Published Papers - SAKAMOTO Takashi

Tripodal Quinone-Cyanine G-Quadruplex Ligands as Novel Photosensitizers on Photoinduced Cancer Cell Death

Junya Muramoto, Takashi Sakamoto （Part： Last author,　Corresponding author )

Molecules     2024.10  [Refereed]  [Invited]

DOI

Near-Infrared Fluorescent Switch-On Probe for Guanine-Quadruplex Imaging with Extremely Large Stokes Shift

Yuka Muraoka, Junya Muramoto, Yu Yasuhara, Mayuko Kawatake, Takashi Sakamoto （Part： Last author,　Corresponding author )

Analytical Chemistry ( American Chemical Society (ACS) )  95 ( 47 ) 17162 - 17165   2023.11  [Refereed]

DOI

Tripodal Quinone-cyanine Fluorescent Dye as a Tool for Analyzing Structural Dynamics of DNA Guanine-quadruplex

Takashi Sakamoto, Zehui Yu （Part： Lead author,　Corresponding author )

Chemistry Letters ( The Chemical Society of Japan )  51 ( 12 ) 1139 - 1142   2022.12  [Refereed]

DOI

Dual-Color Fluorescence Switch-On Probe for Imaging G-Quadruplex and Double-Stranded DNA in Living Cells

Takashi Sakamoto, Zehui Yu, Yuto Otani （Part： Lead author,　Corresponding author )

Analytical Chemistry ( American Chemical Society ({ACS}) )  94 ( 10 ) 4269 - 4276   2022.03  [Refereed]

DOI

Simultaneous Amino Acid Analysis Based on ¹⁹F NMR Using a Modified OPA-Derivatization Method

Takashi Sakamoto, Zhiyong Qiu, Miyu Inagaki, Kenzo Fujimoto （Part： Lead author,　Corresponding author )

Analytical Chemistry ( American Chemical Society (ACS) )  92 ( 2 ) 1669 - 1673   2019.12  [Refereed]

DOI

Front Cover: Label‐Free in Situ Monitoring of the DNA Hybridization Chain Reaction by Using Sequence‐Selective Minor‐Groove‐Binding Fluorophores (ChemBioChem 10/2019)

Takashi Sakamoto, Rikuto Yamada

ChemBioChem ( Wiley )  20 ( 10 ) 1206 - 1206   2019.05

DOI

Photo-cross-linkable artificial nucleic acid: Synthesis and properties of 3-cyanovinylcarbazole-modified nucleic acids and its photo-induced gene-silencing activity in cells

Takashi Sakamoto, Kenzo Fujimoto （Part： Lead author )

Synthesis of Therapeutic Oligonucleotides     171 - 186   2018.12  [Refereed]

　View Summary

© Springer Nature Singapore Pte Ltd. 2018. The inter-strand photo-cross-linking reaction between nucleic acid strands has wide potential for regulating gene expression specifically and spatiotemporally due to its sequence specificity and high photo irradiation operability. Therefore, photo-cross-linkable artificial nucleic acids are required to be specific and effective drugs without adverse effects and also be good tools for investigating gene functions in cells. As one of the most reactive photo-cross-linkable artificial nucleic acids, in this review, 3-cyanovinylcarbazole modified oligodeoxyribonucleotides that can photo-crosslink with their complementary nucleic acid within a few seconds of photoirradiation are examined. The details of the synthetic method, properties and the applications for regulating gene expression in cells are discussed.

DOI

Disassembly-driven signal turn-on probes for bimodal detection of DNA with 19F NMR and fluorescence

Takashi Sakamoto, Daisaku Hasegawa, Kenzo Fujimoto （Part： Lead author,　Corresponding author )

Organic & Biomolecular Chemistry ( Royal Society of Chemistry ({RSC}) )    2018  [Refereed]

DOI

Effect of nucleobase change on cytosine deamination through DNA photo-cross-linking reaction via 3-cyanovinylcarbazole nucleoside.

