Shigeki Sasaki

Name:

Organization: Kyushu University

Department: Graduate School of Pharmaceutical Sciences

Title:

Chemicals
References

Effect of the 3-halo substitution of the 2′-deoxy aminopyridinyl-pseudocytidine derivatives on the selectivity and stability of antiparallel triplex DNA with a CG inversion site

Co-reporter:Lei Wang, Yosuke Taniguchi, Hidenori Okamura, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2017 Volume 25, Issue 14(Issue 14) pp:

Publication Date(Web):15 July 2017

DOI:10.1016/j.bmc.2017.05.035

Triplex formation against a target duplex DNA has the potential to become a tool for the genome research. However, there is an intrinsic restriction on the duplex DNA sequences capable of forming the triplex DNA. Recently, we demonstrated the selective formation of the stable antiparallel triplexes containing the CG inversion sites using the 2′-deoxy-1-methylpseudocytidine derivative (ΨdC), whose amino group was conjugated with the 2-aminopyridine at its 5-position as an additional hydrogen bonding unit (AP-ΨdC). The 1-N of 2-aminopyridine was supposed to be protonated to form the hydrogen bond with the guanine of the CG inversion site. In this study, to test the effect of the 3-substitution of the 2-aminopyridine unit of AP-ΨdC on the triplex stability, we synthesized the 3-halogenated 2-aminopyridine derivatives of AP-ΨdC. The pKa values 1-N of the 2-aminopyridine unit of AP-ΨdC as the monomer nucleoside were determined to be 6.3 for 3-CH3 (MeAP-ΨdC), 6.1 for 3-H (AP-ΨdC), 4.3 for 3-Cl (ClAP-ΨdC), 4.4 for 3-Br (BrAP-ΨdC), and 4.7 for 3-I (IAP-ΨdC), suggesting that all the halogenated AP-ΨdCs are not protonated under neutral conditions. Interestingly, although the recognition selectivity depends on the sequence context, the TFO having the sequence of the 3′-G-(IAP-ΨdC)-A-5′ context showed the selective triplex formation with the CG inversion site. These results suggest that the protonation at the 1-N position plays an important role in the stable and selective triplex formation of AP-ΨdC derivatives in any sequences.Download high-res image (114KB)Download full-size image

Synthetic receptor molecules for selective fluorescence detection of 8-oxo-dGTP in aqueous media

Co-reporter:Yasufumi Fuchi, Takashi Fukuda and Shigeki Sasaki

Organic & Biomolecular Chemistry 2016 vol. 14(Issue 33) pp:7949-7955

Publication Date(Web):29 Jul 2016

DOI:10.1039/C6OB01485B

A series of 9-hydroxy-1,3-diazaphenoxazine-2-one derivatives were synthesized as fluorescent receptor molecules for 8-oxo-dGTP, which attach the cyclen-zinc complex at the 3-N position as the binding site for the triphosphate and the (2-aryloxycarbonylamino)ethyl group at the 9-O position as the hydrogen bonding site for 8-oxoguanine. Among these molecules, the receptor molecule 5a-Zn constructed of the ethyl linker at 3-N and the (2-benzyloxycarbonyl amino)ethyl group at 9-O displayed the best recognition ability for 8-oxoguanosine triphosphate (8-oxo-dGTP) in aqueous media. The receptor 5a-Zn was also shown to selectively detect 8-oxo-dGTP in a cell lysate solution.

DNA cleavage at the AP site via β-elimination mediated by the AP site-binding ligands

Co-reporter:Yukiko S. Abe, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2016 Volume 24(Issue 4) pp:910-914

Publication Date(Web):15 February 2016

DOI:10.1016/j.bmc.2016.01.016

DNA is continuously damaged by endogenous and exogenous factors such as oxidation and alkylation. In the base excision repair pathway, the damaged nucleobases are removed by DNA N-glycosylase to form the abasic sites (AP sites). The alkylating antitumor agent exhibits cytotoxicity through the formation of the AP site. Therefore blockage or modulation of the AP site repair pathway may enhance the antitumor efficacy of DNA alkylating agents. In this study, we have examined the effects of the nucleobase–polyamine conjugated ligands (G-, A-, C- and T-ligands) on the cleavage of the AP site. The G- and A-ligands cleaved DNA at the AP site by promoting β-elimination in a non-selective manner by the G-ligand, and in a selective manner for the opposing dT by the A-ligand. These results suggest that the nucleobase–polyamine conjugate ligands may have the potential for enhancement of the cytotoxicities of the AP site.

