Genomes and Genes
Summary: Incorporation of biotinyl groups into molecules.
- Nonne N, Ameyar Zazoua M, Souidi M, Harel Bellan A. Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res. 2010;38:e20 pubmed publisher..Our 'TAP-Tar' procedure allows the specific pull down of mRNA targets of miRNA. It is useful for validation of targets predicted in silico, and, potentially, for discovery of previously uncharacterized targets. ..
- Baeza A, Izquierdo Barba I, Vallet Regi M. Biotinylation of silicon-doped hydroxyapatite: a new approach to protein fixation for bone tissue regeneration. Acta Biomater. 2010;6:743-9 pubmed publisher..Bioceramic biotinylation has been performed by esterification reaction between the OH groups of hydroxyapatite and COOH groups of ..
- Huang B, Chen C. Detection of protein S-nitrosation using irreversible biotinylation procedures (IBP). Free Radic Biol Med. 2010;49:447-56 pubmed publisher..Then we developed irreversible biotinylation procedures (IBP) to prevent this interference, in which irreversible biotinylation was used to instead of ..
- Matthies H, Moore J, Saunders C, Matthies D, Lapierre L, Goldenring J, et al. Rab11 supports amphetamine-stimulated norepinephrine transporter trafficking. J Neurosci. 2010;30:7863-77 pubmed publisher..Our data demonstrate that AMPH leads to an increase of NET in endosomes of single boutons and varicosities in a Rab11-dependent manner. ..
- So P, Kalber T, Hunt D, Farquharson M, Al Ebraheem A, Parkes H, et al. Efficient and rapid labeling of transplanted cell populations with superparamagnetic iron oxide nanoparticles using cell surface chemical biotinylation for in vivo monitoring by MRI. Cell Transplant. 2010;19:419-29 pubmed publisher..No significant detrimental effects on cell viability or death were observed following cell biotinylation. SPIO-labeled cells exhibited signal loss compared to non-SPIO-labeled cells by MRI in vitro...
- Pestinger V, Wijeratne S, Rodriguez Melendez R, Zempleni J. Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes. J Nutr Biochem. 2011;22:328-33 pubmed publisher..We previously reported biotinylation of lysine (K) residues in histones H2A, H3 and H4 by holocarboxylase synthetase and demonstrated that K12-..
- Kahnt J, Aguiluz K, Koch J, Treuner Lange A, Konovalova A, Huntley S, et al. Profiling the outer membrane proteome during growth and development of the social bacterium Myxococcus xanthus by selective biotinylation and analyses of outer membrane vesicles. J Proteome Res. 2010;9:5197-208 pubmed publisher..First, outer membrane proteins were enriched by biotinylation of intact cells using the reagent NHS (N-hydroxysuccinimide)-PEO(12) (polyethylene oxide)-biotin with ..
- Purushothaman S, Annamalai K, Tyagi A, Surolia A. Diversity in functional organization of class I and class II biotin protein ligase. PLoS ONE. 2011;6:e16850 pubmed publisher..This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL...
- Ingaramo M, Beckett D. Biotinylation, a post-translational modification controlled by the rate of protein-protein association. J Biol Chem. 2011;286:13071-8 pubmed publisher..enzyme-substrate pairs the bimolecular rate of association of enzyme with substrate limits post-translational biotinylation. In addition, in noncognate reactions the three enzymes displayed a range of selectivities...
- Petris G, Vecchi L, Bestagno M, Burrone O. Efficient detection of proteins retro-translocated from the ER to the cytosol by in vivo biotinylation. PLoS ONE. 2011;6:e23712 pubmed publisher..We observed specific mono-biotinylation of cytosolically dislocated molecules, resulting in a novel, reliable way of determining the extent of retro-..
- Zheng W, Zou H, Tan Y, Cai W. Identification of microRNA target genes in vivo. Mol Biotechnol. 2011;47:200-4 pubmed publisher..It is useful for validation of targets predicted in silico, and, potentially, for discovery of previously uncharacterized targets. ..