Sethi S, Ooe M, Sakamoto T, Fujimoto K

    2017.04  [Refereed]

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Sethi S, Ooe M, Sakamoto T, Fujimoto K, Molecular bioSystems, 2017, 2017

DOI

Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy.

Bao HL, Ishizuka T, Sakamoto T, Fujimoto K, Uechi T, Kenmochi N, Xu Y

    2017.02  [Refereed]

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Bao HL, Ishizuka T, Sakamoto T, Fujimoto K, Uechi T, Kenmochi N, Xu Y, Nucleic acids research, 2017, 2017

DOI

UVA-responsive Anticancer Prodrugs Based on Photoinduced Electron Injection into Oligonucleotide Having 5-Halouracils

Fujimoto, Kenzo, Furusawa, Mirei, Nakamura, Shigetaka, Sakamoto, Takashi （Part： Last author )

Chemistry Letters ( The Chemical Society of Japan )  45 ( 9 ) 1078 - 1080   2016.06  [Refereed]

DOI

Simultaneous detection of single-nucleotide polymorphisms in a DNA bulge structure using a fluorine-modified bisbenzimide derivative

Sakamoto, Takashi, Hasegawa, Daisaku, Fujimoto, Kenzo （Part： Lead author,　Corresponding author )

Analyst ( Royal Society of Chemistry )  141 ( 4 ) 1214 - 1217   2016.02  [Refereed]

DOI

Photo-Cross-Linking Reaction in Nucleic Acids: Chemistry and Applications

Sakamoto, Takashi, Fujimoto, Kenzo （Part： Lead author )

Modified Nucleic Acids ( Springer )    145 - 157   2016  [Refereed]

RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes

Fujimoto, Kenzo, Toyosato, Kei, Nakamura, Shigetaka, Sakamoto, Takashi （Part： Last author )

Bioorganic & Medicinal Chemistry Letters ( Pergamon )  26 ( 21 ) 5312 - 5314   2016  [Refereed]

DOI

Critical effect of base pairing of target pyrimidine on the interstrand photo-cross-linking of DNA via 3-cyanovinylcarbazole nucleoside

Sakamoto, Takashi, Ooe, Minako, Fujimoto, Kenzo （Part： Lead author )

Bioconjugate chemistry ( ACS Publications )  26 ( 8 ) 1475 - 1478   2015  [Refereed]

DOI

DNA photo-cross-linking using 3-cyanovinylcarbazole modified oligonucleotide with threoninol linker

Sakamoto, Takashi, Tanaka, Yuya, Fujimoto, Kenzo （Part： Lead author )

Organic letters ( ACS Publications )  17 ( 4 ) 936 - 939   2015  [Refereed]

DOI

Changing blue fluorescent protein to green fluorescent protein using chemical RNA editing as a novel strategy in genetic restoration

Vu, Luyen T, Nguyen, Thanh TK, Alam, Shafiul, Sakamoto, Takashi, Fujimoto, Kenzo, Suzuki, Hitoshi, Tsukahara, Toshifumi

Chemical biology & drug design ( Wiley Online Library )  86 ( 5 ) 1242 - 1252   2015  [Refereed]

DOI

Fluorine-modified bisbenzimide derivative as a molecular probe for bimodal and simultaneous detection of DNAs by 19 F NMR and fluorescence

Sakamoto, Takashi, Hasegawa, Daisaku, Fujimoto, Kenzo （Part： Lead author,　Corresponding author )

Chemical Communications ( Royal Society of Chemistry )  51 ( 42 ) 8749 - 8752   2015  [Refereed]

DOI

Short oligonucleotide prodrug having 5-fluoro and 5-iodouracil inhibits the proliferation of cancer cells in a photo-responsive manner

Fujimoto, Kenzo, Takematsu, Yu-ki, Shigeno, Atsuo, Furusawa, Mirei, Sakamoto, Takashi （Part： Last author )

