Co-reporter:Aya Ogata, Yusuke Maeda, Yoshihito Ueno
Bioorganic & Medicinal Chemistry 2017 Volume 25, Issue 7(Issue 7) pp:
Publication Date(Web):1 April 2017
DOI:10.1016/j.bmc.2017.01.051
The synthesis of oligonucleotide (ON) analogs, which can be used as antisense molecules, has recently gained much attention. Here, we report the synthesis and properties of an ON analog containing acyclic thymidine and cytidine analogs with a 4-pentyl-1,2-diol instead of the d-ribofuranose moiety. The incorporation of these analogs into the ON improved its nuclease resistance to 3′-exonucleases. Furthermore, it was found that the incorporation of the acyclic thymidine analog into a DNA/RNA duplex accelerates the RNA cleavage of a DNA/RNA duplex by Escherichia coli RNase H.Download high-res image (79KB)Download full-size image
Co-reporter:Chika Yokoyama, Kosuke Nakamoto, Yoshihito Ueno
Bioorganic & Medicinal Chemistry 2017 Volume 25, Issue 13(Issue 13) pp:
Publication Date(Web):1 July 2017
DOI:10.1016/j.bmc.2017.05.013
Photoinduced electron transfer (PeT)-based hybridization probe is a linear and quencher-free oligonucleotide (ON) probe for DNA or RNA detection. In this report, we designed and synthesized novel adenosine analogues for PeT-based hybridization probe. In particular, the analogue containing a piperazinomethyl moiety showed effective quenching property under physiological conditions. When the probe containing the analogue was hybridized with a complementary DNA or RNA, the fluorescence increased 3- or 4-fold, respectively, compared to the single-stranded state.Download high-res image (110KB)Download full-size image
Co-reporter:Nazuki Niwa;Saki Shimizu;Yusuke Maeda;Hidekazu Hiroak
RSC Advances (2011-Present) 2017 vol. 7(Issue 41) pp:25378-25386
Publication Date(Web):2017/05/10
DOI:10.1039/C7RA03896H
This paper describes the synthesis and properties of benzene-glycol nucleic acid (BGNA)–DNA chimeras containing four nucleoside analogs – thymidine, cytidine, adenosine, and guanosine – with a base-benzene-glycol structure. We found that the BGNA–DNA chimeras are able to form thermally and thermodynamically stable duplexes with complementary RNAs, and have base-discriminating abilities. The BGNA–DNA chimeras were 20-fold more stable in a buffer containing 30% bovine serum than unmodified DNA. Furthermore, BGNA–DNA chimera/RNA duplexes were found to be good substrates for human RNase H. Thus, BGNA–DNA chimeras are good candidates for the development of therapeutic antisense molecules.
Co-reporter:Kosuke Nakamoto, Koichiro Minami, Yukihiro Akao and Yoshihito Ueno
Chemical Communications 2016 vol. 52(Issue 40) pp:6720-6722
Publication Date(Web):19 Apr 2016
DOI:10.1039/C6CC01360K
To identify target mRNAs of an miRNA, we synthesized photo-reactive miRNA probes, which contained a photo-reactive nucleoside analog, 1-O-[4-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-D-ribofuranose, in the middle of the strand. The photo-reactive miRNA-145 probe was found to specifically label the target mRNAs, FSCN1 and KLF4, by UV-A irradiation in human colon cancer DLD-1 cells.
Co-reporter:Nazuki Niwa;Keisuke Ueda
European Journal of Organic Chemistry 2016 Volume 2016( Issue 14) pp:2435-2443
Publication Date(Web):
DOI:10.1002/ejoc.201600189
Abstract
In this study, we report the synthesis of benzene-glycol nucleic acids and studies of their biophysical and biological properties. Using (S)-mandelic acid as the starting material, we prepared phosphoramidite units for the synthesis of benzene-glycol nucleic acids. The benzene-glycol moieties effectively replace the sugar groups ordinarily found in DNA and RNA monomers. Oligonucleotides (ONs) containing these nucleoside analogues formed thermally and thermodynamically stable duplexes with complementary DNA and RNA strands and proved to be more resistant (i.e. less susceptible) to 3′-exonuclease than their “natural” counterparts. Furthermore, we demonstrated that a duplex composed of a modified ON and its complementary strand of RNA very effectively elicits RNase H activity.