Recognition and detection of 8-oxo-rG in RNA using the DNA/OMeRNA chimera probes containing fluorescent adenosine-diazaphenoxazine analog

Co-reporter:Yohei Koga, Yosuke Taniguchi, Yoshiya Kikukawa, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2016 Volume 24(Issue 6) pp:1308-1313

Publication Date(Web):15 March 2016

DOI:10.1016/j.bmc.2016.02.001

Recent studies indicate that oxidative damage to RNA results in dysfunction of translation and eventual pathogenesis. A representative oxidized base in RNA is 8-hydroxyguanosine (8-oxo-rG), however, unlike its DNA counterpart (8-oxo-dG), its role in pathogenesis has not attracted much attention until recently. The 2′-deoxyadenosine derivative with a diazaphenoxazine skeleton at the 6-amino group (Adap) was shown to be selective for 8-oxo-dG in DNA. In this study, the 2′-O-methoxy derivative of Adap (2′-OMeAdap) was designed as a selective molecule for 8-oxo-rG in RNA. 8-Oxo-rG in the homopurine RNA was selectively recognized by the ODN probe incorporating Adap. In contrast, although it was not possible by the Adap-containing ODN prove due to the instability of the corresponding duplex, 8-oxo-rG in homopyrimidine RNA was selectively detected by the 2′-OMeRNA probe incorporating 2′-OMeAdap.

Stabilization of the i-motif structure by the intra-strand cross-link formation

Co-reporter:Kenji Kikuta, Haishun Piao, John Brazier, Yosuke Taniguchi, Kazumitsu Onizuka, Fumi Nagatsugi, Shigeki Sasaki

Bioorganic & Medicinal Chemistry Letters 2015 Volume 25(Issue 16) pp:3307-3310

Publication Date(Web):15 August 2015

DOI:10.1016/j.bmcl.2015.05.064

The i-motif structures are formed by oligonucleotides containing cytosine tracts under acidic conditions. The folding of the i-motif under physiological conditions is of great interest because of its biological role. In this study, we investigated the effect of the intra-strand cross-link on the stability of the i-motif structure. The 4-vinyl-substituted analog of thymidine (T-vinyl) was incorporated into the 5′-end of the human telomere complementary strand, which formed the intra-strand cross-link with the internal adenine. The intra-strand cross-linked i-motif displayed CD spectra similar to that of the natural i-motif at acidic pH, which was transformed into a random coil with the increasing pH. The pH midpoint for the transition from the i-motif to random coil increased from pH 6.1 for the natural one to pH 6.8 for the cross-linked one. The thermodynamic parameters were obtained by measuring the thermal melting behaviors by CD and UV, and it was determined that the intra-strand cross-linked i-motif is stabilized due to a favorable entropy effect. Thus, this study has clearly indicated the validity of the intra-strand cross-linking for stabilization of the i-motif structure.

Strong positive cooperativity in binding to the A3T3 repeat by Hoechst 33258 derivatives attaching the quinoline units at the end of a branched linker

Co-reporter:Hironori Koda, John Alan Brazier, Ippei Onishi, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2015 23(15) pp: 4583-4590

Publication Date(Web):

DOI:10.1016/j.bmc.2015.05.056

Efficient Covalent Capture of 8-Nitroguanosine via a Multiple Hydrogen-Bonded Complex

Co-reporter:Yasufumi Fuchi and Shigeki Sasaki

Organic Letters 2014 Volume 16(Issue 6) pp:1760-1763

Publication Date(Web):March 7, 2014

DOI:10.1021/ol500452r

A novel 1,3-diazaphenoxazine nucleoside derivative (nitroG-Grasp) bearing a thiol group with a urea linker forms multiple hydrogen-bonded complexes with 8-nitroguanosine and efficiently displaces the nitro group; thus, it is the first molecule that can covalently capture 8-nitroguanosine.

An Isocytidine Derivative with a 2-Amino-6-methylpyridine Unit for Selective Recognition of the CG Interrupting Site in an Antiparallel Triplex DNA

Co-reporter:Hidenori Okamura;Dr. Yosuke Taniguchi; Shigeki Sasaki

ChemBioChem 2014 Volume 15( Issue 16) pp:2374-2378

Publication Date(Web):

DOI:10.1002/cbic.201402328

Abstract

Sequence-specific recognition of duplex DNA mediated by triple helix formation offers a potential basis for oligonucleotide therapy and biotechnology. However, triplex formation is limited mostly to homopurine strands, due to poor stabilization at CG or TA base pairs in the target duplex DNA sequences. Several non-natural nucleosides have been designed for the recognition of CG or TA base pairs within an antiparallel triplex DNA. Nevertheless, problems including low selectivity and high dependence on the neighboring bases remain unsolved. We thus synthesized N²-arylmethyl isodC derivatives and incorporated them into triplex-forming oligonucleotides (TFOs) for the selective recognition of the CG base pair within antiparallel triplex DNA. It was shown that an isodC derivative bearing a 2-amino-6-methylpyridine moiety (AP-isodC) recognizes the CG base pair with high selectivity in antiparallel triplex DNA irrespective of the flanking base pairs.