- Bao B, Pestinger V, Hassan Y, Borgstahl G, Kolar C, Zempleni J. Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18. J Nutr Biochem. 2011;22:470-5 pubmed publisher..We tested the hypothesis that HCS interacts physically with histone H3 for subsequent biotinylation. Co-immunoprecipitation experiments were conducted and provided evidence that HCS co-localizes with histone H3 ..
- Maeda Y, Yoshino T, Matsunaga T. In vivo biotinylation of bacterial magnetic particles by a truncated form of Escherichia coli biotin ligase and biotin acceptor peptide. Appl Environ Microbiol. 2010;76:5785-90 pubmed publisher..coli biotin ligase can attach biotin molecules to a lysine residue of biotin acceptor peptide (BAP), and biotinylation of particular BAP-fused proteins in cells was carried out by coexpression of E...
- Schliemann C, Roesli C, Kamada H, Borgia B, Fugmann T, Klapper W, et al. In vivo biotinylation of the vasculature in B-cell lymphoma identifies BST-2 as a target for antibody-based therapy. Blood. 2010;115:736-44 pubmed publisher..Here, we describe the results of a chemical proteomic study, based on the in vivo biotinylation of vascular proteins in lymphoma-bearing mice followed by mass spectrometric and bioinformatic analysis, to ..
- Smelyanski L, Gershoni J. Site directed biotinylation of filamentous phage structural proteins. Virol J. 2011;8:495 pubmed publisher..The in vivo and in vitro biotinylation of the various phages were compared...
- Huang C, Jacobson K. Detection of protein-protein interactions using nonimmune IgG and BirA-mediated biotinylation. Biotechniques. 2010;49:881-6 pubmed publisher..Since this method does not require specific antibodies and is inexpensive, sensitive, and reliable, it should be useful for detecting protein-protein interactions in cells. ..
- Filenko N, Kolar C, West J, Smith S, Hassan Y, Borgstahl G, et al. The role of histone H4 biotinylation in the structure of nucleosomes. PLoS ONE. 2011;6:e16299 pubmed publisher..It has been shown that biotinylation of histone H4 at lysine-12 in histone H4 (K12Bio-H4) is associated with repression of a number of genes...
- Guo Y, Ye J, Divin C, Huang B, Thomas T, Baker J, et al. Real-time biomolecular binding detection using a sensitive photonic crystal biosensor. Anal Chem. 2010;82:5211-8 pubmed publisher..By all important metrics for sensitivity, we anticipate this photonic crystal biosensor will provide new capabilities for highly sensitive measurements of biomolecular binding. ..
- Strübbe G, Popp C, Schmidt A, Pauli A, Ringrose L, Beisel C, et al. Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci U S A. 2011;108:5572-7 pubmed publisher..the dynamic aspects underlying PcG composition and function we have established an inducible version of the biotinylation tagging approach to purify Polycomb and associated factors from Drosophila embryos...
- Kuroishi T, Rios Avila L, Pestinger V, Wijeratne S, Zempleni J. Biotinylation is a natural, albeit rare, modification of human histones. Mol Genet Metab. 2011;104:537-45 pubmed publisher..Recently, a team of investigators failed to detect biotinylated histones and proposed that biotinylation is not a natural modification of histones, but rather an assay artifact...
- Zempleni J, Chew Y, Bao B, Pestinger V, Wijeratne S. Repression of transposable elements by histone biotinylation. J Nutr. 2009;139:2389-92 pubmed publisher..Here, we review recent findings that biotinylation of lysine-12 in histone H4 (H4K12bio) is an epigenetic mechanism to repress long terminal repeat (LTR) ..
- Xu W, Cao L, Chen L, Li J, Zhang X, Qian H, et al. Isolation of circulating tumor cells in patients with hepatocellular carcinoma using a novel cell separation strategy. Clin Cancer Res. 2011;17:3783-93 pubmed publisher..It is likely clinically useful in diagnosis and monitoring of HCC and may have a role in clinical decision making. ..
- Bao B, Rodriguez Melendez R, Zempleni J. Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells. J Nutr Biochem. 2012;23:635-9 pubmed publisherHolocarboxylase synthetase (HCS) plays an essential role in catalyzing the biotinylation of carboxylases and histones...