Co-reporter:Aya Hayai, Yusuke Maeda, Yoshihito Ueno
Bioorganic & Medicinal Chemistry Letters 2016 Volume 26(Issue 15) pp:3552-3555
Publication Date(Web):1 August 2016
DOI:10.1016/j.bmcl.2016.06.024
Here, we report the synthesis of a fluorescence resonance energy transfer (FRET)-based probe for single nucleotide polymorphism (SNP) typing. The probe contains a fluorescent tricyclic base, 8-amino-3-(2,3-dihydroxypropyl)imidazo[4′,5′:5,6]pyrido[2,3-d]pyrimidine, as a donor molecule and 7-diethylaminocoumarin-3-carboxylic acid as an acceptor molecule. FRET was observed between the donor and acceptor molecules on the probe. The identity of the target bases on DNA and RNA strands could be determined using the probe.
Co-reporter:Natsumi Inada, Kosuke Nakamoto, Takashi Yokogawa, Yoshihito Ueno
European Journal of Medicinal Chemistry 2015 Volume 103() pp:460-472
Publication Date(Web):20 October 2015
DOI:10.1016/j.ejmech.2015.09.011
•Synthesis of the siRNAs containing acetal-type nucleoside analogs is described.•The siRNA containing the trifluoroethyl group is more potent than a natural siRNA.•The trifluoroethyl-modified RNA is more nuclease-resistant than a natural RNA.In this study, we aimed to create small interfering RNAs (siRNAs) with increased silencing activities and nuclease resistance properties. Therefore, we designed and synthesized five types of siRNA containing acetal-type nucleoside analogs at their 3′-dangling ends. We found that the siRNA containing 1-O-(2,2,2-trifluoroethyl)-β-D-ribofuranose at the 3′-dangling end was the most potent among the synthesized siRNAs and showed more resistance to nucleolytic degradation by a 3′ exonuclease than a natural RNA did. Thus, modification of siRNAs by addition of 1-O-(2,2,2-trifluoroethyl)-β-D-ribofuranose may hold promise as a means of improving the silencing activity and nuclease resistance of siRNAs.
Co-reporter:Aya Ogata, Yoshihito Ueno
Bioorganic & Medicinal Chemistry Letters 2015 25(12) pp: 2574-2578
Publication Date(Web):
DOI:10.1016/j.bmcl.2015.04.034
Co-reporter:Kan Takahashi, Shun Ito, Kosuke Nakamoto, Yasutomo Ito, and Yoshihito Ueno
The Journal of Organic Chemistry 2015 Volume 80(Issue 17) pp:8561-8570
Publication Date(Web):August 10, 2015
DOI:10.1021/acs.joc.5b01132
Here, we report the synthesis of a hybridization probe for detection of RNA and DNA based on photoinduced electron transfer (PeT). We designed and synthesized an oligonucleotide containing an adenosine analogue with a 9-(N,N-dimethylaminomethyl)anthracenyl moiety at its 6-position via an ethynylene linker as the hybridization probe. When the probe was hybridized with a complementary RNA or DNA, the fluorescence intensity increased 3-fold or 4.5-fold, respectively, compared to the single-stranded state.
Co-reporter:Kosuke Nakamoto and Yoshihito Ueno
The Journal of Organic Chemistry 2014 Volume 79(Issue 6) pp:2463-2472
Publication Date(Web):February 26, 2014
DOI:10.1021/jo402738t
Here, we report the applicability of diazirine-containing RNA photo-cross-linking probes for the identification of microRNA (miRNA) targets. The RNA cross-linking probes were synthesized by substituting the RNA nucleobases with nucleoside analogues such as 1-O-[3-(3-trifluoromethyl-3H-diazirin-3-yl)]benzyl-β-d-ribofuranose or 1-O-[4-(3-trifluoromethyl-3H-diazirin-3-yl)]benzyl-β-d-ribofuranose that carry aryl trifluoromethyl diazirine moieties. The probes were successfully cross-linked with synthetic RNAs containing the four natural nucleosides on the opposite site of the nucleoside analogues. Furthermore, it was found that miRNAs containing these analogues were effective in regulating the expression of their target genes. Thus, RNAs containing the nucleoside analogues are promising candidates as photo-cross-linking probes to identify the target mRNAs of miRNAs.