Bioorganic & medicinal chemistry letters ( Elsevier )  24 ( 16 ) 3736 - 3738   2014  [Refereed]

DOI

Photo-regulation of constitutive gene expression in living cells by using ultrafast photo-cross-linking oligonucleotides

Sakamoto, Takashi, Shigeno, Atsuo, Ohtaki, Yuichi, Fujimoto, Kenzo （Part： Lead author )

Biomaterials Science ( Royal Society of Chemistry )  2 ( 9 ) 1154 - 1157   2014  [Refereed]

DOI

Details of the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside: cis--trans isomeric effect and the application for SNP-based genotyping

Fujimoto, Kenzo, Yamada, Asuka, Yoshimura, Yoshinaga, Tsukaguchi, Tadashi, Sakamoto, Takashi （Part： Last author )

Journal of the American Chemical Society ( ACS Publications )  135 ( 43 ) 16161 - 16167   2013  [Refereed]

DOI

Diamine Derivatives Accelerate Photochemical C→ U Transition in DNA Double Strand

Fujimoto, Kenzo, Futamura, Daiki, Sakamoto, Takashi （Part： Last author )

Chemistry Letters ( The Chemical Society of Japan )  42 ( 3 ) 289 - 291   2013  [Refereed]

DOI

Quick and reversible photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside in a DNA triplex

Fujimoto, Kenzo, Yoshinaga, Hiroki, Yoshio, Yasumasa, Sakamoto, Takashi （Part： Last author )

Organic & biomolecular chemistry ( Royal Society of Chemistry )  11 ( 31 ) 5065 - 5068   2013  [Refereed]

DOI

Quick, selective and reversible photocrosslinking reaction between 5-methylcytosine and 3-cyanovinylcarbazole in DNA double strand

Fujimo, Kenzo, Konishi-Hiratsuka, Kaoru, Sakamoto, Takashi （Part： Last author )

International journal of molecular sciences ( Multidisciplinary Digital Publishing Institute )  14 ( 3 ) 5765 - 5774   2013  [Refereed]

DOI

Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex

Fujimoto, Kenzo, Kishi, Satomi, Sakamoto, Takashi （Part： Last author )

Photochemistry and photobiology ( Wiley Online Library )  89 ( 5 ) 1095 - 1099   2013  [Refereed]

DOI

Development about photochemical DNA and RNA crosslinking via 3-cyanovinylcarbazole

Satomi Kishi, Daiki Futamura, Kaoru Hiratsuka, Takashi Sakamoto, Kenzo Fujimoto

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY ( AMER CHEMICAL SOC )  243   2012.03  [Refereed]

Regulation of gene expression by photocrosslinking oligonucleotide containing of carbazole

Atsuo Shigeno, Sakamoto Takashi, Kenzo Fujimoto

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY ( AMER CHEMICAL SOC )  243   2012.03  [Refereed]

Quick regulation of mRNA functions by a few seconds of photoirradiation

Shigeno, Atsuo, Sakamoto, Takashi, Yoshimura, Yoshinaga, Fujimoto, Kenzo

Organic & biomolecular chemistry ( Royal Society of Chemistry )  10 ( 38 ) 7820 - 7825   2012  [Refereed]

DOI

Specific and reversible photochemical labeling of plasmid DNA using photoresponsive oligonucleotides containing 3-cyanovinylcarbazole

Fujimoto, Kenzo, Hiratsuka-Konishi, Kaoru, Sakamoto, Takashi, Ohtake, Tomoko, Shinohara, Ken-ichi, Yoshimura, Yoshinaga

Molecular BioSystems ( Royal Society of Chemistry )  8 ( 2 ) 491 - 494   2012  [Refereed]

DOI

Signal turn-on probe for nucleic acid detection based on 19 F nuclear magnetic resonance