- Emerman A, Zhang Z, Chakrabarti O, Hegde R. Compartment-restricted biotinylation reveals novel features of prion protein metabolism in vivo. Mol Biol Cell. 2010;21:4325-37 pubmed publisher..Thus, spatiotemporal tagging has uncovered novel aspects of normal and mutant PrP metabolism and should be readily applicable to the analysis of minor topologic isoforms of other proteins. ..
- Ooi S, Henikoff J, Henikoff S. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res. 2010;38:e26 pubmed publisher..elegans H3.3 gene fused to BioTag, a 23-amino-acid peptide serving as a biotinylation substrate for BirA, in vivo in worms. We found that the fusion BioTag::H3...
- Papalia G, Myszka D. Exploring minimal biotinylation conditions for biosensor analysis using capture chips. Anal Biochem. 2010;403:30-5 pubmed publisherUsing Biacore's new regenerateable streptavidin capture (CAP) sensor chips, we investigated a number of biotinylation conditions for target ligands...
- Strassberger V, Trüssel S, Fugmann T, Neri D, Roesli C. A novel reactive ester derivative of biotin with reduced membrane permeability for in vivo biotinylation experiments. Proteomics. 2010;10:3544-8 pubmed publisher..A novel, triply charged biotinylation reagent, NHS-?-Ala-(L-Asp)(3)-biotin, was synthesized and validated in terms of its applicability for in vivo ..
- ..These protocols can be applied not only to labeling in vitro or in tissue culture, but also to in vivo labeling of whole laboratory animals or to ex vivo labeling of surgically resected organs. ..
- Takatsuki H, Tanaka H, Rice K, Kolli M, Nalabotu S, Kohama K, et al. Transport of single cells using an actin bundle-myosin bionanomotor transport system. Nanotechnology. 2011;22:245101 pubmed publisher..Cargo unloading from bundles was achieved by incubation with Triton X-100. These data suggest that actin bundling may improve the ability of the myosin motor system for nanotransport applications...
- Bratthauer G. The avidin-biotin complex (ABC) method and other avidin-biotin binding methods. Methods Mol Biol. 2010;588:257-70 pubmed publisher..Finally, biotinylated tyramide used in conjunction with peroxidase precipitates even greater amounts of biotin molecules for detection by enzyme-labeled avidin molecules. ..
- Volkmann G, Liu X. Protein C-terminal labeling and biotinylation using synthetic peptide and split-intein. PLoS ONE. 2009;4:e8381 pubmed publisher..Protein biotinylation and immobilization on a streptavidin-coated surface were also achieved in a cell lysate without prior ..
- Delli Bovi T, Spalding M, Prigge S. Overexpression of biotin synthase and biotin ligase is required for efficient generation of sulfur-35 labeled biotin in E. coli. BMC Biotechnol. 2010;10:73 pubmed publisher..7 Ci/mmol, two orders of magnitude higher than previously published methods. The biotinylation domain (PfBCCP-79) from the Plasmodium falciparum acetyl-CoA carboxylase (ACC) was expressed in E...
- Zhang Y, Bekku Y, Dzhashiashvili Y, Armenti S, MENG X, Sasaki Y, et al. Assembly and maintenance of nodes of ranvier rely on distinct sources of proteins and targeting mechanisms. Neuron. 2012;73:92-107 pubmed publisher..In mature nodes, components turnover slowly and are replenished via transport. ..
- Ibrahim E, Babaei Jadidi R, Nateri A. The streptavidin/biotinylated DNA/protein bound complex protocol for determining the association of c-JUN protein with NANOG promoter. Curr Protoc Stem Cell Biol. 2013;Chapter 1:Unit 1B.10 pubmed publisher..This streptavidin/biotinylated DNA/protein-bound complex protocol can be used for detecting the interactions between multiple transcription factors and their DNA binding sites. ..
- Liu J, Chen L, Lie P, Dun B, Zeng L. A universal biosensor for multiplex DNA detection based on hairpin probe assisted cascade signal amplification. Chem Commun (Camb). 2013;49:5165-7 pubmed publisher..The implementation of tag/anti-tag DNA and gold nanoparticle reporters permits a universal platform for multiplex genotyping without instrumentation. ..
