201
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Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S. A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition. Nucleic Acids Res 2009; 37:1225-38. [PMID: 19136459 PMCID: PMC2651773 DOI: 10.1093/nar/gkn1062] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 12/15/2008] [Accepted: 12/16/2008] [Indexed: 11/13/2022] Open
Abstract
Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.
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Affiliation(s)
| | | | | | | | | | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
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202
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Kodama T, Matsuo C, Ori H, Miyoshi T, Obika S, Miyashita K, Imanishi T. Design, synthesis, and evaluation of a novel bridged nucleic acid, 2′,5′-BNAON, with S-type sugar conformation fixed by N–O linkage. Tetrahedron 2009. [DOI: 10.1016/j.tet.2008.12.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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203
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Obika S, Kodama T, Sugaya K, Baba T, Imanishi T. Synthesis of a Novel trans-3’,4’-BNA Monomer Bearing a 4,8-Dioxa-5-azabicyclo[5.3.0]decane Skeleton. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(d)58] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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204
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Obika S, Kodama T, Sugaya K, Harada Y, Mitsuoka Y, Imanishi T. Synthesis and Properties of 2’-Deoxy-trans-3’,4’-BNA with S-Type Sugar Puckering. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(f)99] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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205
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Obika S, Rahman SMA, Song B, Onoda M, Koizumi M, Morita K, Imanishi T. Synthesis and properties of 3'-amino-2',4'-BNA, a bridged nucleic acid with a N3'-->P5' phosphoramidate linkage. Bioorg Med Chem 2008; 16:9230-7. [PMID: 18812260 DOI: 10.1016/j.bmc.2008.09.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/01/2008] [Accepted: 09/05/2008] [Indexed: 01/09/2023]
Abstract
The synthesis and properties of a bridged nucleic acid analogue containing a N3'-->P5' phosphoramidate linkage, 3'-amino-2',4'-BNA, is described. A heterodimer containing a 3'-amino-2',4'-BNA thymine monomer, and thymine and methylcytosine monomers of 3'-amino-2',4'-BNA and their 5'-phosphoramidites, were synthesized efficiently. The dimer and monomers were incorporated into oligonucleotides by conventional 3'-->5' assembly, and 5'-->3' reverse assembly phosphoramidite protocols, respectively. Compared to a natural DNA oligonucleotide, modified oligonucleotides containing the 3'-amino-2',4'-BNA residue formed highly stable duplexes and triplexes with single-stranded DNA (ssDNA), single-stranded RNA (ssRNA), and double-stranded DNA (dsDNA) targets, with the average increase in melting temperature (T(m)) against ssDNA, ssRNA and dsDNA being +2.7 to +4.0 degrees C, +5.0 to +7.0 degrees C, and +5.0 to +11.0 degrees C, respectively. These increases are comparable to those observed for 2',4'-BNA-modified oligonucleotides. In addition, an oligonucleotide modified with a single 3'-amino-2',4'-BNA thymine residue showed extraordinarily high resistance to nuclease degradation, much higher than that of 2',4'-BNA and substantially higher even than that of 3'-amino-DNA and phosphorothioate oligonucleotides. The above properties indicate that 3'-amino-2',4'-BNA has significant potential for antisense and antigene applications.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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206
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Morita K, Kaneko M, Obika S, Imanishi T, Kitade Y, Koizumi M. Biologically stable 2-5A analogues containing 3'-O,4'-C-bridged adenosine as potent RNase L agonists. ChemMedChem 2008; 2:1703-7. [PMID: 17910011 DOI: 10.1002/cmdc.200700150] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Koji Morita
- Exploratory Chemistry Research Laboratories, Sankyo Co., Ltd.,Tokyo 140-8710, Japan
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207
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Kuwahara M, Obika S, Nagashima JI, Ohta Y, Suto Y, Ozaki H, Sawai H, Imanishi T. Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides. Nucleic Acids Res 2008; 36:4257-65. [PMID: 18583360 PMCID: PMC2490744 DOI: 10.1093/nar/gkn404] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 06/07/2008] [Accepted: 06/09/2008] [Indexed: 11/16/2022] Open
Abstract
In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of thermostable DNA polymerases used, Taq, Phusion HF, Vent(exo-), KOD Dash and KOD(exo-), the KOD Dash and KOD(exo-) DNA polymerases could smoothly read through the modified templates containing 2'-O,4'-C-methylene-linked nucleotides at intervals of a few nucleotides, even at standard enzyme concentrations for 5 min. Although the Vent(exo-) DNA polymerase also read through these modified templates, kinetic study indicates that the KOD(exo-) DNA polymerase was found to be far superior to the Vent(exo-) DNA polymerase in accurate incorporation of nucleotides. When either of the DNA polymerase was used, the presence of 2',4'-bridged nucleotides on a template strand substantially decreased the reaction rates of nucleotide incorporations. The modified templates containing sequences of seven successive 2',4'-bridged nucleotides could not be completely transcribed by any of the DNA polymerases used; yields of longer elongated products decreased in the order of steric bulkiness of the modified sugars. Successive incorporation of 2',4'-bridged nucleotides into extending strands using 2',4'-bridged nucleoside-5'-triphospates was much more difficult. These data indicate that the sugar modification would have a greater effect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template as well, as in base modification.