Sakamoto, Takashi, Shimizu, Yu-ki, Sasaki, Jun, Hayakawa, Hikaru, Fujimoto, Kenzo （Part： Lead author )

Bioorganic & medicinal chemistry letters ( Elsevier )  21 ( 1 ) 303 - 306   2011  [Refereed]

DOI

5-Methylcytosine selective photoligation using photoresponsive oligonucleotides containing various 5-vinyl-2′-deoxyuridines having an aromatic group

Sakamoto, Takashi, Ami, Takehiro, Fujimoto, Kenzo （Part： Lead author )

Chemistry Letters ( The Chemical Society of Japan )  41 ( 1 ) 47 - 49   2011  [Refereed]

DOI

Development of a Potassium Ion Sensor for 19F Magnetic Resonance Chemical Shift Imaging Based on Fluorine-labeled Thrombin Aptamer

Sakamoto, Takashi, Hayakawa, Hikaru, Fujimoto, Kenzo （Part： Lead author )

Chemistry Letters ( The Chemical Society of Japan )  40 ( 7 ) 720 - 721   2011  [Refereed]

DOI

1P346 DNA computing based on photochemical DNA manipulation(Miscellaneous topics,The 48th Annual Meeting of the Biophysical Society of Japan)

Ogasawara Shinji, Sakamoto Takashi, Nakamura Shigetaka, Fujimoto Kenzo

Seibutsu Butsuri ( The Biophysical Society of Japan General Incorporated Association )  50 ( 2 ) S81   2010

DOI

Site-specific photochemical RNA editing

Fujimoto, Kenzo, Konishi-Hiratsuka, Kaoru, Sakamoto, Takashi, Yoshimura, Yoshinaga

Chemical Communications ( Royal Society of Chemistry )  46 ( 40 ) 7545 - 7547   2010  [Refereed]

DOI

Site-Specific Cytosine to Uracil Transition by Using Reversible DNA Photo-crosslinking

Fujimoto, Kenzo, Konishi-Hiratsuka, Kaoru, Sakamoto, Takashi, Yoshimura, Yoshinaga

ChemBioChem ( Wiley Online Library )  11 ( 12 ) 1661 - 1664   2010  [Refereed]

DOI

Molecular recognition, fluorescence sensing, and biological assay of phosphate anion derivatives using artificial Zn (II)--Dpa complexes

Sakamoto, Takashi, Ojida, Akio, Hamachi, Itaru （Part： Lead author )

Chemical Communications ( Royal Society of Chemistry )  ( 2 ) 141 - 152   2009  [Refereed]

DOI

Self-assembling nanoprobes that display off/on 19F nuclear magnetic resonance signals for protein detection and imaging

Takaoka, Yousuke, Sakamoto, Takashi, Tsukiji, Shinya, Narazaki, Michiko, Matsuda, Tetsuya, Tochio, Hidehito, Shirakawa, Masahiro, Hamachi, Itaru

Nature chemistry ( Nature Publishing Group )  1 ( 7 ) 557 - 561   2009  [Refereed]

DOI

Fluorescent BODIPY-based Zn (II) complex as a molecular probe for selective detection of neurofibrillary tangles in the brains of Alzheimer’s disease patients

Ojida, Akio, Sakamoto, Takashi, Inoue, Masa-aki, Fujishima, Sho-hei, Lippens, Guy, Hamachi, Itaru

Journal of the American Chemical Society ( ACS Publications )  131 ( 18 ) 6543 - 6548   2009  [Refereed]

DOI

Real-time fluorescence monitoring of GSK3$β$-catalyzed phosphoryation by use of a BODIPY-based Zn (II)--Dpa chemosensor

Sakamoto, Takashi, Inoue, Masa-aki, Ojida, Akio, Hamachi, Itaru （Part： Lead author )

Bioorganic & medicinal chemistry letters ( Elsevier )  19 ( 15 ) 4175 - 4177   2009  [Refereed]

