Selection of RNA aptamers against mouse embryonic stem cells.

Abstract:

:Embryonic stem cells (ESCs) are capable of unlimited self-renewal and differentiation into multiple cell types. Recent large-scale analyses have identified various cell surface molecules on ESCs. Some of them are considered to be beneficial markers for characterization of cellular phenotypes and/or play an essential role for regulating the differentiation state. Thus, it is desired to efficiently produce affinity reagents specific to these molecules. In this study, to develop such reagents for mouse ESCs (mESCs), we selected RNA aptamers against intact, live mESCs using several selection strategies. The initial selection provided us with several anti-mESC aptamers of distinct sequences, which unexpectedly react with the same molecule on mESCs. Then, to isolate aptamers against different surface markers on mESCs, one of the selected aptamers was used as a competitor in the subsequent selections. In addition, one of the selections further employed negative selection against differentiated mouse cells. Consequently, we successfully isolated three classes of anti-mESC aptamers that do not compete with one another. The isolated aptamers were shown to distinguish mESCs from differentiated mouse cell lines and trace the differentiation process of mESCs. These aptamers could prove useful for developing molecular probes and manipulation tools for mESCs.

journal_name

Biochimie

journal_title

Biochimie

authors

Iwagawa T,Ohuchi SP,Watanabe S,Nakamura Y

doi

10.1016/j.biochi.2011.10.017

subject

Has Abstract

pub_date

2012-01-01 00:00:00

pages

250-7

issue

1

eissn

0300-9084

issn

1638-6183

pii

S0300-9084(11)00413-5

journal_volume

94

pub_type

杂志文章
  • Activation of a cryptic splice site in the tax gene of HTLV-I by a single nucleotide change.

    abstract::We identified a T-to-C mutation 2 nucleotides (nt) upstream from the AG in a GT-AG intron between exons 2 and 3 in the human T-cell leukemia virus type I (HTLV-I) tax mRNA. This mutation resulted in the preferential usage of an alternative splice site, causing a 75-nt elongation of tax mRNA and reduced production of v...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2005.07.013

    authors: Ohsugi T

    更新日期:2006-02-01 00:00:00

  • Molecular cloning and characterization of neutral ceramidase homologue from the red flour beetle, Tribolium castaneum.

    abstract::Ceramidase plays an important role in regulating the metabolism of sphingolipids, such as ceramide, sphingosine (SPH), and sphingosine-1-phosphate (S1P), by controlling the hydrolysis of ceramide. Here we report the cloning and biochemical characterization of a neutral ceramidase from the red flour beetle Tribolium ca...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2011.03.009

    authors: Zhou Y,Lin XW,Yang Q,Zhang YR,Yuan JQ,Lin XD,Xu R,Cheng J,Mao C,Zhu ZR

    更新日期:2011-07-01 00:00:00

  • Does histone H1 bind specifically to the nuclear factor I recognition sequence?

    abstract::The issue of whether histone H1 possesses specificity of binding to certain nucleotide sequences in DNA is of fundamental importance to the suggested role of the linker histone in the regulation of gene transcription. The purpose of the present study was to reinvestigate the specificity of binding of histone H1 to the...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(93)90116-a

    authors: Yaneva JN,Zlatanova JS

    更新日期:1993-01-01 00:00:00

  • Regulation of the human Suv3 helicase on DNA by inorganic cofactors.

    abstract::Mitochondria are essential organelles and consequently proper expression and maintenance of the mitochondrial genome are indispensable for proper cell function. The mitochondrial Suv3 (SUPV3L1) helicase is known to have a central role in mitochondrial RNA metabolism and to be essential for maintenance of mitochondrial...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2014.11.003

    authors: Venø ST,Witt MB,Kulikowicz T,Bohr VA,Stevnsner T

    更新日期:2015-01-01 00:00:00

  • Aldehyde dehydrogenase and HSP90 co-localize in human glioblastoma biopsy cells.

    abstract::The concept of a stem cell subpopulation as understood from normal epithelial tissue or bone marrow function has been extended to our understanding of cancer tissue and is now the target of treatment efforts specifically directed to this subpopulation. In glioblastoma, as well as in other cancers, increased expression...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2012.11.007

    authors: Rappa F,Cappello F,Halatsch ME,Scheuerle A,Kast RE

    更新日期:2013-04-01 00:00:00

  • Small RNAs derived from longer non-coding RNAs.