- Maruta C, Saito Y, Hata S, Gotoh N, Suzuki T, Yamamoto T. Constitutive cleavage of the single-pass transmembrane protein alcadein? prevents aberrant peripheral retention of Kinesin-1. PLoS ONE. 2012;7:e43058 pubmed publisher..This role might exemplify the functional relevance of the constitutive cleavage of single-pass transmembrane proteins. ..
- McNamara M, Tzeng S, Maier C, Zhang L, Bermudez L. Surface proteome of "Mycobacterium avium subsp. hominissuis" during the early stages of macrophage infection. Infect Immun. 2012;80:1868-80 pubmed publisher..In this study, the selective biotinylation of surface-exposed proteins, streptavidin affinity purification, and shotgun mass spectrometry were used to ..
- Tanaka K, Yokoi S, Morimoto K, Iwata T, Nakamoto Y, Nakayama K, et al. Cell surface biotinylation by azaelectrocyclization: easy-handling and versatile approach for living cell labeling. Bioorg Med Chem. 2012;20:1865-8 pubmed publisher..Versatile method for living cell labeling has been established. Cell surfaces are initially biotinylated by azaelectrocyclization, and then treated with the fluorescence-labeled avidin or the anti-biotin antibody. ..
- Yu F, Järver P, Nygren P. Tailor-making a protein a-derived domain for efficient site-specific photocoupling to Fc of mouse IgG?. PLoS ONE. 2013;8:e56597 pubmed publisher..To exemplify functionalization of a mIgG? antibody via site-specific biotinylation, the Z(F5I-Q32C-MBP) protein was first biotinylated using an amine reactive reagent and subsequently ..
- Senevirathne C, Pflum M. Biotinylated phosphoproteins from kinase-catalyzed biotinylation are stable to phosphatases: implications for phosphoproteomics. Chembiochem. 2013;14:381-7 pubmed publisher..Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag...
- Altgärde N, Nilebäck E, de Battice L, Pashkuleva I, Reis R, Becher J, et al. Probing the biofunctionality of biotinylated hyaluronan and chondroitin sulfate by hyaluronidase degradation and aggrecan interaction. Acta Biomater. 2013;9:8158-66 pubmed publisher..b>Biotinylation is a convenient method for immobilizing molecules to surfaces...
- Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M. Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy. Methods Enzymol. 2014;535:167-77 pubmed publisher..Labeled PDGF was successfully validated and can be utilized in various microscopical techniques. ..
- Moeller H, Slengerik Hansen J, Aroankins T, Assentoft M, MacAulay N, Moestrup S, et al. Regulation of the Water Channel Aquaporin-2 via 14-3-3Î¸ and -Î¶. J Biol Chem. 2016;291:2469-84 pubmed publisher..In conclusion, this study demonstrates phosphorylation-dependent interactions of AQP2 with 14-3-3Î¸ and -Î¶. These interactions play divergent roles in modulating AQP2 trafficking, phosphorylation, ubiquitylation, and degradation. ..
- Karhemo P, Ravela S, Laakso M, Ritamo I, Tatti O, Mäkinen S, et al. An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis. J Proteomics. 2012;77:87-100 pubmed publisher..The unbiased identification and validation of both known and novel metastasis-associated proteins indicate a reliable approach for the identification of differentially expressed surface proteins. ..
- Lau P, Cheung P. Elucidating combinatorial histone modifications and crosstalks by coupling histone-modifying enzyme with biotin ligase activity. Nucleic Acids Res. 2013;41:e49 pubmed publisher..PTMs and crosstalks among histone PTMs, we have developed a novel nucleosome purification method called Biotinylation-assisted Isolation of CO-modified Nucleosomes (BICON)...
- Sato A, Aoki J, Ebina K. Synthetic biotinylated peptide compound, BP21, specifically recognizes lysophosphatidylcholine micelles. Chem Biol Drug Des. 2012;80:417-25 pubmed publisher..Further study of the interaction between biotinylated P21 and lysophosphatidylcholine micelles may provide important information for the prevention and treatment for many inflammatory diseases caused by lysophosphatidylcholine micelles. ..