DOI

Microarray-based label-free detection of RNA using bispyrene-modified 2′-O-methyl oligoribonucleotide as capture and detection probe

Sakamoto, Takashi, Kobori, Akio, Murakami, Akira （Part： Lead author )

Bioorganic & medicinal chemistry letters ( Elsevier )  18 ( 8 ) 2590 - 2593   2008  [Refereed]

DOI

Transcriptome analysis device based on liquid phase detection by fluorescently labeled nucleic acid probes

Yokokawa, Ryuji, Tamaoki, Soichiro, Sakamoto, Takashi, Murakami, Akira, Sugiyama, Susumu

Biomedical microdevices ( Springer )  9 ( 6 ) 869 - 875   2007  [Refereed]

DOI

Real-time monitoring of antibody secretion from B-cells on a microchip stimulated with a minute amount of mitogen

Munaka, Tatsuya, Abe, Hirohisa, Kanai, Masaki, Sakamoto, Takashi, Nakanishi, Hiroaki, Shoji, Shuichi, Kimura, Shinya, Maekawa, Taira, Murakami, Akira

Analyst ( Royal Society of Chemistry )  132 ( 6 ) 512 - 514   2007  [Refereed]

DOI

Homogeneous Fluorescence Assays for RNA Diagnosis by Pyrene-Conjugated 2′-O-Methyloligoribonucleotides

Sakamoto, Takashi, Kobori, Akio, Shigezawa, Masako, Amitani, Yasutaka, Higuchi, Maiko, Murakami, Akira （Part： Lead author )

Nucleosides, Nucleotides, and Nucleic Acids ( Taylor \& Francis )  26 ( 10-12 ) 1659 - 1664   2007  [Refereed]

DOI

Highly-sensitive detection of immunoreactions by time-resolved fluorescence anisotropy analysis

Takashi Sakamoto, Nobuyuki Fujihara, Akio Kobori, Akira Murakami, Miharu Kishi, Koichi Yamagata

Polymer Preprints, Japan   55 ( 2 ) 4933   2006

　View Summary

Long-lifetime fluorophore is useful for the highly-sensitive detection of immunoreactions based on time-resolved fluorescence anisotropy analysis. We focused on pyrene-β-cyclodextrin conjugate (Py-β-CD) as a long-lifetime fluorescent label. Py-β-CD-NHS-ester was used to label human serum albumin (HSA). The steady-state fluorescence anisotropy of Py-β-CD-labeled HSA (Py-β-CD-HSA) was measured in the presence of various proteins. The fluorescence anisotropy of Py-β-CD-HSA increased upon the addition of anti-HSA monoclonal IgG or anti-HSA polyclonal IgG. On the other hand, the addition of anti-IgG IgG or HSA did not affect the fluorescence anisotropy of Py-β-CD-HSA. Time-resolved fluorescence anisotropy analysis of the Py-β-CD-HSA was carried out in the presence or absence of anti-HSA polyclonal IgG. The fluorescence anisotropy of the Py-β-CD-HSA from 0 to 200 nsec after pulse excitation significantly increased by the addition of anti-HSA polyclonal IgG. These results indicated that Py-β-CD-HSA bound to its specific IgG and that Py-β-CD-HSA was useful for highly-sensitive detection of immunoreactions based on time-resolved fluorescence anisotropy analysis.