    abstract::Posttranscriptional gene regulation by small RNAs and its crucial impact on development, apoptosis, stem cell self-renewal and differentiation gained tremendous scientific attention since the discovery of RNA interference (RNAi) and microRNAs (miRNAs). However, in the last few years, many more examples for regulatory ...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2011.07.032

    authors: Röther S,Meister G

    更新日期:2011-11-01 00:00:00

  • Eicosapentaenoic acid modifies lipid composition in caveolae and induces translocation of endothelial nitric oxide synthase.

    abstract::Endothelial nitric oxide synthase (eNOS) plays a crucial role in the regulation of a variety of cardiovascular functions. Many studies have shown that dietary n-3 polyunsaturated fatty acids (PUFAs) have beneficial effects on coronary atherosclerosis. However, the mechanisms of n-3 PUFAs regulation in eNOS activation ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2006.10.009

    authors: Li Q,Zhang Q,Wang M,Zhao S,Ma J,Luo N,Li N,Li Y,Xu G,Li J

    更新日期:2007-01-01 00:00:00

  • Eukaryote-specific motif of ribosomal protein S15 neighbors A site codon during elongation and termination of translation.

    abstract::The eukaryotic ribosomal protein S15 is a key component of the decoding site in contrast to its prokaryotic counterpart, S19p, which is located away from the mRNA binding track on the ribosome. Here, we determined the oligopeptide of S15 neighboring the A site mRNA codon on the human 80S ribosome with the use of mRNA ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2010.02.031

    authors: Khairulina J,Graifer D,Bulygin K,Ven'yaminova A,Frolova L,Karpova G

    更新日期:2010-07-01 00:00:00

  • [Gratuitous induction of beta-glucuronidase of Escherichia coli K 12 and the double repression mechanism].

    abstract::Using natural inducers of beta-glucuronidase, methyl-glucuronide and fructuronate, under gratuitous conditions (without metabolic conversion of these two compounds), we corroborate the fact that both molecules are required simultaneously in order to derepress the enzyme synthesis to a maximum level. Structurally relat...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(77)80287-3

    authors: Mandrand-Berthelot MA,Novel G,Novel M

    更新日期:1977-01-01 00:00:00

  • The adaptive response in E. coli.

    abstract::The adaptive response appears in E. coli after exposure to low levels of alkylating agents. This system is under the positive control of the ada gene. At least two enzymes are induced during the response: 3-methyladenine DNA glycosylase II and O6-methylguanine DNA methyltransferase. The latter is also the product of t...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/s0300-9084(85)80080-8

    authors: Defais M

    更新日期:1985-03-01 00:00:00

  • [Characterization of cell wall constituents involved in the flocculation of Saccharomyces uvarum yeast strains].

    abstract::Cell walls of flocculent strains (0006) and non flocculent strains (0019) of Saccharomyces uvarum (Carlsbergensis), grown in different media and taken in both growth and stationary phases, were treated with water and with 2 per cent (W/V) potassium hydroxide. This treatment yielded four fractions (FI, FII, FIII and FR...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(81)80055-7

    authors: Amri MA,Bonaly R,Duteurtre B,Moll M

    更新日期:1981-07-01 00:00:00

  • Spin-labelled sulfur containing neoglycolipids.

    abstract::A neoglycolipid of structure beta-D-Glcp-S-(CH2)3N(OH)(CH2)4-O-cholest-5-en-3 beta-yl has been prepared in fair overall yield by reduction of the nitrone obtained by condensation of beta-D-Glcp-S-(CH2)3NHOH and OCH-(CH2)3-O-cholest-5-en-3 beta-yl. This synthetic procedure is very flexible, allowing a large range of le...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(92)90184-g

    authors: Tronchet JM,Zsély M,Ricca A,Barbalat-Rey F,Geoffroy M

    更新日期:1992-01-01 00:00:00

  • FasL on the surface of Tag7 (PGRP-S)-activated lymphocytes induces necroptosis in HLA-negative tumor cells with the involvement of lysosomes and mitochondria.

    abstract::Recently we have found that cytokine IL-2 and innate immunity protein Tag7 activate cytotoxic lymphocytes that kill HLA-negative tumor cells, inducing both apoptosis and necroptosis. Here we decrypt the processes, taking part in necroptosis execution after FasL-Fas interaction. Necroptosis begins with RIPK1 activation...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2018.07.003

    authors: Sharapova TN,Romanova EA,Sashchenko LP,Yashin DV

    更新日期:2018-09-01 00:00:00

  • Some novel transcription attenuation mechanisms used by bacteria.