2,6-Diaminopurine nucleoside derivative of 9-ethyloxy-2-oxo-1,3-diazaphenoxazine (2-amino-Adap) for recognition of 8-oxo-dG in DNA

Co-reporter:Yosuke Taniguchi, Keitaro Fukabori, Yoshiya Kikukawa, Yohei Koga, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2014 22(5) pp: 1634-1641

Publication Date(Web):

DOI:10.1016/j.bmc.2014.01.024

Synthesis of 8-halogenated-7-deaza-2′-deoxyguanosine as an 8-oxo-2′-deoxyguanosine analogue and evaluation of its base pairing properties

Co-reporter:Yizhen Yin, Yosuke Taniguchi, Shigeki Sasaki

Tetrahedron 2014 70(11) pp: 2040-2047

Publication Date(Web):

DOI:10.1016/j.tet.2014.01.047

N-(Guanidinoethyl)-2′-deoxy-5-methylisocytidine exhibits selective recognition of a CG interrupting site for the formation of anti-parallel triplexes

Co-reporter:Hidenori Okamura, Yosuke Taniguchi and Shigeki Sasaki

Organic & Biomolecular Chemistry 2013 vol. 11(Issue 23) pp:3918-3924

Publication Date(Web):16 Apr 2013

DOI:10.1039/C3OB40472B

The development of novel nucleoside analogues for the formation of triplex DNA containing pyrimidine–purine inversion sites has been a challenging field. In this paper, we describe the design and synthesis of non-natural nucleoside analogues, N-substituted-2′-deoxy-5-methylisocytidine derivatives, and their evaluation for triplex formation. It has been shown that N-(guanidinoethyl)-2′-deoxy-5-methylisocytidine exhibits selective recognition of a CG interrupting site and potentiates the formation of anti-parallel triplexes.

Synthesis of 1′-phenyl-2′-OMe ribose analogues connecting the thymine base at the 1′ position through a flexible linker for the formation of a stable anti-parallel triplex DNA

Co-reporter:Yosuke Taniguchi, Hidenori Okamura, Norihiko Fujino, Shigeki Sasaki

Tetrahedron 2013 69(2) pp: 600-606

Publication Date(Web):

DOI:10.1016/j.tet.2012.11.016

An efficient antigene activity and antiproliferative effect by targeting the Bcl-2 or survivin gene with triplex forming oligonucleotides containing a W-shaped nucleoside analogue (WNA-βT)

Co-reporter:Yosuke Taniguchi and Shigeki Sasaki

Organic & Biomolecular Chemistry 2012 vol. 10(Issue 41) pp:8336-8341

Publication Date(Web):18 Sep 2012

DOI:10.1039/C2OB26431E

Triplex forming oligonucleotides (TFOs) are some of the most promising tools in the antigene strategy for the development of gene targeting therapeutics. However, the stable triplex formation is restricted to the homopurine sequences consisting of purine nucleosides, dG and dA. Therefore, the T or dC nucleoside in the homopurine strand inhibits the stable triplex formation. We have developed W-shaped nucleoside analogues (WNAs) for the formation of the unnatural type triplex DNA, with sequences containing the interrupting site in an antiparallel triplex formation. In the present study, we tested the antigene effect of TFOs having WNA-βT, which increased the stability of the triplex formation with a target sequence including the TA interrupting site. We designed the GU TFO (WNA) and GU TFO (natural) for targeting sequences of the Bcl-2 or survivin oncogene. The gel shift assay showed that the TFO (WNA) formed more stable triplexes than the natural TFO. Remarkably, the Bcl-2- or survivin-targeted TFO (WNA) inhibited the cell proliferation and induced a caspase-dependent apoptosis. It was confirmed that the survivin-targeted TFO (WNA) more effectively decreased the number of survivin products in the A549 cell than the natural TFOs.

Synthesis and binding properties of new selective ligands for the nucleobase opposite the AP site

Co-reporter:Yukiko Abe, Osamu Nakagawa, Rie Yamaguchi, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2012 Volume 20(Issue 11) pp:3470-3479

Publication Date(Web):1 June 2012

DOI:10.1016/j.bmc.2012.04.009

DNA is continuously damaged by endogenous and exogenous factors such as oxidative stress or DNA alkylating agents. These damaged nucleobases are removed by DNA N-glycosylase and form apurinic/apyrimidinic sites (AP sites) as intermediates in the base excision repair (BER) pathway. AP sites are also representative DNA damages formed by spontaneous hydrolysis. The AP sites block DNA polymerase and a mismatch nucleobase is inserted opposite the AP sites by polymerization to cause acute toxicities and mutations. Thus, AP site specific compounds have attracted much attention for therapeutic and diagnostic purposes. In this study, we have developed nucleobase–polyamine conjugates as the AP site binding ligand by expecting that the nucleobase part would play a role in the specific recognition of the nucleobase opposite the AP site by the Watson–Crick base pair formation and that the polyamine part should contribute to the access of the ligand to the AP site by a non-specific interaction to the DNA phosphate backbone. The nucleobase conjugated with 3,3′-diaminodipropylamine (A-ligand, G-ligand, C-ligand, T-ligand and U-ligand) showed a specific stabilization of the duplex containing the AP site depending on the complementary combination with the nucleobase opposite the AP site; that is A-ligand to T, G-ligand to C, C-ligand to G, T- and U-ligand to A. The thermodynamic binding parameters clearly indicated that the specific stabilization is due to specific binding of the ligands to the complementary AP site. These results have suggested that the complementary base pairs of the Watson–Crick type are formed at the AP site.