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Affiliation(s)
- Masayasu Kuwahara
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Gunma 376-8515, Japan.
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208
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Roongjang S, Takahashi K, Obika S, Imanishi T. Inhibition of bcl-xL expression by antisense oligonucleotides containing various bridged nucleic acids (BNAs). ACTA ACUST UNITED AC 2008:113-4. [PMID: 18029612 DOI: 10.1093/nass/nrm057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recently, we described the antisense activity of 2',4'-BNA oligonucleotides in living cells.(1) Here, we examine the antisense effect of 2',4'-BNA, 2',4'-(COC) and 3'-amino-2',4'-BNA oligonucleotides targeting the bcl-xL gene. The results showed that while S-oligo had a slightly inhibiting effect on bcl-xL expression and natural DNA had no effect, an antisense oligonucleotide (AON) containing six 2',4'-(COC) nucleotides reduced the bcl-xL mRNA level to 64% of the untreated level. Interestingly, several types of AON-those containing nine 2',4'-BNA(COC) nucleotides, 2',4'-BNA and 3'-amino-2',4'-BNA- completely inhibited expression of the target gene. These data show that, compared with the corresponding natural DNA and S-oligo, BNA-based AONs are efficient inhibitors of bcl-xL expression.
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Affiliation(s)
- Somjing Roongjang
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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209
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Tachibana K, Katayama T, Ueda C, Sumitomo M, Tagami M, Ishimoto K, Yamasaki D, Tanaka T, Hamakubo T, Sakai J, Kodama T, Obika S, Imanishi T, Doi T. Antisense activity of 2',4'-BNA targeted to PPAR gamma in THP-1 and HCT116 cells. ACTA ACUST UNITED AC 2008:441-2. [PMID: 18029776 DOI: 10.1093/nass/nrm221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) is a nucleic acid analogue that has high affinity binding to its complementary RNA. Peroxisome proliferator-activated receptor (PPAR) y belongs to the nuclear hormone receptor superfamily and is a drug target in the treatment of type 2 diabetes. Here, we show the antisense effects of 2',4'-BNA oligonucleotides against PPARy in the human monocytic leukaemia cell line THP-1 and the human colorectal tumor cell line HCT116.
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Affiliation(s)
- Keisuke Tachibana
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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210
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Nagashima JI, Minezaki S, Obika S, Imanishi T, Kuwahara M, Sawai H. Polymerisation of a DNA strand using oligo-DNA template with modified bases, sugars and phosphates. ACTA ACUST UNITED AC 2008:55-6. [PMID: 18029583 DOI: 10.1093/nass/nrm028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have attempted to synthesise a complimentary strand using oligo-DNA with modified bases, sugars and phosphates as a template strand by polymerase reaction. Analogues bearing C5-substituted uracil, those with amide linkage [-CH2C=ONH-] in place of phospho-diester linkage and those bearing 2'-O, 4'-C-bridged sugar were used. Primer extension reactions were carried out to synthesise complimentary DNA strands. The reactions depended on the thermostable DNA polymerase used, the type of modification or the number of the modified position on the template strand.
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Affiliation(s)
- Jun-Ichi Nagashima
- Graduate School of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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211
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Sugaya K, Harada Y, Mitsuoka Y, Osaki T, Obika S, Kodama T, Imanishi T. Synthesis and properties of a 2'-deoxy analogue of trans-3',4'-BNA with an S-type sugar conformation. ACTA ACUST UNITED AC 2008:155-6. [PMID: 18029633 DOI: 10.1093/nass/nrm078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We previously synthesized bridged nucleic acid (BNA) analogues possessing an S-type sugar conformation. Recently, we achieved the synthesis of a 2'-deoxy analogue of trans-3',4'-BNA. The structure of this compound was confirmed by X-ray crystallography, which indicated that its sugar ring had an S-type conformation. The hybridization ability of the 2'-deoxy-trans-3',4'-BNA-modified oligonucleotide with DNA and RNA complements was evaluated, and it was found that 2'-deoxy-trans-3',4'-BNA showed superior hybridization ability compared with other BNA analogues with S-type sugar conformation.
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Affiliation(s)
- Kensaku Sugaya
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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212
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Kodama T, Matsuo C, Ori H, Obika S, Miyashita K, Imanishi T. Synthesis and evaluation of a novel 2',5'-bridged nucleic acid with sugar conformation fixed to S-type by N-O linkage. ACTA ACUST UNITED AC 2008:159-60. [PMID: 18029635 DOI: 10.1093/nass/nrm080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Our work involves the design and synthesis of various types of bridged nucleic acid (BNA). Here, we describe a novel 2'-O, 5'-N-bridged nucleic acid, 2',5'-BNA(ON), whose sugar puckering is fixed to the S-type conformation by N-O linkage. A 2',5'-BNA(ON)-containing dimer unit was synthesized via a coupling reaction between a protected 2',5'-BNA(ON)-U monomer and a thymidine derivative. Introduction of 2',5'-BNA(ON)-U into DNA was carried out using conventional phosphoramidite chemistry with a DNA synthesizer. The hybridization abilities of 2',5'-BNA(ON)-U-modified oligonucleotides with their DNA or RNA complements were evaluated.