Co-reporter:Kinji Furukawa, Mayumi Hattori, Tokimitsu Ohki, Yoshiaki Kitamura, Yukio Kitade, Yoshihito Ueno
Bioorganic & Medicinal Chemistry 2012 Volume 20(Issue 1) pp:16-24
Publication Date(Web):1 January 2012
DOI:10.1016/j.bmc.2011.11.045
The development of a reliable and simple method for detecting single nucleotide polymorphisms (SNPs), common genetic variations in the human genome, is currently an important research area because SNPs are important for identifying disease-causing genes and for pharmacogenetic studies. Here, we developed a novel method for SNP detection. We designed and synthesized DNA probes containing a fluorescent tricyclic base-linked acyclonucleoside P. The type of nucleobases involved in the SNP sites in the DNA and RNA targets could be determined using four DNA probes containing P. Thus, this system would provide a novel and simple method for detecting SNPs in DNA and RNA targets.
Co-reporter:Mayumi Hattori, Tokimitsu Ohki, Emiko Yanase, Yoshihito Ueno
Bioorganic & Medicinal Chemistry Letters 2012 Volume 22(Issue 1) pp:253-257
Publication Date(Web):1 January 2012
DOI:10.1016/j.bmcl.2011.11.022
A reliable and simple method for detecting nucleobase mutations is very important clinically because sequence variations in human DNA cause genetic diseases and genetically influenced traits. A majority of sequence variations are attributed to single nucleotide polymorphisms (SNPs). Here, we developed a method for SNP detection using DNA probes that contained a fluorescent tricyclic base-linked acyclonucleoside N. The type of nucleobases involved in the SNP sites in an RNA target could be determined using four DNA probes containing N. Further, we found that the SNP in the RNA target could be detected by a visible color. Thus, this system would provide a novel and simple method for detecting SNPs in an RNA target.
Co-reporter:Aya Shibata, Yoshihito Ueno, Mari Iwata, Haruka Wakita, Akira Matsuda, Yukio Kitade
Bioorganic & Medicinal Chemistry Letters 2012 Volume 22(Issue 8) pp:2681-2683
Publication Date(Web):15 April 2012
DOI:10.1016/j.bmcl.2012.03.024
This Letter describes the synthesis and properties of double-stranded antisense oligonucleotides connected with a pentaerythritol linker. We found that double-stranded antisense oligonucleotides with aminomethyl residues have high affinity for single-stranded DNA or RNA in buffer solutions with and without MgCl2. Thus, these oligonucleotides would be useful as antisense oligonucleotides for targeting single-stranded RNA through triplex formation.
Co-reporter:Kayo Yoshikawa, Aya Ogata, Chiho Matsuda, Michinori Kohara, Hideo Iba, Yukio Kitade, and Yoshihito Ueno
Bioconjugate Chemistry 2011 22(1) pp: 42-49
Publication Date(Web):December 9, 2010
DOI:10.1021/bc100301w
Small interfering RNA (siRNA) is a noncoding RNA with considerable potential as a new therapeutic drug for intractable diseases. siRNAs can be rationally designed and synthesized if the sequences of the disease-causing genes are known. In this paper, we describe the synthesis and properties of siRNAs modified with biaryl units. We found that incorporation of biaryl units into the 5′ and 3′ ends of sense and antisense strands of siRNA duplexes improved strand selectivity and nuclease resistance.
Co-reporter:Satoru Kuboe, Mayuko Yoda, Aya Ogata, Yukio Kitade, Yukihide Tomari and Yoshihito Ueno
Chemical Communications 2010 vol. 46(Issue 39) pp:7367-7369
Publication Date(Web):06 Sep 2010
DOI:10.1039/C0CC02450C
We here report the synthesis and characterization of small interfering RNAs with aryl trifluoromethyl diazirine moieties in the 3′-overhang regions, which allow sensitive detection of interacting proteins during assembly of the effector ribonucleoprotein complex by irradiation with minimally destructive long-wavelength ultraviolet light.