Efficient DNA Strand Displacement by a W-Shaped Nucleoside Analogue (WNA-T) Containing an ortho-Methyl-Substituted Phenyl Ring

Co-reporter:Eriko Aoki;Dr. Yosuke Taniguchi;Yasumasa Wada; Shigeki Sasaki

ChemBioChem 2012 Volume 13( Issue 8) pp:1152-1160

Publication Date(Web):

DOI:10.1002/cbic.201200066

Abstract

Molecules that can target duplex DNA with sequence selectivity have the potential to be useful tools in genomic research and also as therapeutic agents. Homopurine–homopyrimidine stretches in duplex DNA can be recognized by homopurine or homopyrimidine TFOs (triplex-forming oligonucleotides) through the formation of triplex DNA. We have previously developed bicyclic nucleoside analogues (WNAs) for the formation of stable triplexes in the formation of stable antiparallel triplexes containing a TA or a CG interrupting site. In this study, we investigated the effects on triplex DNA formation of ortho-, meta-, and para-methyl substituent groups on the aromatic ring of the WNA analogue. It was found that the homopurine TFO containing meta- and para-methyl-substituted WNA-βT (mMe-WNA-βT, pMe-WNA-βT) stabilized triplexes containing a TA interrupting site or a GC site, respectively. Interestingly, the ortho-methyl-substituted WNA-βT (oMe-WNA-βT) efficiently promoted DNA strand displacement to form the TFO/pyrimidine duplex. A detailed investigation showed that the duplex was in the antiparallel orientation and that its formation took place prior to triplex formation with the need for a magnesium cation. NOESY measurements indicated a significant difference in the rotation flexibilities of the phenyl rings of WNA-βTs: that is, the conformation of the ortho-methylated phenyl ring was stable in a temperature-independent manner. It was speculated that the initial formation of a ternary complex was followed by strand displacement and then the formation of the TFO/pyrimidine duplex together with the TFO₂/pyrimidine triplex formation during the early stage, and that the equilibrium shifted to the triplex during the later stage. Although the detailed role is still uncertain, the fixed phenyl ring of oMe-WNA-βT might play a role in the displacement reaction.

The oligodeoxynucleotide probes for the site-specific modification of RNA

Co-reporter:Shigeki Sasaki, Kazumitsu Onizuka and Yosuke Taniguchi

Chemical Society Reviews 2011 vol. 40(Issue 12) pp:5698-5706

Publication Date(Web):07 Jun 2011

DOI:10.1039/C1CS15066A

As the knowledge of the biological functions of RNA expands, the demand for research tools to investigate intracellular RNA is increasing. Oligonucleotides can be rationally designed for the target RNA sequence, and therefore, have become a reliable platform for the development of specific molecules for RNA. The chemical modification of RNA has a strong impact on RNA research; the fluorescent labeling of RNA is useful to monitor RNA production, processing, relocation in the cell, interaction with other intracellular components and degradation, etc. Chemical modification may affect the RNA function through a variety of pathways, and therefore, would be potentially useful for biological research, therapeutic approach and artificial manipulation of the RNA function. This tutorial review starts with an introduction of the biological relevance of modified RNA, and focuses on the recent progress of the oligodeoxynucleotide probes for the covalent modifications of RNA. The prospects of this new technology are also discussed.

Adenosine-1,3-diazaphenoxazine Derivative for Selective Base Pair Formation with 8-Oxo-2′-deoxyguanosine in DNA

Co-reporter:Yosuke Taniguchi ; Ryota Kawaguchi

Journal of the American Chemical Society 2011 Volume 133(Issue 19) pp:7272-7275

Publication Date(Web):April 27, 2011

DOI:10.1021/ja200327u

The selective detection of 8-oxo-2′-deoxyguanosine (8-oxo-dG) in DNA without chemical or enzymatic treatment is an attractive tool for genomic research. We designed and synthesized the non-natural nucleoside analogue, the adenosine-1,3-diazaphenoxazine (Adap) derivative, for selective recognition of 8-oxo-dG in DNA. This study clearly showed that Adap has a highly selective stabilizing effect on the duplex containing the Adap–8-oxo-dG base pair. Furthermore, the fluorescent property of Adap was shown to be useful for the selective detection of 8-oxo-dG in the duplex DNA. To the best of our knowledge, this is the first successful demonstration of a non-natural nucleoside with a high selectivity for 8-oxo-dG in DNA.