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Affiliation(s)
- Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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213
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Rahman SMA, Seki S, Utsuki K, Obika S, Miyashita K, Imanishi T. 2',4'-BNA(NC): a novel bridged nucleic acid analogue with excellent hybridizing and nuclease resistance profiles. Nucleosides Nucleotides Nucleic Acids 2008; 26:1625-8. [PMID: 18066840 DOI: 10.1080/15257770701548980] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Oligonucleotides modified with 2 ',4 '-BNA(NC) (N-H)/(N-Me) monomers exhibited excellent hybridizing and nuclease resistance properties. Duplex and triplex thermal stabilities were greatly enhanced by incorporating 2',4'-BNA(NC) (N-H) and (N-Me) monomers and nuclease resistance was tremendously higher than that of natural oligonucleotide.
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Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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214
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Rahman SMA, Seki S, Obika S, Yoshikawa H, Miyashita K, Imanishi T. Design, synthesis, and properties of 2',4'-BNA(NC): a bridged nucleic acid analogue. J Am Chem Soc 2008; 130:4886-96. [PMID: 18341342 DOI: 10.1021/ja710342q] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The novel bridged nucleic-acid analogue 2',4'-BNA(NC) (2'-O,4'-C-aminomethylene bridged nucleic acid), containing a six-membered bridged structure with an N-O linkage, was designed and synthesized efficiently, demonstrating a one-pot intramolecular NC bond-forming key reaction to construct a perhydro-1,2-oxazine ring (11 and 12). Three monomers of 2',4'-BNA(NC) (2',4'-BNA(NC)[NH], [NMe], and [NBn]) were synthesized and incorporated into oligonucleotides, and their properties were investigated and compared with those of 2',4'-BNA (LNA)-modified oligonucleotides. Compared to 2',4'-BNA (LNA)-modified oligonucleotides, 2',4'-BNA(NC) congeners were found to possess: (i) equal or higher binding affinity against an RNA complement with excellent single-mismatch discriminating power, (ii) much better RNA selective binding, (iii) stronger and more sequence selective triplex-forming characters, and (iv) immensely higher nuclease resistance, even higher than the S(p)-phosphorthioate analogue. 2',4'-BNA(NC)-modified oligonucleotides with these excellent profiles show great promise for applications in antisense and antigene technologies.
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Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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215
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Osaki T, Obika S, Harada Y, Mitsuoka Y, Sugaya K, Sekiguchi M, Roongjang S, Imanishi T. Synthesis of novel 2'-deoxy type trans-3',4'-bridged nucleic acid. Nucleosides Nucleotides Nucleic Acids 2008; 26:1079-82. [PMID: 18058540 DOI: 10.1080/15257770701516235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We newly designed and synthesized a 2'-deoxy type trans-3',4'-bridged nucleic acid (trans-3',4'-BNA) analogues bearing a 4,7-dioxabicyclo[4.3.0]nonane structure. The synthesis of the trans-3',4'-BNA was carried out successfully from thymidine over 21 steps. The structure of trans-3',4'-BNA was confirmed by x-ray crystallographic analysis, indicating that the furanose ring has a typical S-type conformation with C(3')-exo puckering.
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Affiliation(s)
- Tomohisa Osaki
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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216
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Obika S, Tomizu M, Negoro Y, Osaki T, Orita A, Ueyama Y, Nakagawa O, Imanishi T. Acid-mediated cleavage of oligonucleotide P3' --> N5' phosphoramidates triggered by sequence-specific triplex formation. Nucleosides Nucleotides Nucleic Acids 2008; 26:893-6. [PMID: 18058503 DOI: 10.1080/15257770701505741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The P-N bond in oligonucleotide P3' --> N5' phosphoramidates (5'-amino-DNA) is known to be chemoselectively cleaved under mild acidic conditions. We prepared homopyrimidine oligonucleotides containing 5'-amino-5'-deoxythymidine (5'-amino-DNA thymine monomer) or its conformationally locked congener, 5'-amino-2',4'-BNA thymine monomer, at midpoint of the sequence. The effect of triplex formation with homopurineohomopyrimidine dsDNA targets on acid-mediated hydrolysis of the P3' --> N5' phosphoramidate linkage was evaluated. Very interestingly, it was found that the triplex formation significantly accelerates the P-N bond cleavage.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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217
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Obika S, Tomizu M, Negoro Y, Orita A, Nakagawa O, Imanishi T. Double-stranded DNA-templated oligonucleotide digestion triggered by triplex formation. Chembiochem 2008; 8:1924-8. [PMID: 17868159 DOI: 10.1002/cbic.200700430] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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218
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Obika S, Inohara H, Hari Y, Imanishi T. Recognition of T.A interruption by 2',4'-BNAs bearing heteroaromatic nucleobases through parallel motif triplex formation. Bioorg Med Chem 2007; 16:2945-54. [PMID: 18255299 DOI: 10.1016/j.bmc.2007.12.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Revised: 12/19/2007] [Accepted: 12/20/2007] [Indexed: 11/29/2022]
Abstract
2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) monomers bearing novel unnatural nucleobases, 4-(3-benzamidophenyl)-2-pyridone and 2-(N-methylbenzamido)thiazole, were synthesized and successfully incorporated into oligonucleotides. UV melting experiments showed that the corresponding oligonucleotide derivatives formed stable triplexes with dsDNA targets even in the presence of a T.A interruption.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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219
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Abstract
Introduction of the 2',4'-BNA monomer into oligonucleotides significantly enhanced binding affinity toward ssRNA and resistance to nuclease degradation. Here, we evaluated the antisense activity of 2',4'-BNA oligonucleotides against bcl-xL in HepG2 cells. Our data revealed that 2',4'-BNA antisense oligonucleotides remarkably inhibited the expression of bcl-xL in HepG2 cells compared to the natural DNA antisense oligonucleotide. The inhibitory effect of 2',4'-BNA antisense oligonucleotide was dose-dependent and highly sequence-specific.