Properties of novel antisense oligonucleotides containing 2′-O-modified adenosine with a photo-reactive group

Higuchi Maiko, Sakamoto Takashi, Kobori Akio, Murakami Akira

Nucleic Acids Symposium Series   50 ( 1 ) 301 - 2   2006  [Refereed]

　View Summary

In order to enhance the efficiency of antisense molecules for target RNA regulation, a novel photo-reactive antisense oligonucleotide was developed. We designed and synthesized a photo-reactive antisense oligonucleotide containing an adenosine in which 2'-OH was modified with 4,5',8-trimethylpsoralen (Ps) via an ethoxymethylene linkage (2'-Ps-eom). We evaluated the photo-cross-linking efficiency and sequence specificity toward complementary RNA (match-RNA). 2'-Ps-eom was selectively photo-cross-linked to the match-RNA. The photo-cross-linking efficiency was about 75% upon UVA-irradiation (365 nm) for 10 min. Previously, we reported oligonucleotides that had an adenosine anchoring Ps at 2'-O-position via a methylene linkage (2'-Ps-met). The photo-cross-linking efficiency of 2'-Ps-met and match-RNA was about 35% upon UVA-irradiation for 120 min. The photo-cross-linking efficiency of 2'-Ps-eom was dramatically enhanced in comparison with the one of 2'-Ps-met.

Solid-phase detection of RNA using bispyrene-modified RNA probe

Sakamoto Takashi, Kobori Akio, Murakami Akira （Part： Lead author )

Nucleic Acids Symposium Series   50 ( 1 ) 215 - 6   2006  [Refereed]

　View Summary

Bispyrene modified 2'-O-methyl oligoRNA (OMUpy2), which is a useful fluorescent probe for specific RNA detection, was immobilized on a glass substrate via various linker molecules to develop a more convenient RNA detection chip for gene expression study. As the fluorescence intensity of OMUpy2 enhanced greatly when it hybridized with its complementary RNA, it was expected that RNA detection by OMUpy2-immobilized chip (RNA-chip) required neither fluorescent labels to target nucleic acid nor washing protocol after the hybridization. As the linker molecules, oligo(dT), agarose, and poly(ethylene glycol) (PEG) were chosen, and the fluorescence from the chip was measured by a fluorescence microscope. Results indicated that the RNA-chip was able to detect the complementary oligoribonucleotide (cORN) without target labeling and washing protocols. Furthermore, the background emission was reduced as the length of the linker increased. In the case of PEG linker, 25-fold enhancement of the fluorescence intensity of the OMUpy2 was observed upon the addition of cORN.

Monitoring cellular events in living mast cells stimulated with an extremely small amount of fluid on a microchip

Munaka, Tatsuya, Abe, Hirohisa, Kanai, Masaki, Sakamoto, Takashi, Nakanishi, Hiroaki, Yamaoka, Tetsuji, Shoji, Shuichi, Murakami, Akira

Japanese journal of applied physics ( IOP Publishing )  45 ( 7L ) L634   2006  [Refereed]

DOI

Real-time monitoring of antibody secretion from hybridomas on a microchip by time-resolved luminescence anisotropy analysis

Munaka, Tatsuya, Abe, Hirohisa, Kanai, Masaki, Sakamoto, Takashi, Nakanishi, Hiroaki, Yamaoka, Tetsuji, Shoji, Shuichi, Murakami, Akira

Analytical biochemistry ( Elsevier )  353 ( 1 ) 1 - 6   2006  [Refereed]

DOI

Development of the cell analysis chip (II)

Tatsuya Munaka, Masaki Kanai, Hirohisa Abe, Hiroaki Nakanishi, Takashi Sakamoto, Akio Kobori, Tetsuji Yamaoka, Shuichi Shoji, Akira Murakami

Polymer Preprints, Japan   54 ( 1 ) 2329   2005  [Refereed]

　View Summary

In recent years, cell analysis has attracted increased attention in bioanalytical and biotechnological applications. On the other hand, microchip techniques, which are called micro total analysis systems (μTAS), have been developed especially in chemical and biochemical analysis fields. We took advantage of a feature of μ TAS and developed a system that can detect a small amount of the protein released by a cell without bound/free (B/F) separation protocol and with high sensitivity. In this report, we describe the continuous monitoring of immunoglobulin G (lgG) production of hybridoma cells stimulated by the serum.