Optimization of fluorescence property of the 8-oxodGclamp derivative for better selectivity for 8-oxo-2′-deoxyguanosine

Co-reporter:Yohei Koga, Yasufumi Fuchi, Osamu Nakagawa, Shigeki Sasaki

Tetrahedron 2011 67(35) pp: 6746-6752

Publication Date(Web):

DOI:10.1016/j.tet.2011.03.111

Activation and Alteration of Base Selectivity by Metal Cations in the Functionality-Transfer Reaction for RNA Modification

Co-reporter:Kazumitsu Onizuka, Yosuke Taniguchi and Shigeki Sasaki

Bioconjugate Chemistry 2010 Volume 21(Issue 8) pp:1508

Publication Date(Web):June 29, 2010

DOI:10.1021/bc100131j

Previously, we reported that the 2-methylidene-1,3-diketone unit of 6-thioguanosine transferred selectively to the amino group of cytosine at pH 7.0 and that its selectivity was changed to the guanine base at pH 9.6. In this study, it was found that the functionality-transfer reaction enhanced selectivity for the guanine base in the presence of divalent transition metal cations such as Ni2+ and Co2+ at pH 7.4.

The alkyl-connected 2-amino-6-vinylpurine (AVP) crosslinking agent for improved selectivity to the cytosine base in RNA

Co-reporter:Yosuke Taniguchi, Yusuke Kurose, Takamasa Nishioka, Fumi Nagatsugi, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2010 Volume 18(Issue 8) pp:2894-2901

Publication Date(Web):15 April 2010

DOI:10.1016/j.bmc.2010.03.008

We have previously reported that the 2-amino-6-vinylpurine (AVP) nucleoside exhibits a highly efficient and selective crosslinking reaction toward cytosine and displayed an improved antisense inhibition in cultured cells. In this study, we further investigated the alkyl-connected AVP nucleoside analogs for more efficient crosslinking to the cytosine base (rC) of the target RNA. We synthesized three AVP analogs which connect the 2-amino-6-vinylpurine unit to the 2′-deoxyribose through a methylene, an ethylene, or a butylene linker. The ODN incorporating the AVP analog with the methylene or the butylene linker showed a slightly higher crosslinking to the target rC of RNA than the original AVP with no linker. In contrast, the AVP with the ethylene linker formed a selective and efficient crosslink to the rC of the target RNA.The ethylene-connected 2-amino-6-vinylpurine (AVP) crosslinking agent exhibited improved reactivity and selectivity to the cytosine base in RNA.

The ODN probes conjugating the Cu(II) complex enhance the luminol chemiluminescence by assembling on the DNA template

Co-reporter:Yosuke Taniguchi, Akiko Nitta, Sun Min Park, Akiko Kohara, Takahiro Uzu, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2010 Volume 18(Issue 24) pp:8614-8617

Publication Date(Web):15 December 2010

DOI:10.1016/j.bmc.2010.10.007

Potent peroxidase-like activity of the β-ketoenamine (1)–dicopper (II) complex (2) for the chemiluminescence (CL) of luminol either in the presence or absence of H2O2 has been previously demonstrated by our group. In this study, the β-ketoenamine (1) as the ligand unit for copper(II) was incorporated into the oligonucleotide (ODN) probes. It has been shown that the catalytic activity of the ODN probes conjugating the ligand–Cu(II) complex is activated by hybridization with the target DNA with the complementary sequence. Thus, this study has successfully demonstrated the basic concept for the sensitive detection of nucleic acids by CL based on the template-inductive activation of the catalytic unit for CL.

Synthesis of new derivatives of 8-oxoG-Clamp for better understanding the recognition mode and improvement of selective affinity

Co-reporter:Zhichun Li, Osamu Nakagawa, Yohei Koga, Yosuke Taniguchi, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2010 Volume 18(Issue 11) pp:3992-3998

Publication Date(Web):1 June 2010

DOI:10.1016/j.bmc.2010.04.025

8-Oxoguanosine (8-oxoG) is a representative metabolite derived by the oxidation of guanosine (G) and is regarded as a marker of oxidative stress in the cells. We previously reported the 8-oxoG-clamp as the first fluorescent probe for detection of 8-oxoG. In this study, new 8-oxoG-clamp derivatives having a variety of N-functional groups were synthesized and their recognition properties were investigated. The sp3 oxygen atom of the carbamate unit was revealed to play a significant role in the hydrogen bonding interactions, and the pyrene group produced higher stability with 8-oxoG compared with the original 8-oxoG-clamp.8-OxoG-clamp derivatives having a variety of N-functional groups were synthesized to clarify the suitable structure for more selective recognition, and 2-pyrene-1-yl-ethoxycarbonyl unit was found to produce higher stability with 8-oxoG.