Co-reporter:Aya Ogata, Chihiro Furukawa, Kouhei Sakurai, Hideo Iba, Yukio Kitade, Yoshihito Ueno
Bioorganic & Medicinal Chemistry Letters 2010 20(24) pp: 7299-7302
Publication Date(Web):
DOI:10.1016/j.bmcl.2010.10.077
Co-reporter:Yoshihito Ueno, Akihiro Kawamura, Keiji Takasu, Shinji Komatsuzaki, Takumi Kato, Satoru Kuboe, Yoshiaki Kitamura and Yukio Kitade
Organic & Biomolecular Chemistry 2009 vol. 7(Issue 13) pp:2761-2769
Publication Date(Web):12 May 2009
DOI:10.1039/B901631G
This paper describes the synthesis and properties of a novel molecular beacon (MB) containing a benzene-phosphate backbone at its stem moiety. The fluorescence intensity of MBs was found to stabilize by the introduction of the benzene-phosphate backbone at its stem moiety. Furthermore, an MB containing the benzene-phosphate backbone was more resistant to DNase I (endonuclease) than an MB comprising natural DNA and 2′-O-methyl-RNA. These results indicate that the MB with the benzene-phosphate backbone is superior as a molecular beacon as compared to the MB composed of natural DNA and 2′-O-methyl-RNA.
Co-reporter:Yoshihito Ueno;Shinji Komatsuzaki;Keiji Takasu;Satoru Kawai;Yoshiaki Kitamura;Yukio Kitade
European Journal of Organic Chemistry 2009 Volume 2009( Issue 28) pp:4763-4769
Publication Date(Web):
DOI:10.1002/ejoc.200900567
Abstract
We describe the synthesis and properties of oligonucleotides (ONs) containing biaryl units, which are composed of a bis(hydroxymethyl)benzene residue and a naphthalene or pyrene moiety. We found that by introducing the biaryl units into the ONs, the aromatic chromophores were suitably arrayed in the DNAs. Further, we succeeded in the detection of a single-base mismatch in RNA by using the ON containing the biaryl unit as a molecular beacon. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Co-reporter:Yoshihito Ueno;Shinji Komatsuzaki;Keiji Takasu;Satoru Kawai;Yoshiaki Kitamura;Yukio Kitade
European Journal of Organic Chemistry 2009 Volume 2009( Issue 28) pp:
Publication Date(Web):
DOI:10.1002/ejoc.200990078
Abstract
The cover picture shows a DNA duplex containing a biaryl unit, which is made up of benzene and pyrene moieties; an excimer is formed between the biaryl units, which results in the formation of a duplex. In the article by Y. Ueno et al. on p. 4763 ff the synthesis of the monomer units and oligonucleotides containing the biaryl units and the thermal stabilities of the duplexes, as well as their absorption and fluorescence properties, are discussed. The authors would like to thank Yoichiro Kato for his help in designing the cover picture.
Co-reporter:Yoshihito Ueno, Kayo Yoshikawa, Yoshiaki Kitamura, Yukio Kitade
Bioorganic & Medicinal Chemistry Letters 2009 Volume 19(Issue 3) pp:875-877
Publication Date(Web):1 February 2009
DOI:10.1016/j.bmcl.2008.11.107
Unintended (off-target) transcript silencing is a critical problem associated with RNA interference (RNAi)-based therapeutic applications. This paper shows that the incorporation of appropriate alkyl linkers at the center of the sense strands can suppress the off-target effects induced by the sense strands without reducing the RNAi-inducing activity of the antisense strands.