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Affiliation(s)
- Somjing Roongjang
- Graduate School of Pharmaceutical Science, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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220
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Mitsuoka Y, Ohnishi R, Hari Y, Obika S, Imanishi T. Synthesis of 2',4'-BNACOC bearing a purine nucleobase. ACTA ACUST UNITED AC 2007:13-4. [PMID: 17150793 DOI: 10.1093/nass/nrl007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Recently, we have synthesized pyrimidine derivatives of 2',4'-BNA(COC) monomer, the sugar conformation of which was restricted in N-form by a seven-membered bridged structure. The oligonucleotides containing these monomers showed high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. For an application to antisense methodology, it is important to synthesize 2',4'-BNA(COC) monomers bearing a purine nucleobase. However, the formation of methyleneoxymethylene (COC) linkage in the purine derivatives failed under the acidic conditions used for the synthesis of 2',4'-BNA(COC) with pyrimidine nucleobases. After several examinations, we successfully achieved the synthesis of 2',4'-BNA(COC) monomers bearing a purine nucleobase via the formation of COC linkage using Pummerer-type reaction.
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Affiliation(s)
- Yasunori Mitsuoka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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221
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Rahman SMA, Seki S, Utsuki K, Obika S, Miyashita K, Imanishi T. High-affinity RNA mimicking binding of 2',4'-BNANC towards complementary strands: a comparative study with 2',4'-BNA/LNA. ACTA ACUST UNITED AC 2007:195-6. [PMID: 17150884 DOI: 10.1093/nass/nrl097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
2',4'-BNA(NC), a bridged nucleic acid analogue, which was designed and synthesized in our laboratory, showed very high binding affinity towards complementary RNA and DNA strands. Its duplex-forming ability towards a single-stranded RNA was similar to or slightly higher than that of 2',4'-BNA and the overall triplex-forming ability against a double-stranded DNA was also better than that of 2',4'-BNA. 2',4'-BNA(NC) exhibited higher RNA selectivity than 2',4'-BNA.
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Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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222
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Inohara H, Obika S, Imanishi T. 2',4'-BNA derivatives bearing an unnatural nucleobase: synthesis and application to triplex-forming oligonucleotides. ACTA ACUST UNITED AC 2007:63-4. [PMID: 17150479 DOI: 10.1093/nass/48.1.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recognition of dsDNA by a triplex-forming oligonucleotide (TFO) is limited to homopurine x homopyrimidine sequences. Therefore, it is necessary to develop novel nucleoside analogues which recognize pyrimidine x purine basepairs (C x G or T x A). We have designed and synthesized novel 2',4'-BNA/LNA monomers bearing 3-hydroxybenzene and indole as a nucleobase (3HB(B) and In(B)), and these nucleoside analogues have been introduced into TFOs. On melting temperature (Tm) measurements, 3HB(B) and In(B) were found to interact with T x A base pair interruption with moderate binding affinity.
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Affiliation(s)
- Hiroyasu Inohara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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223
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Miyashita K, Rahman SMA, Seki S, Obika S, Imanishi T. N-Methyl substituted 2',4'- BNANC: a highly nuclease-resistant nucleic acid analogue with high-affinity RNA selective hybridization. Chem Commun (Camb) 2007:3765-7. [PMID: 17851621 DOI: 10.1039/b707352f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides modified with a novel BNA analogue, 2', 4'-BNA(NC)[N-Me], were synthesized, and in comparison to 2',4'-BNA (LNA), have similarly high RNA affinity, better RNA selectivity and much higher resistance to nuclease degradation, suggesting that the novel BNA analogue may be particularly useful for antisense approaches.
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Affiliation(s)
- Kazuyuki Miyashita
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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224
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Abstract
We have recently designed and synthesized a novel bridged nucleic acid analogue 2',4'-BNA(NC), bearing an N-O bridged structure, which furnished both higher duplex and triplex-forming abilities and sequence selectivity towards complementary RNA and/or DNA, respectively, and showed excellent resistance against nuclease degradation. Duplex and triplex-forming abilities were slightly higher or similar to those of 2',4'-BNA and nuclease resistance was as high as that of S-oligo.