The SpermineBisaryl Conjugate as a Potent Inducer of B- to Z-DNA Transition

Co-reporter:Issei Doi;Genichiro Tsuji;Kyoko Kawakami;Dr. Osamu Nakagawa;Dr. Yosuke Taniguchi ; Shigeki Sasaki

Chemistry - A European Journal 2010 Volume 16( Issue 39) pp:11993-11999

Publication Date(Web):

DOI:10.1002/chem.201000947

Abstract

DNA containing alternating purine and pyrimidine repeats has the potential to adopt the Z-DNA structure, one of the well-studied structures besides A- and B-DNA. Despite a number of molecular models that have been proposed to explain the mechanism for BZ transition, there is continued discussion on the mechanism and physiological role of this transition. In this study, we have found that the bis(2-naphthyl)-maleimide–spermine conjugate (3 c) exhibits a remarkable ability to cause the BZ transition of d(CGCGCG)₂ at low salt concentrations. Using isothermal titration calorimetry (ITC) we show that the BZ transition induced by 3 c is both enthalpically and entropically favorable. The ligand might effect the dehydration of B-DNA, which leads to the BZ transition. Interestingly, an intermediate CD between the B and Z forms was observed in the pH-dependent transition in the presence of the ligand. The unique structure and characteristics of the ligand designed in this investigation will be useful for the study of Z-DNA.

Site-Specific Covalent Modification of RNA Guided by Functionality-Transfer Oligodeoxynucleotides

Co-reporter:Kazumitsu Onizuka, Yosuke Taniguchi and Shigeki Sasaki

Bioconjugate Chemistry 2009 Volume 20(Issue 4) pp:799

Publication Date(Web):March 6, 2009

DOI:10.1021/bc900009p

Efficient methods for the covalent modification of large RNA molecules should find significance utility as innovative biological tools as well as therapeutic methods. In this study, the development of a general method for site-specific RNA modification guided by the functional ODN template has been investigated. The ODN probe containing 6-thioguanosine was modified by the methylenediketone derivative to form the S-functionalized ODN. Site-specific and cytosine-selective RNA modifications were achieved by the functionality-transfer reaction from the sulfur atom of the functionalized probe to the amino group of the cytosine base of the target strand. It was shown that the base and site selectivity were due to the close proximity of the reactants in the DNA-RNA duplexes.

Recognition of CG interrupting site by W-shaped nucleoside analogs (WNA) having the pyrazole ring in an anti-parallel triplex DNA

Co-reporter:Yosuke Taniguchi, Yuko Uchida, Tomoko Takaki, Eriko Aoki, Shigeki Sasaki

Bioorganic & Medicinal Chemistry 2009 Volume 17(Issue 19) pp:6803-6810

Publication Date(Web):1 October 2009

DOI:10.1016/j.bmc.2009.08.040

We have previously developed W-shaped nucleoside analogs (WNA) for recognition of TA and CG interrupting sites, which are the intrinsic limitation for the formation of a stable triplex DNA by the natural triplex-forming oligonucleotide (TFO). However, the stabilization effect of WNA is dependent on the neighboring nucleobases at both sides of the WNA analogs within the TFO. Considering that the base is located at the hindered site constructed of three bases of the target duplex and the TFO, it was expected that replacement of the pyrimidine base of the WNA analog with a smaller pyrazole ring might avoid steric repulsion to produce a greater stability for the triplex. In this study, the new WNA analogs bearing the pyrazole ring, 3-aminopyrazole (AP), and 4-methyl-3-pyrazole-5-on (MP) were synthesized, incorporated into the TFOs, then their stabilizing effects on the triplexes were evaluated. A remarkable success was illustrated by the fact that the TFO containing WNA-βAP in the 3′G-WNA-G-5′ sequence formed a stable triplex with selectivity to the CG interrupting site where the previous WNA-βC did not induce the triplex formation.

Selective fluorescence quenching of the 8-oxoG-clamp by 8-oxodeoxyguanosine in ODN

Co-reporter:Tamer Nasr, Zhichun Li, Osamu Nakagawa, Yosuke Taniguchi, Sayaka Ono, Shigeki Sasaki

Bioorganic & Medicinal Chemistry Letters 2009 Volume 19(Issue 3) pp:727-730

Publication Date(Web):1 February 2009

DOI:10.1016/j.bmcl.2008.12.036

The 8-oxoG-clamp, a specific fluorescent probe for 8-oxo-deoxyguanosine (8-oxo-dG), was incorporated into the oligodeoxynucleotide (ODN) within or at the 3′-end of the purine and the pyrimidine sequences. Based on the UV-melting temperature, the 8-oxoG-clamp showed slightly lower stabilizing effects on the duplexes containing 8-oxo-dG at the complementary site than that with dG. On the other hand, 8-oxo-dG in DNA was selectively detected by fluorescence quenching of the 8-oxoG-clamp.The 8-oxoG-clamp, a specific fluorescence probe for 2′-deoxy-8-oxoguanosine (8-oxo-dG) in solutions, was incorporated into the ODN, which was shown to be a selective fluorescence probe for 8-oxo-dG in DNA.