Analytical method for estimation of kinetics of oligonucleotide/RNA hybridization using fluorescence depolarization spectroscopy

Sakamoto, Takashi, Mahara, Atsushi, Iwase, Reiko, Yamaoka, Tetsuji, Murakami, Akira （Part： Lead author )

Analytical biochemistry ( Academic Press )  340 ( 2 ) 369 - 372   2005  [Refereed]

DOI

Transcriptome Analyzing Chip Based on Liquid-phase Detection Using Fluorescence Labeled Nucleic Acid Probe

Tamaoki S, Sugiyama S, Sakamoto T, Murakami A

PROCEEDINGS OF THE SENSOR SYMPOSIUM ON SENSORS MICROMACHINES AND APPLIED SYSTEMS   22   270   2005  [Refereed]

Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution

Sakamoto, Takashi, Mahara, Atsushi, Yamagata, Koichi, Iwase, Reiko, Yamaoka, Tetsuji, Murakami, Akira （Part： Lead author )

Biophysical journal ( Elsevier )  89 ( 6 ) 4122 - 4128   2005  [Refereed]

DOI

Luminescence anisotropy-based detection of nucleic acids and proteins using long-lifetime Ru(II) complex as a luminescent label.

Takashi Sakamoto, Atsushi Mahara, Kobori Akio, Tetsuji Yamaoka, Akira Murakami （Part： Lead author )

Nucleic acids symposium series (2004)   49 ( 49 ) 203 - 204   2005  [Refereed]

　View Summary

Luminescence anisotropy-based methods are powerful tool for the detection of biomolecules in homogeneous physiological media without Bound/Free separation. However, analyses based on the method are always disturbed by the autofluorescence from biological specimen. This disturbance limits the sensitivity of the method. To improve the detection limit of the method, a long-lifetime luminophore was adopted as the label. Because of the lifetime of the autofluorescence is below 10 ns, it is expected that the use of the long-lifetime luminophore enables us to avoid the disturbance by adopting time-resolved luminescence anisotropy measurement. To verify this concept, oligodeoxyribonucleotides and Staphylococcus aureus protein A were labeled with Ru(II) complex (tau approximately 500 nsec) and used for the detection of Escherichia coli 16S ribosomal RNA (16S rRNA) and immunoglobulin G (IgG), respectively. Results indicated that the methods were useful for the detection of rRNA and IgG without disturbance of the autofluorescence.

Time-resolved luminescence anisotropy-based detection of immunoglobulin G using long-lifetime Ru (II) complex-labeled protein A

Sakamoto, Takashi, Mahara, Atsushi, Munaka, Tatsuya, Yamagata, Koich, Iwase, Reiko, Yamaoka, Tetsuji, Murakami, Akira （Part： Lead author )

Analytical biochemistry ( Academic Press )  329 ( 1 ) 142 - 144   2004  [Refereed]

DOI

Transcriptome analysis using fluorescence-labeled oligonucleotide.

Naohiko Shimada, Atsushi Mahara, Takashi Sakamoto, Tetsuji Yamaoka, Akira Murakami

Nucleic acids symposium series (2004)   48 ( 48 ) 301 - 302   2004  [Refereed]

　View Summary

In our previous studies, the fluorescence intensity at 480 nm of the bispyrene-labeled 2'-O-methyl-oligoribonucleotide (OMUpy2) was drastically enhanced only when it was hybridized with its complementary RNA. In this study, we demonstrated the potential of the OMUpy2 for transcriptome analysis in the cell free system and in the living cell. For the analysis in the cell free system, the micro-chamber was designed and used to evaluate the detection limit of the target RNA. The detection limit of oligo-RNA was approximately 15 fmol. For the analysis of the living cells, C-OMUpy2 was introduced to the cervical carcinoma cells, C4II, and the fluorescence from C-OMUpy2 was monitored. The fluorescence from the cells began to be observed 5 min after the serum stimulation, and the fluorescence was decreased after 20 min. These results seemed to be consistent with the results from the RT-PCR analysis and suggested that OMUpy2 could be a useful tool for the transcriptome analysis.