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Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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225
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Tsuda N, Matsumoto A, Ito A, Uneda T, Tanabe A, Obika S, Imanishi T. Antigene-block strategy: effective regulation of gene expression by 2',4'-BNA-modified TFOs with an additional stem-loop structure. ACTA ACUST UNITED AC 2007:335-6. [PMID: 17150770 DOI: 10.1093/nass/49.1.335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Antigene strategy is promising technology to regulate gene expression. We have previously reported that 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotides (TFOs) significantly enhanced the binding affinity towards the target dsDNA. In spite of its usefulness, the TFO-binding site may not completely overlay the protein-binding site because of the limitation of TFOs targeting sequences. To overcome this problem, we developed an antigene-based new methodology called "antigene-block" strategy. In this methodology, the TFOs bearing a bulky hairpin tail are used for efficient inhibition of protein-DNA interaction. The antigene-block TFOs having 2',4'-BNA modifications formed stable triplexes with the homopurine-homopyrimidine sequence which partially overlap the transcription factor NF-kappaB binding site. In addition, the antigene-block TFOs significantly reduced the expression level of the target-gene in living cells, while conventional 2',4'-BNA-modified or unmodified TFOs showed no effect on the target-gene expression.
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Affiliation(s)
- Naoto Tsuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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226
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Matsugu S, Inohara H, Obika S, Imanishi T. Synthesis and triplex-forming properties of 2',4'-BNA derivatives bearing pyridines as an unnatural nucleobase. ACTA ACUST UNITED AC 2007:159-60. [PMID: 17150682 DOI: 10.1093/nass/49.1.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Triplex-forming oligonucleotide (TFO) could serve as a potential tool to regulate gene expression. However, stability of the triplex is relatively low, and the sequence of the target dsDNA is severely regulated. In an attempt to overcome these problems, we have designed and synthesized 2',4'-BNA monomers bearing a 6-aminopyridin-3-yl (aPy(B)) and pyridin-2-yl group (Py(B)) as a nucleobase. These monomers were successfully incorporated into natural TFOs, and the triplex-forming property of the modified TFOs was evaluated by UV melting experiments.
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Affiliation(s)
- Sachiko Matsugu
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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227
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Rahman SMA, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T. Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue. Angew Chem Int Ed Engl 2007; 46:4306-9. [PMID: 17469090 DOI: 10.1002/anie.200604857] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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228
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Rahman S, Seki S, Obika S, Haitani S, Miyashita K, Imanishi T. Highly Stable Pyrimidine-Motif Triplex Formation at Physiological pH Values by a Bridged Nucleic Acid Analogue. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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229
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Nishida M, Kodama T, Obika S, Imanishi T. Synthesis and chemical properties of a novel 2',4'-bridged nucleic acid analogue with a seven-membered cyclic carbamate structure. Nucleic Acids Symp Ser (Oxf) 2007; 51:157-158. [PMID: 18029634 DOI: 10.1093/nass/nrm079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
BNA We designed and synthesized a novel bridged nucleic acid (BNA) with N-type sugar conformation, possessing a seven-membered cyclic carbamate structure (2',4'-(CNC) monomer). The monomer shows interesting chemical properties, such as prompt migration of the carbamate bridge from the 2'-to the 3'-position and consequent conformational change of the furanose moiety. These chemical behaviors of 2',4'-BNA(CNC) were investigated by (1)H-NMR analysis, and the structure of the compound after migration was confirmed by X-ray crystallographic analysis.
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Affiliation(s)
- Masaru Nishida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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230
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Sekiguchi M, Obika S, Harada Y, Osaki T, Somjing R, Mitsuoka Y, Shibata N, Masaki M, Imanishi T. Synthesis and properties of trans-3',4'-bridged nucleic acids having typical S-type sugar conformation. J Org Chem 2006; 71:1306-16. [PMID: 16468776 DOI: 10.1021/jo051187l] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of nucleoside analogues with a conformationally restricted sugar moiety is of great interest. The present research describes the synthesis of BNA (bridged nucleic acid) monomers 1 and 2 bearing a 4,7-dioxabicyclo[4.3.0]nonane skeleton and a methoxy group at the C2' position. Conformational analysis showed that the sugar moiety of these monomers is restricted in a typical S-type conformation. It was difficult to synthesize the phosphoramidite derivative of the ribo-type monomer 1, while the phosphoramidite of the arabino-type monomer 2 was successfully prepared and incorporated into oligodeoxynucleotides (ODNs). The hybridization ability of the obtained ODN derivatives containing 2 with complementary strands was evaluated by melting temperature (T(m)) measurements. As a result, the ODN derivatives hybridized with DNA and RNA complements in a sequence-selective manner, though the stability of the duplexes was lower than that of the corresponding natural DNA/DNA or DNA/RNA duplex.