Synthesis and Evaluation of the Luciferase-Oligodeoxynucleotide for the Sequence-Selective Detection of Nucleic Acids

Co-reporter:Fumi Nagatsugi;Ryusuke Nakahara;Kaori Inoue

Archiv der Pharmazie 2008 Volume 341( Issue 9) pp:562-567

Publication Date(Web):

DOI:10.1002/ardp.200800031

Abstract

A new method for the synthesis of ODN-luciferase conjugate was investigated as a signal-amplifying sensor of the target nucleic acids. The conjugation of the luciferase was successfully achieved between the cysteine residue and the 2-amino-6-vinylpurine nucleoside of the ODN probe without significant inactivation of luciferase. The ODN-luciferase conjugate modified with PEG retained the luciferase activity and selectivity during the hybridization with the target ODN.

Specific Fluorescent Probe for 8-Oxoguanosine

Co-reporter:Osamu Nakagawa Dr.;Sayaka Ono;Zhichun Li;Akira Tsujimoto Dr.

Angewandte Chemie International Edition 2008 Volume 47( Issue 47) pp:

Publication Date(Web):

DOI:10.1002/anie.200890244

No abstract is available for this article.

Specific Fluorescent Probe for 8-Oxoguanosine

Co-reporter:Osamu Nakagawa Dr.;Sayaka Ono;Zhichun Li;Akira Tsujimoto Dr.

Angewandte Chemie 2008 Volume 120( Issue 47) pp:

Publication Date(Web):

DOI:10.1002/ange.200890293

No abstract is available for this article.

Specific Fluorescent Probe for 8-Oxoguanosine

Co-reporter:Osamu Nakagawa Dr.;Sayaka Ono;Zhichun Li;Akira Tsujimoto Dr.

Angewandte Chemie International Edition 2007 Volume 46(Issue 24) pp:

Publication Date(Web):10 MAY 2007

DOI:10.1002/anie.200700671

Marking mutations: Complete discrimination of 8-oxoguanosine (8-oxoG) from other nucleosides has been achieved with a new fluorescent probe, named “8-oxoG-clamp” (see picture). The complex structure between 8-oxoG-clamp and 8-oxoG was confirmed by ¹H NMR titration and 2D NMR measurements. A preliminary investigation with use of a detergent for solubilization indicates that 8-oxoG-clamp may be applicable in aqueous media.

Specific Fluorescent Probe for 8-Oxoguanosine

Co-reporter:Osamu Nakagawa Dr.;Sayaka Ono;Zhichun Li;Akira Tsujimoto Dr.

Angewandte Chemie 2007 Volume 119(Issue 24) pp:

Publication Date(Web):10 MAY 2007

DOI:10.1002/ange.200700671

Mutationen markiert: Die eindeutige Unterscheidung von 8-Oxoguanosin (8-oxoG) von anderen Nucleosiden gelingt mit der neuen Fluoreszenzsonde „8-oxoG-clamp“ (siehe Bild). Die Struktur des Komplexes aus 8-oxoG-clamp und 8-oxo-dG wurde durch ¹H-NMR-Titration und 2D-NMR-Messungen bestätigt. Ein Test mit einem Tensid zur Solubilisierung spricht dafür, dass 8-oxoG-clamp in wässrigen Medien eingesetzt werden kann.

Intracellular Inducible Alkylation System That Exhibits Antisense Effects with Greater Potency and Selectivity than the Natural Oligonucleotide

Co-reporter:Md. Monsur Ali Dr.;Motoi Oishi Dr.;Fumi Nagatsugi Dr.;Kenya Mori Dr.;Yukio Nagasaki Dr.;Kazunori Kataoka Dr. Dr.

Angewandte Chemie 2006 Volume 118(Issue 19) pp:

Publication Date(Web):30 MAR 2006

DOI:10.1002/ange.200504441

Eine Fehlpaarung in der mRNA-Zielsequenz wird durch ein System zur induzierbaren Alkylierung erkannt, das auf Sulfidvorstufen des Nucleosids 2-Amino-6-vinylpurin beruht (siehe Schema). Die reaktiven Oligonucleotide werden als Polyethylenglycol(PEG)-Konjugate in Polyionkomplex(PIC)-Micellen in die Zellen geschleust. Ihre Antisense-Aktivität ist hoch selektiv und übertrifft diejenige natürlicher Antisense-Oligonucleotide.