    abstract::A variety of transcription attenuation mechanisms are used by bacteria to regulate gene and operon expression. This review summarizes previous and current studies designed to elucidate the features of the specific attenuation mechanisms that regulate expression of the tryptophanase (tna) operon of Escherichia coli and...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/s0300-9084(97)86725-9

    authors: Yanofsky C,Konan KV,Sarsero JP

    更新日期:1996-01-01 00:00:00

  • Proteins involved in sleep homeostasis: Biophysical characterization of INC and its partners.

    abstract::The insomniac protein of Drosophila melanogaster (INC) has a crucial role in sleep homeostasis as flies lacking the inc gene exhibit strikingly reduced and poorly consolidated sleep. Nevertheless, in vitro characterizations of INC biophysical properties and partnerships have not been yet reported. Here we report the h...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2016.09.013

    authors: Pirone L,Smaldone G,Esposito C,Balasco N,Petoukhov MV,Spilotros A,Svergun DI,Di Gaetano S,Vitagliano L,Pedone EM

    更新日期:2016-12-01 00:00:00

  • Use of a new integrational vector to investigate compartment-specific expression of the Bacillus subtilis spoIIM gene.

    abstract::The product of the spoIIM gene of Bacillus subtilis is required for complete septum migration and forespore engulfment during sporulation. To investigate whether expression of spoIIM is required in the forespore compartment of the sporangium, we have constructed a new integrational vector, pKSV7, which contains temper...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(92)90143-3

    authors: Smith K,Youngman P

    更新日期:1992-07-01 00:00:00

  • Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA.

    abstract::A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicu...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/0300-9084(93)90014-j

    authors: Felden B,Florentz C,Westhof E,Giegé R

    更新日期:1993-01-01 00:00:00

  • Conformational features of bradykinin. A circular dichroism study of some peptide fragments and structural analogues of bradykinin.

    abstract::The vasoactive hormone bradykinin, its N-and C-terminal fragments and some structural analogues were studied by Circular Dichroism. Conformational features of the peptide can be detected by comparative analysis of the various CD spectra recorded as a function of aqueous pH, solvent and temperature. It is shown that th...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(79)80316-8

    authors: Lintner K,Fermandjian S,Regoli D

    更新日期:1979-01-01 00:00:00

  • Attenuated mitochondrial NADP+-dependent isocitrate dehydrogenase activity induces apoptosis and hypertrophy of H9c2 cardiomyocytes.

    abstract::Oxidative stress, characterized by the accumulation of reactive oxygen species (ROS), is known to have numerous detrimental effects on the myocardium such as the induction of apoptotic cell death, hypertrophy, fibrosis, dysfunction, and dilatation. Over the past several years, we have shown that mitochondrial NADP(+)-...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2013.11.016

    authors: Lee JH,Park JW

    更新日期:2014-04-01 00:00:00

  • Expression of the MuIFN alpha 7 gene in Bacillus subtilis using the levansucrase system.

    abstract::The mouse interferon alpha 7 gene, the signal sequence of which has been removed by oligonucleotide-directed mutagenesis, was introduced into a Bacillus subtilis secretion vector containing the promoter and the signal sequence of the B. subtilis levansucrase gene. Different B. subtilis strains were transformed with th...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/0300-9084(89)90091-6

    authors: Dion M,Rapoport G,Doly J

    更新日期:1989-06-01 00:00:00

  • cDNA sequence and molecular modeling of a nerve growth factor from Bothrops jararacussu venomous gland.

    abstract::The complete nucleotide sequence of a nerve growth factor precursor from Bothrops jararacussu snake (Bj-NGF) was determined by DNA sequencing of a clone from cDNA library prepared from the poly(A) + RNA of the venom gland of B. jararacussu. cDNA encoding Bj-NGF precursor contained 723 bp in length, which encoded a pre...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(02)01429-3

    authors: Kashima S,Soares AM,Roberto PG,Pereira JO,Astolfi-Filho S,Cintra AO,Fontes MR,Giglio JR,de Castro França S

    更新日期:2002-07-01 00:00:00

  • Amino acid sequence of rat thymus histone H2B and identification of the in vitro phosphorylation sites.