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Affiliation(s)
- Mitsuaki Sekiguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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231
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Fujii S, Obika S, Imanishi T. Effects of the 2',4'-BNA modification on the sequence specificity of molecular beacons. Nucleic Acids Symp Ser (Oxf) 2006:211-2. [PMID: 17150708 DOI: 10.1093/nass/49.1.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Molecular beacons (MBs) are stem-loop hairpin oligonucleotide probes with an internally quenched fluorophore. These probes recognize their targets with higher specificity than conventional linear probes. To further enhance sequence-specificity of MBs, we have designed and synthesized MBs having 2',4'-BNA modification. Thermodynamic analysis revealed that the MBs with the 2',4'-BNA-modified stem region have high sequence-specificity. In addition, the 2',4'-BNA modification in the loop region was also found to be efficient for discrimination of one base mismatch.
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Affiliation(s)
- Shiho Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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232
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Obika S, Sekiguchi M, Somjing R, Imanishi T. Adjustment of the gamma dihedral angle of an oligonucleotide P3'-->N5' phosphoramidate enhances its binding affinity towards complementary strands. Angew Chem Int Ed Engl 2006; 44:1944-7. [PMID: 15678433 DOI: 10.1002/anie.200461942] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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233
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Obika S, Hiroto A, Nakagawa O, Imanishi T. Presence of 2',5'-linkages in a homopyrimidine DNA oligonucleotide promotes stable triplex formation under physiological conditions. Nucleosides Nucleotides Nucleic Acids 2005; 24:1055-8. [PMID: 16248091 DOI: 10.1081/ncn-200060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We prepared 15-mer homopyrimidine oligonucleotides containing three or four 2',5'-linked DNA units, and their ability as a triplex-forming oligonucleotide (TFO) was analyzed in detail UV melting experiments showed that replacement of a 3',5'-linkage by a 2',5'-linkage at every third or fourth residue in TFO significantly promoted stable triplex formation under physiological conditions.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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234
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Torigoe H, Katayama T, Obika S, Maruyama A, Imanishi T. Combination of poly(L-lysine)-graft-dextran copolymer and 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification synergistically stabilizes pyrimidine motif triplex at neutral pH. Nucleosides Nucleotides Nucleic Acids 2005; 24:635-8. [PMID: 16248002 DOI: 10.1081/ncn-200060113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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235
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Sekiguchi M, Obika S, Somjing R, Imanishi T. Synthesis and properties of a novel bridged nucleic acid analogue, 5'-amino-3',5'-BNA. Nucleosides Nucleotides Nucleic Acids 2005; 24:1097-100. [PMID: 16248099 DOI: 10.1081/ncn-200061836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An oligonucleotide P3'-->N5' phosphoramidate (5'-amino-DNA) attracts much attention because of its potential for application to DNA sequencing; however, its ability to hybridize with complementary strands is low. To overcome this drawback of the 5-amino-DNA, we have designed and successfully synthesized a novel nucleic acid analogue having a P3'-->N5' phosphoramidate linkage and a constrained sugar moiety, 5'-amino-3'-C,5'-N-methylene bridged nucleic acid (5'-amino-3',5'-BNA). The binding affinity of the 5'-amino-3',5'-BNA towards complementary DNA and RNA strands was investigated by UV melting experiments. The melting temperature (Tm) of the duplex comprising the 5'-amino-3',5'-BNA and its complementary strand was much higher than that of the duplex containing the corresponding 5-amino-DNA.
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Affiliation(s)
- Mitsuaki Sekiguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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236
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Hari Y, Obika S, Ohnishi R, Eguchi K, Osaki T, Ohishi H, Imanishi T. Synthesis and properties of 2'-O,4'-C-methyleneoxymethylene bridged nucleic acid. Bioorg Med Chem 2005; 14:1029-38. [PMID: 16213732 DOI: 10.1016/j.bmc.2005.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2005] [Revised: 09/05/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
A novel bridged nucleic acid (BNA) analogue, 2'-O,4'-C-methyleneoxymethylene bridged nucleic acid (2',4'-BNA(COC)), was synthesized and incorporated into oligonucleotides. The 2',4'-BNA(COC) modified oligonucleotides showed high binding affinity with an RNA complement and significant enzymatic stability against snake venom phosphodiesterase.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
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237
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Abstract
In the last decade, increased efforts have been directed toward the development of oligonucleotide-based technologies for genome analyses, diagnostics, or therapeutics. Among them, an antigene strategy is one promising technology to regulate gene expression in living cells. Stable triplex formation between the triplex-forming oligonucleotide (TFO) and the target double-stranded DNA (dsDNA) is fundamental to the antigene strategy. However, there are two major drawbacks in triplex formation by a natural TFO: low stability of the triplex and limitations of the target DNA sequence. To overcome these problems, we have developed various bridged nucleic acids (BNAs), and found that the 2',4'-BNA modification of oligonucleotides strongly promotes parallel motif triplex formation under physiological conditions. Some nucleobase analogues to extend the target DNA sequence were designed, synthesized, and introduced into the 2',4'-BNA structure. The obtained 2',4'-BNA derivatives with unnatural nucleobases effectively recognized a pyrimidine-purine interruption in the target dsDNA. Some other examples of nucleic acid analogues for stable triplex formation and extension of the target DNA sequence are also summarized.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan.