Co-reporter:Yoshihito Ueno, Yuuji Watanabe, Aya Shibata, Kayo Yoshikawa, Takashi Takano, Michinori Kohara, Yukio Kitade
Bioorganic & Medicinal Chemistry 2009 17(5) pp: 1974-1981
Publication Date(Web):
DOI:10.1016/j.bmc.2009.01.033
Co-reporter:Yoshihito Ueno, Koshi Kawada, Tomoharu Naito, Aya Shibata, Kayo Yoshikawa, Hye-Sook Kim, Yusuke Wataya, Yukio Kitade
Bioorganic & Medicinal Chemistry 2008 Volume 16(Issue 16) pp:7698-7704
Publication Date(Web):15 August 2008
DOI:10.1016/j.bmc.2008.07.010
Short-interfering RNAs (siRNAs) conjugated with lipophilic groups at their 3′-termini were synthesized. The properties of the synthesized siRNAs were examined in detail, and it was found that at low concentrations, their silencing abilities were dependent on the positions of the modifications and the types of organic molecules attached. Although the modification of siRNAs with palmitic acid or oleic acid at the 3′-end slightly reduced their silencing activities, siRNAs had enough abilities to induce RNAi at 10 nM concentrations. On the other hand, the modification of siRNAs with cholesterol at the 3′-end of the passenger strand was tolerated; however, the modification at the guide strand significantly reduces its silencing activity. The siRNAs modified with the lipophilic groups did not possess ability to penetrate the plasma membranes of HT-1080 cells without the transfection reagent. However, the results described in this report will aid in designing novel siRNAs with cell membrane-permeable molecules.Figure optionsDownload full-size imageDownload as PowerPoint slide
Co-reporter:Yoshihito Ueno, Takumi Inoue, Mahito Yoshida, Kayo Yoshikawa, Aya Shibata, Yoshiaki Kitamura, Yukio Kitade
Bioorganic & Medicinal Chemistry Letters 2008 Volume 18(Issue 19) pp:5194-5196
Publication Date(Web):1 October 2008
DOI:10.1016/j.bmcl.2008.08.086
We describe the synthesis and silencing activities of siRNA possessing N1-[3,5-bis(hydroxymethyl)phenyl]thymine (bt) in their 3′-overhang regions. We found that an siRNA possessing bt in the 3′-overhang region was more effective than an siRNA with natural nucleosides and the siRNA possessing 1,3-bis(hydroxymethyl)benzene (b) without a nucleobase at the 3′-overhang region in in vitro experiment using HeLa cells system. Furthermore, the RNA possessing bt at its 3′-end was more resistant to nucleolytic hydrolysis by snake venom phosphodiesterase (a 3′-exonuclease) than the RNA possessing the natural nucleoside 2′-deoxythymidine at the 3′-end. Thus, the compound bt will be a novel 3′-overhang moiety that can enhance the silencing activity and nuclease-resistant property of siRNAs.
Co-reporter:Satoru Kuboe, Mayuko Yoda, Aya Ogata, Yukio Kitade, Yukihide Tomari and Yoshihito Ueno
Chemical Communications 2010 - vol. 46(Issue 39) pp:NaN7369-7369
Publication Date(Web):2010/09/06
DOI:10.1039/C0CC02450C
We here report the synthesis and characterization of small interfering RNAs with aryl trifluoromethyl diazirine moieties in the 3′-overhang regions, which allow sensitive detection of interacting proteins during assembly of the effector ribonucleoprotein complex by irradiation with minimally destructive long-wavelength ultraviolet light.
Co-reporter:Kosuke Nakamoto, Koichiro Minami, Yukihiro Akao and Yoshihito Ueno
Chemical Communications 2016 - vol. 52(Issue 40) pp:NaN6722-6722
Publication Date(Web):2016/04/19
DOI:10.1039/C6CC01360K
To identify target mRNAs of an miRNA, we synthesized photo-reactive miRNA probes, which contained a photo-reactive nucleoside analog, 1-O-[4-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-β-D-ribofuranose, in the middle of the strand. The photo-reactive miRNA-145 probe was found to specifically label the target mRNAs, FSCN1 and KLF4, by UV-A irradiation in human colon cancer DLD-1 cells.
Co-reporter:Yoshihito Ueno, Akihiro Kawamura, Keiji Takasu, Shinji Komatsuzaki, Takumi Kato, Satoru Kuboe, Yoshiaki Kitamura and Yukio Kitade
Organic & Biomolecular Chemistry 2009 - vol. 7(Issue 13) pp:NaN2769-2769
Publication Date(Web):2009/05/12
DOI:10.1039/B901631G
This paper describes the synthesis and properties of a novel molecular beacon (MB) containing a benzene-phosphate backbone at its stem moiety. The fluorescence intensity of MBs was found to stabilize by the introduction of the benzene-phosphate backbone at its stem moiety. Furthermore, an MB containing the benzene-phosphate backbone was more resistant to DNase I (endonuclease) than an MB comprising natural DNA and 2′-O-methyl-RNA. These results indicate that the MB with the benzene-phosphate backbone is superior as a molecular beacon as compared to the MB composed of natural DNA and 2′-O-methyl-RNA.