    abstract::The amino acid sequence of rat thymus histone obtained in highly purified form by preparative electrophoresis, was determined. This sequence is identical to the sequence of calf thymus histone H2B. The in vitro phosphorylation of the rat histone with a cyclic AMP-dependent protein kinase isolated from rat pancreas led...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(79)80313-2

    authors: Martinage A,Mangeat P,Sautière P,Marchis-Mouren G,Biserte G

    更新日期:1979-01-01 00:00:00

  • Insights into the fatty acid chain length specificity of the carboxylesterase PA3859 from Pseudomonas aeruginosa: A combined structural, biochemical and computational study.

    abstract::The open reading frame PA3859 of Pseudomonas aeruginosa encodes an intracellular carboxylesterase belonging to a group of microbial enzymes (EC 3.1.1.1) that catalyze the hydrolysis of aliphatic and aromatic esters with a broad substrate specificity. With few exceptions, for this class of enzymes, belonging to the α/β...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2010.09.001

    authors: Pesaresi A,Lamba D

    更新日期:2010-12-01 00:00:00

  • Thiolation of low-density lipoproteins and their interaction with L2C leukemic lymphocytes.

    abstract::We present here, a new method for coupling sulfhydryl groups (SH) to low-density lipoprotein (LDL) surface. This method uses homocysteine thiolactone (HCTL) which reacts with lysine residues in a very mild manner, and permits the selection of the number of SH bound per LDL. Under our experimental conditions (8 SH/LDL)...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(86)80166-3

    authors: Vidal M,Sainte-Marie J,Philippot J,Bienvenue A

    更新日期:1986-05-01 00:00:00

  • The influence of adenosine on intermediary metabolism of isolated hepatocytes.

    abstract::The effect of adenosine was tested on the energetic metabolism of fed rat liver cells after isolation. The cells were incubated in a buffered saline medium with glucose (5 mM) and adenosine (1 mM) for 30 minutes at 37 degrees C. This increased the concentration of the adenylic nucleotides ATP (+57 per cent, ADP (+39 p...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/s0300-9084(80)80286-0

    authors: Marchand JC,Lavoinne A,Giroz M,Matray F

    更新日期:1979-01-01 00:00:00

  • Prostaglandin E synthases: Understanding their pathophysiological roles through mouse genetic models.

    abstract::Prostaglandin E synthase (PGES), which converts cyclooxygenase (COX)-derived prostaglandin H(2) (PGH(2)) to PGE(2), is known to comprise a group of at least three structurally and biologically distinct enzymes. Two of them are membrane-bound and have been designated as mPGES-1 and mPGES-2. mPGES-1 is a perinuclear pro...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2010.02.007

    authors: Hara S,Kamei D,Sasaki Y,Tanemoto A,Nakatani Y,Murakami M

    更新日期:2010-06-01 00:00:00

  • The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells.

    abstract::Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2005.03.015

    authors: Forterre P

    更新日期:2005-09-01 00:00:00

  • Alterations of endogenous sphingolipid metabolism in cardiometabolic diseases: Towards novel therapeutic approaches.

    abstract::The increasing prevalence of obesity and metabolic diseases is a worldwide public health concern, and the advent of new analytical technologies has made it possible to highlight the involvement of some molecules, such as sphingolipids (SL), in their pathophysiology. SL are constituents of cell membranes, lipoproteins ...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2019.10.003

    authors: Le Barz M,Boulet MM,Calzada C,Cheillan D,Michalski MC

    更新日期:2020-02-01 00:00:00

  • Impact of protein dynamics on secondary structure prediction.

    abstract::Protein 3D structures support their biological functions. As the number of protein structures is negligible in regards to the number of available protein sequences, prediction methodologies relying only on protein sequences are essential tools. In this field, protein secondary structure prediction (PSSPs) is a mature ...

    journal_title:Biochimie

    pub_type: 杂志文章

    doi:10.1016/j.biochi.2020.09.006

    authors: de Brevern AG

    更新日期:2020-12-01 00:00:00

  • Expanding the role of Src and protein-tyrosine phosphatases balance in modulating osteoblast metabolism: lessons from mice.

    abstract::The widespread nature of protein phosphorylation/dephosphorylation underscores its key role in cell signaling metabolism, growth and differentiation. Tyrosine phosphorylation of cytoplasmic proteins is a critical event in the regulation of intracellular signaling pathways activated by external stimuli. An adequate bal...

    journal_title:Biochimie

    pub_type: 杂志文章,评审

    doi:10.1016/j.biochi.2010.01.002

    authors: Zambuzzi WF,Milani R,Teti A

    更新日期:2010-04-01 00:00:00