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238
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Obika S, Hiroto A, Nakagawa O, Imanishi T. Promotion of stable triplex formation by partial incorporation of 2',5'-phosphodiester linkages into triplex-forming oligonucleotides. Chem Commun (Camb) 2005:2793-5. [PMID: 15928760 DOI: 10.1039/b417688j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Pentadecamer homopyrimidine oligonucleotides containing three or more 2',5'-phosphodiester linkages in different modes were prepared and used to evaluate the ability as a triplex-forming oligonucleotide (TFO), and it was found that discontinuous replacement of the 3',5'-phosphodiester linkages in TFO by 2',5'-linkages significantly stabilizes parallel-motif triplexes.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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239
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Obika S, Sekiguchi M, Somjing R, Imanishi T. Adjustment of the? Dihedral Angle of an Oligonucleotide P3??N5? Phosphoramidate Enhances Its Binding Affinity towards Complementary Strands. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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240
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Abstract
The completion of the human genome sequencing project will greatly accelerate the development of novel and practical technologies for genome-analysis, diagnostics or therapeutics. Oligonucleotides are playing an important role in these genome technologies, because of their sequence-specific hybridization ability toward the complementary strand. Besides the sequence-specific duplex formation, oligonucleotides are able to form stable triplex structures, which is fundamental to the antigene strategy to regulate gene expression in a living cell. However, two major drawbacks are known in the triplex formation by a natural oligonucleotide: low stability of the triplex and limitations of the target DNA sequence. One promising strategy to overcome these problems is chemical modification of the oligonucleotides. We have developed various bridged nucleic acids (BNAs), and found that the oligonucleotides containing 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification form a stable parallel motif triplex with the double-stranded DNA target under physiological conditions. Some nucleobase analogues to extend the target DNA sequence were designed, synthesized and incorporated into the 2',4'-BNA structure. The obtained 2',4'-BNA derivatives containing modified nucleobases effectively recognized a pyrimidine-purine interruption. Some other examples of nucleic acid analogues to overcome the two major drawbacks in the triplex-forming oligonucleotides are also summarized.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871, Japan.
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241
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Hari Y, Obika S, Inohara H, Ikejiri M, Une D, Imanishi T. Synthesis and Triplex-Forming Ability of 2',4'-BNAs Bearing Imidazoles as a Nucleobase. Chem Pharm Bull (Tokyo) 2005; 53:843-6. [PMID: 15997150 DOI: 10.1248/cpb.53.843] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To expand the sequence of double-stranded DNA (dsDNA) targets in a triplex formation, 2',4'-BNAs (2'-O,4'-C-methylene bridged nucleic acids) having imidazoles as a nucleobase were synthesized and incorporated into oligonucleotides. Triplex-forming ability of the modified oligonucleotides was evaluated by using melting temperature (Tm) measurements.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
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242
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Tomizu M, Nakagawa O, Obika S, Imanishi T. Promotion of acid-mediated cleavage of oligonucleotide P3'->N5' phosphoroamidates by triplex formation: a novel approach to sequence-specific DNA detection. Nucleic Acids Symp Ser (Oxf) 2005:157-8. [PMID: 17150681 DOI: 10.1093/nass/49.1.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The 5'-amino-2',4'-BNA, bearing a locked N-type sugar conformation and a P3'-->N5' phosphoramidate linkage, was found to be rapidly cleaved by acid-mediated hydrolysis when they formed a triplex with the target dsDNA. The fluorophore and quencher moieties were introduced into the 5'-amino-2',4'-BNA-modified oligonucleotide which was used as a novel and innovative DNA detection probe.
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Affiliation(s)
- Masaharu Tomizu
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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243
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Obika S, Osaki T, Sekiguchi M, Somjing R, Harada Y, Imanishi T. Synthesis and conformation of a novel bridged nucleic acid having a trans -fused 3,5,8-trioxabicyclo[5.3.0]decane structure. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.04.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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244
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Katayama T, Maruyama A, Obika S, Imanishi T, Torigoe H. Synergistic stabilization of triplex by combination of comb-type cationic copolymer and 2',4'-BNA. Nucleic Acids Symp Ser (Oxf) 2004:139-40. [PMID: 17150517 DOI: 10.1093/nass/48.1.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We examined the effect of the combination of the two triplex-stabilizing factors, poly(L-lysine)-graft-dextran (PLL-g-Dex) copolymer and 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) backbone modification of triplex-forming oligonucleotide (TFO), on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The combination of both stabilizing factors that was the triplex involving the 2',4'-BNA TFO in the presence of the copolymer synergistically increased the thermal stability of the pyrimidine motif triplex at neutral pH. The present results certainly support the idea that the combination of the stabilizing factors can be a key method for triplex stabilization and may lead to progress in therapeutic applications of the antigene strategy in vivo.
