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Minato-ku, Japan

Nomura Y.,Chiba Institute of Technology | Nomura Y.,Japan Science and Technology Agency | Sugiyama S.,Osaka University | Sugiyama S.,Japan Science and Technology Agency | And 24 more authors.
Nucleic Acids Research | Year: 2010

Aptamers are short single-stranded nucleic acids with high affinity to target molecules and are applicable to therapeutics and diagnostics. Regardless of an increasing number of reported aptamers, the structural basis of the interaction of RNA aptamer with proteins is poorly understood. Here, we determined the 2.15 crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer. The aptamer adopts a characteristic structure fit to hFc1 that is stabilized by a calcium ion, and the binding activity of the aptamer can be controlled many times by calcium chelation and addition. Importantly, the aptamer-hFc1 interaction involves mainly van der Waals contacts and hydrogen bonds rather than electrostatic forces, in contrast to other known aptamer-protein complexes. Moreover, the aptamer-hFc1 interaction involves human IgG-specific amino acids, rendering the aptamer specific to human IgGs, and not crossreactive to other species IgGs. Hence, the aptamer is a potent alternative for protein A affinity purification of Fc-fusion proteins and therapeutic antibodies. These results demonstrate, from a structural viewpoint, that conformational plasticity and selectivity of an RNA aptamer is achieved by multiple interactions other than electrostatic forces, which is applicable to many protein targets of low or no affinity to nucleic acids. © 2010 The Author(s). Source


Nakamura Y.,University of Tokyo | Nakamura Y.,Tokyo Medical University | Nakamura Y.,Ribomic Inc.
Advances in Polymer Science | Year: 2012

Aptamers are short single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries on the basis of their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases superior to, those of antibodies from several viewpoints. This review summarizes the recent achievements in aptamer programs developed in our laboratory against basic as well as therapeutic protein targets. Through these studies, we became aware of RNA's remarkable conformational plasticity, which the literature has not shed light on even though this is evidently a crucial feature for the strong specificity and affinity of RNA aptamers. © 2011 Springer-Verlag Berlin Heidelberg. Source


Soeno Y.,The Nippon Dental University | Fujita K.,The Nippon Dental University | Kudo T.,Hyogo College of Medicine | Asagiri M.,Kyoto University | And 14 more authors.
PLoS ONE | Year: 2013

Box C/D-type small nucleolar RNAs (snoRNAs) are functional RNAs responsible for mediating 2′-O-ribose methylation of ribosomal RNAs (rRNAs) within the nucleolus. In the past years, evidence for the involvement of human U50 snoRNA in tumorigenesis has been accumulating. We previously identified U50HG, a non-protein-coding gene that hosted a box C/D-type U50 snoRNA, in a chromosomal breakpoint in a human B-cell lymphoma. Mouse genome analysis revealed four mouse U50 (mU50) host-genes: three mU50HG-a gene variants that were clustered in the genome and an mU50HG-b gene that we supposed to be the U50HG ortholog. In this study, to investigate the physiological importance of mU50 snoRNA and its involvement in tumorigenesis, we eliminated mU50 snoRNA sequences from the mU50HG-b gene. The established mouse line (ΔmU50(HG-b)) showed a significant reduction of mU50 snoRNA expression without alteration of the host-gene length and exon-intron structure, and the corresponding target rRNA methylation in various organs was reduced. Lifelong phenotypic monitoring showed that the ΔmU50(HG-b) mice looked almost normal without accelerated tumorigenicity; however, a notable difference was the propensity for anomalies in the lymphoid organs. Transcriptome analysis showed that dozens of genes, including heat shock proteins, were differentially expressed in ΔmU50(HG-b) mouse lymphocytes. This unique model of a single snoRNA knockdown with intact host-gene expression revealed further new insights into the discrete transcriptional regulation of multiple mU50 host-genes and the complicated dynamics involved in organ-specific processing and maintenance of snoRNAs. © 2013 Soeno et al. Source


Shan L.,Glaxosmithkline | Shan L.,Tianjin University of Traditional Chinese Medicine | Noritake S.,Glaxosmithkline | Fujiwara M.,Glaxosmithkline | And 9 more authors.
Inflammation | Year: 2012

Airway epithelium is a key component for airway integrity. Previously, we found that expression of the Sec14l3 gene that encodes a 45-kDa secretory protein is inversely associated with the progression of experimentally induced airway inflammation and degeneration/necrosis of alveolar epithelium. In this report, using in situ hybridization we demonstrated that the ciliated cells in mouse lung selectively express Sec14l3 mRNA. In a three-dimensional culture of mouse tracheal epithelial cells, levels of the Sec14l3 mRNA correlated with the differentiation of ciliated cells. Intranasal infection of adult mice with influenza virus resulted in a 20-fold, progressive decrease in Sec14l3 mRNA expression over 10 days post infection. These results enhance the potential value of Sec14l3 as a ciliated epithelial cell-specific biomarker for the progression of airway inflammations such as airway viral infection and asthma. © 2011 Springer Science+Business Media, LLC. Source


Patent
Ribomic Inc. and Otsuka Pharmaceutical Factory Inc. | Date: 2013-11-21

The present invention provides an aptamer binding to midkine and capable of forming a potential secondary structure represented by the formula (I): wherein

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