In situ Cell Monitoring on a Microchip using Time-Resolved Fluorescence Anisotropy Analysis

Sakamoto Takashi, Mahara Atsushi, Yamayoshi Asako

Seibutsu Butsuri ( The Biophysical Society of Japan General Incorporated Association )  43   S222   2003.10  [Refereed]

DOI

RNAの機能・構造解析に用いる螢光RNAプローブの開発

村上 章, 坂本 隆, 馬原 淳

化学と生物 ( Japan Society for Bioscience, Biotechnology, and Agrochemistry )  41 ( 8 ) 549 - 556   2003.08

DOI

Detection of acceptor sites for antisense oligonucleotides on native folded RNA by fluorescence-labeled oligonucleotide.

Atsushi Mahara, Takashi Sakamoto, Tatsuya Munaka, Reiko Iwase, Tetsuji Yamaoka, Akira Murakami

Nucleic acids research. Supplement (2001)   3 ( 3 ) 73 - 74   2003  [Refereed]

　View Summary

Pyrene-labeled 2'-O-methyloligoribonucleotide (OMUpy) and 5'-Ru(II) complex labeled oligodeoxyribonucleotie (Ru-probe) were prepared as the fluorescence probes to detect acceptor sites of antisense molecules on native folded RNA under the physiological condition. OMUpy showed the remarkable increase of the fluorescence intensity (334-fold at 375 nm) only when hybridized with complementary oligoRNA. When OMUpy was applied to E. coli 16S-rRNA, the fluorescence intensities were increased in a sequence specific manner. The rotational correlation time of Ru-probe complementary to 16S-rRNA were largely dependent on the sequence of Ru-probe. These results suggest that the accessibility of the antisense molecules for RNA can be evaluated by those fluorescent probes.

Detection of acceptor sites for antisense oligonucleotides on native folded RNA by fluorescence spectroscopy

Mahara, Atsushi, Iwase, Reiko, Sakamoto, Takashi, Yamaoka, Tetsuji, Yamana, Kazushige, Murakami, Akira

Bioorganic & medicinal chemistry ( Elsevier )  11 ( 13 ) 2783 - 2790   2003  [Refereed]

DOI

Bispyrene-conjugated 2'-O-methyloligonucleotide as a highly specific RNA-recognition probe.

Atsushi Mahara, Reiko Iwase, Takashi Sakamoto, Kazushige Yamana, Tetsuji Yamaoka, Akira Murakami

Angewandte Chemie (International ed. in English)   41 ( 19 ) 3648 - 50   2002.10

Bispyrene-Conjugated 2′-O-Methyloligonucleotide as a Highly Specific RNA-Recognition Probe

Mahara, Atsushi, Iwase, Reiko, Sakamoto, Takashi, Yamana, Kazushige, Yamaoka, Tetsuji, Murakami, Akira

Angewandte Chemie ( WILEY-VCH Verlag )  114 ( 19 ) 3800 - 3802   2002  [Refereed]

DOI

Study on structure of ribosomal RNA by time-resolved luminescence anisotropy analysis.

T. Sakamoto, A. Mahara, R. Iwase, T. Yamaoka, A. Murakami （Part： Lead author )

Nucleic acids research. Supplement (2001)   1 ( 1 ) 143 - 144   2001  [Refereed]

　View Summary

Evaluation of the folded structure of E.coli 16S-rRNA was performed using 5'-Ru(II) complex labeled oligodeoxyribonucleotide (Ru-probe) as the probe. This probe could evaluate the dynamic manner of the binding site of Ru-probe by using the time-resolved luminescence anisotropy technique. It was found that the rotational manner of Ru-probe in the presence of 16S-rRNA was markedly dependent on the oligonucleotide sequence, indicating that the microenvironments around the Ru-probes were largely different.

DOI