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Affiliation(s)
- Takuma Katayama
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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245
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Sekiguchi M, Obika S, Somjing R, Imanishi T. Synthesis and properties of a novel bridged nucleic acid analogue bearing a P3'-->N5' phosphoroamidate linkage, 5'-amino-3', 5'-BNA. Nucleic Acids Symp Ser (Oxf) 2004:7-8. [PMID: 17150451 DOI: 10.1093/nass/48.1.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We have designed and successfully synthesized a novel bridged nucleic acid analogue with a P3'-->N5' phosphoramidate linkage, 5'-amino-3',5'-BNA. X-ray crystallographic analysis demonstrated that the 5'-amino-3',5'-BNA had C1-exo-O4-endo sugar puckering and a constrained gamma dihedral angle of 22.8 degrees. The oligonucleotides containing 5'-amino-3',5'-BNA exhibited strong binding affinity towards complementary strands. In addition, the 5'-amino-3',5'-BNA oligonucleotide was easily hydrolyzed at its phosphoramidate linkage under mild acidic conditions.
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Affiliation(s)
- Mitsuaki Sekiguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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246
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Abstract
Molecular dynamics studies have been performed for 3.5 ns on the ETS domain of Ets-1 transcription factor bound to the 14-bp DNA, d(AGTGCCGGAAATGT), comprising the core sequence of high-affinity (GGAA), ETS-GGAA. In like manner, molecular dynamics simulations have been carried out for 3.9 ns on the mutant low-affinity core sequence, GGAG (ETS-GGAG). Analyses of the DNA backbone of ETS-GGAG show conformational interconversions from BI to BII substates. Also, crank shaft motions are noticed at the mutated nucleotide base pair step after 1500 ps of dynamics. The corresponding nucleotide of ETS-GGAA is characteristic of a BI conformation and no crank shaft motions are observed. The single mutation of ETS-GGAA to ETS-GGAG also results in variations of helical parameters and solvent-accessible surface area around the major and minor grooves of the DNA. The presence of water contacts during the entire simulation proximal to the fourth base pair step of core DNA sequence is a characteristic feature of ETS-GGAA. Such waters are more mobile in ETS-GGAG at 100 ps and distant after 1500 ps. Anticorrelated motions between certain amino acids of Ets-1 protein are predominant in ETS-GGAA but less so or absent in the mutant. These motions are reflected in the flexibility of amino acid residues of the protein backbone. We consider that these conformational features and water contacts are involved in stabilizing the hydrogen bond interactions between helix-3 residues of Ets-1 and DNA during the transcription process.
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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Torigoe H, Hari Y, Obika S, Imanishi T. Triplex formation involving 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) with 2-pyridone base analogue: efficient and selective recognition of C:G interruption. Nucleosides Nucleotides Nucleic Acids 2003; 22:1097-9. [PMID: 14565353 DOI: 10.1081/ncn-120022745] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
For the effective recognition of C:G interruption in homopurine-homopyrimidine duplex DNA, we examined triplex-forming ability and sequence-selectivity of a triplex-forming oligonucleotide (TFO) involving of 2'-O,4'-C-methylene bridged nucleic acid with 2-pyridone base analogue. We found that the modified TFO formed stable triplex with high binding affinity and sequence-selectivity.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan.
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Torigoe H, Hari Y, Obika S, Imanishi T. Triplex formation involving 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) with 1-isoquinolone base analogue: efficient and selective recognition of C:G interruption. Nucleosides Nucleotides Nucleic Acids 2003; 22:1571-3. [PMID: 14565468 DOI: 10.1081/ncn-120023036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
For the effective recognition of C x G interruption in homopurine-homopyrimidine duplex DNA, we examined triplex-forming ability and sequence-selectivity of a triplex-forming oligonucleotide (TFO) involving of 2'-O, 4'-C-methylene bridged nucleic acid with 1-isoquinolone base analogue. We found that the modified TFO formed stable triplex with high binding affinity and sequence-selectivity.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan.
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249
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Sekiguchi M, Osaki T, Harada Y, Obika S, Imanishi T. trans-3',4'-BNAs, novel nucleic acid analogues with an S-type conformation: synthesis and incorporation into oligonucleotides. ACTA ACUST UNITED AC 2003:111-2. [PMID: 14510405 DOI: 10.1093/nass/3.1.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We designed and successfully synthesized novel nucleic acid analogues with a C3'-C4' trans-fused six-membered ring, trans-3',4'-BNAs from D-glucose. A 1H-NMR experiment and X-ray crystallographic analysis demonstrated that the sugar puckering of trans-3',4'-BNA was restricted in an S-type conformation. We also achieved its incorporation into oligonucleotides using automated DNA synthesizer.
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Affiliation(s)
- Mitsuaki Sekiguchi
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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250
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Obika S, Nakagawa O, Hiroto A, Hari Y, Imanishi T. Synthesis and properties of a novel bridged nucleic acid with a P3' --> N5' phosphoramidate linkage, 5'-amino-2',4'-BNA. Chem Commun (Camb) 2003:2202-3. [PMID: 13678201 DOI: 10.1039/b307290h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5'-Amino-2',4'-BNA, a novel analogue of BNA series compounds, was successfully synthesized, and its incorporated oligonucleotides showed potent duplex- and triplex-forming ability and resistance against snake venom phosphodiesterase.
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Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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