Intracellular Inducible Alkylation System That Exhibits Antisense Effects with Greater Potency and Selectivity than the Natural Oligonucleotide

Co-reporter:Md. Monsur Ali, Motoi Oishi, Fumi Nagatsugi, Kenya Mori, Yukio Nagasaki, Kazunori Kataoka,Shigeki Sasaki

Angewandte Chemie International Edition 2006 45(19) pp:3136-3140

Publication Date(Web):

DOI:10.1002/anie.200504441

New DNA binding ligands as a model of chromomycin A3

Co-reporter:Shuhei Imoto, Yoshinari Haruta, Kyouichi Watanabe, Shigeki Sasaki

Bioorganic & Medicinal Chemistry Letters 2004 Volume 14(Issue 19) pp:4855-4859

Publication Date(Web):4 October 2004

DOI:10.1016/j.bmcl.2004.07.043

Small molecules with DNA-binding affinity within the minor groove have become of great interest. In this study, new DNA-binding ligands were designed to mimic Chromomycin A3 (CRA3), which contains a hydroxylated tetrahydroanthracene chromophore substituted with di and trisaccharides. The trisaccharide part of CRA3 that is supposed to contribute to form the Mg2+-coordinated dimer was expected to be mimicked by a simple alkyl group attached to the chromophore part as new model compounds. The present study has successfully demonstrated that the new ligands form Mg2+-coordinated dimer complexes to exhibit DNA-binding affinity.

Solid-Phase synthesis of a library constructed of aromatic phosphate, long alkyl chains and tryptophane components, and identification of potent dipeptide telomerase inhibitors

Co-reporter:Shigeki Sasaki, Takeru Ehara, Md Rowshon Alam, Yasuhiro Fujino, Naozumi Harada, Junko Kimura, Hideo Nakamura, Minoru Maeda

Bioorganic & Medicinal Chemistry Letters 2001 Volume 11(Issue 19) pp:2581-2584

Publication Date(Web):8 October 2001

DOI:10.1016/S0960-894X(01)00507-8

Telomerase inhibitors are expected as a new candidate of therapeutic agents for cancer. Recently, we have found novel inhibitors based on the bisindole skeleton. In this study, solid-phase synthesis was applied to construct a library of inhibitors having aromatic phosphate, long alkyl chain and tryptophane components, from which a d,d-ditryptophane derivative has been identified as a new potent telomerase inhibitor with IC50 values of 0.3 μM. A hypothetical binding model for the new inhibitors has been proposed based on the structure–activity relationship.Graphic

Development of novel telomerase inhibitors based on a Bisindole unit

Co-reporter:Shigeki Sasaki, Takeru Ehara, Ikuhiro Sakata, Yasuhiro Fujino, Naozumi Harada, Junko Kimura, Hideo Nakamura, Minoru Maeda

Bioorganic & Medicinal Chemistry Letters 2001 Volume 11(Issue 4) pp:583-585

Publication Date(Web):26 February 2001

DOI:10.1016/S0960-894X(01)00002-6

Telomerase is the enzyme that elongates telomere repeat at the ends of a chromosome. As high telomerase activity is observed in most cancer cells, inhibitors of human telomerase have been expected as new chemotherapeutic agents for cancer. We describe here the discovery of novel inhibitors with IC50 values in the submicromolar range. The structure of the novel inhibitors will be useful as a scaffold for construction of the library in the search for telomerase inhibitors.Graphic

The oligodeoxynucleotide probes for the site-specific modification of RNA

Co-reporter:Shigeki Sasaki, Kazumitsu Onizuka and Yosuke Taniguchi

Chemical Society Reviews 2011 - vol. 40(Issue 12) pp:NaN5706-5706

Publication Date(Web):2011/06/07

DOI:10.1039/C1CS15066A

An efficient antigene activity and antiproliferative effect by targeting the Bcl-2 or survivin gene with triplex forming oligonucleotides containing a W-shaped nucleoside analogue (WNA-βT)

Co-reporter:Yosuke Taniguchi and Shigeki Sasaki

Organic & Biomolecular Chemistry 2012 - vol. 10(Issue 41) pp:NaN8341-8341

Publication Date(Web):2012/09/18

DOI:10.1039/C2OB26431E

N-(Guanidinoethyl)-2′-deoxy-5-methylisocytidine exhibits selective recognition of a CG interrupting site for the formation of anti-parallel triplexes

Co-reporter:Hidenori Okamura, Yosuke Taniguchi and Shigeki Sasaki

Organic & Biomolecular Chemistry 2013 - vol. 11(Issue 23) pp:NaN3924-3924

Publication Date(Web):2013/04/16

DOI:10.1039/C3OB40472B

Synthetic receptor molecules for selective fluorescence detection of 8-oxo-dGTP in aqueous media

Co-reporter:Yasufumi Fuchi, Takashi Fukuda and Shigeki Sasaki

Organic & Biomolecular Chemistry 2016 - vol. 14(Issue 33) pp:NaN7955-7955

Publication Date(Web):2016/07/29

DOI:10.1039/C6OB01485B

2(1H)-Pyrimidinone, 1-[5-O-[bis(4-methoxyphenyl)phenylmethyl]-3-O-[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]-2-deoxy-β-D-erythro-pentofuranosyl]-5-methyl-4-[2-(octylthio)ethyl]-

CAS:1422258-31-8

2(1H)-Pyrimidinone, 1-[5-O-[bis(4-methoxyphenyl)phenylmethyl]-3-O-[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]-2-deoxy-β-D-erythro-pentofuranosyl]-5-methyl-4-[2-(octylthio)ethyl]-