthesized and combined for site-selective RNA hydrolysis by Lu(III). When these conjugates form a ternary complex with complementary RNA, the Lu(III)-iminodiacetate complex is placed near the target phosphodiester linkage of RNA which is in front of the acridine and is activated by noncovalent interactions. The site-selective hydrolysis by these combinations is several times as fast as that achieved by combining unmodified DNA (without iminodiacetate) and the acridine-DNA conjugate.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, 153-8904, Japan
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19
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Kuznetsova IL, Zenkova MA, Gross HJ, Vlassov VV. Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease. Nucleic Acids Res 2005; 33:1201-12. [PMID: 15731340 PMCID: PMC549568 DOI: 10.1093/nar/gki264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1–7 nt) and sequence composition were formed in a 3′ terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulges (up to 4 nt) were readily formed upon oligonucleotide hybridization, whereas hybridization of the RNA to the oligonucleotides designed to produce larger bulges resulted in formation of several alternative structures. A synthetic ribonuclease mimic displaying Pyr–Pu cleavage specificity cleaved CpA motifs located within bulges faster than similar motifs within the rest of the RNA. In the presence of 10 mM MgCl2, 75% of the cleavage products resulted from the attack of this motif. Thus, selective RNA cleavage at a single target phosphodiester bond was achieved by using bulge forming oligonucleotides and a small ribonuclease A mimic.
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Affiliation(s)
| | - Marina A. Zenkova
- To whom correspondence should be addressed. Tel: +7 3832 333761; Fax: +7 3832 333761;
| | - Hans J. Gross
- Institute of Biochemistry, BiocenterAm Hubland, D-97074 Würzburg, Germany
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