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Citations Search

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Am. J. Hum. Genet. 97, 555-66. Biallelic mutations in nuclear pore complex subunit NUP107 cause early-childhood-onset steroid-resistant nephrotic syndrome. 2015

Niyake, N., Tsukaguchi, H., Koshimizu, E., Shono, A., Matsunaga, S., Shiina, M., Mimura, Y., Imamura, S., Hirose, T., Okudela, K., Nozu, K., Akioka, Y., Hattori, M., Yoshikawa, N., Kitamura, A., Cheong, H.I., Kagami, S., Yamashita, M., Fugita, A., Miyatake, S., Tsurusaki, Y., Nakashima, M., Saitsu, H., Ohashi, K., Imamoto, N. and Ryo, A.

Notes: The interaction of NUP107 and NUP133 were investigated by several means. First, in vitro expressed, biotinylated NUP107 was mixed with FLAG-tagged NUP133 and pulled down with Streptavidin MagneSphere® Particles and blotted for reaction with Anti-FLAG antibodies. HeLa cells were transfected with a GFP-NUP107 fusion vector using ViaFect™ Transfection Reagent (no details provided) and immunoprecipitated then blotted to identify NUP133 in the pull down. Subcellular localization of GFP-NUP107 was examined as well. RT-PCR analysis of nup107 splicing variants in zebrafish relied on M-MLV Reverse Transcriptase for cDNA synthesis. (4675)

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Proc. Natl. Acad. Sci. USA 102, 7701-7706. The two-component signal transduction system RR06/HK06 regulates expression of cbpA in Streptococcus pneumoniae. 2005

Standish, A.J., Stroeher, U.H., and Paton, J.C.

Notes: In this study, the binding of the response regulator RR06 to the promoter region of cbpA was investigated. DNA encoding the rr06 gene was cloned into the pGEM®-T Easy vector and transformed into E. coli strain DH5α. Cell lysates were prepared and incubated with a labeled cbpA promoter fragment, and binding was evaluated in an electrophoretic mobility shift assay (EMSA). To further investigate the RR06/cbpA interaction, the cbpA promoter region, or a control rRNA sequence, was biotin labeled and attached to Streptavidin MagneSphere® Paramagnetic Particles. The beads were incubated with E. coli lysates expressing RR06, or with control lysates. After washing, bound proteins were eluted by boiling. Eluted samples were then probed with specific anti-RR06 antisera. (3397)

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J. Biol. Chem. 279(10), 9208-14. Inhibition of HIV-1 replication by cell-penetrating peptides binding Rev. 2004

Roisin A., Robin J.P., Dereuddre-Bosquet N., Vitte A.L., Dormont D., Clayette P. and Jalinot P.

Notes: The authors constructed a library of random heptapeptides using biotin-labeled sense and antisense oligonucleotides. The oligos were then hybridized, filled in with Klenow and cut with BamH I and Xma I, the restriction sites engineered into the oligo ends.  Subsequently, the biotinylated ends were removed by incubation with Streptavidin MagneSphere® Paramagnetic Particles.  Unbound fragments were then ligated upstream of the HIV-1 Tat protein transduction domain and the resultant plasmid transformed into bacteria for propagation. (3079)

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Proc. Natl. Acad. Sci. USA 101(11), 3786-3791. Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system. 2004

Cochella, L. and Green, R.

Notes: The authors initiated translation on a poly(U) mRNA using biotin-labeled phenylalanine tRNA with isolated ribosomes. The reaction was allowed to bind to Streptavidin MagneSphere® Paramagnetic Particles, washed four times and then shaken in buffer to remove the ribosomes.  The isolated rRNA was then extracted with phenol/chloroform, ethanol precipitated and used in RT-PCR. (3082)

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Cell 109, 757-767. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. 2002

Park, J-S, Marr, M.T., and Roberts, J.W.

Notes: Promega's Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to bind a biotinylated DNA template and E. coli RNA polymerase in an open transcriptional complex. The synthesized RNA template was intentionally paused at certain points by nucleotide deprivation. The ability of the DNA repair protein Mfd to assist in elongation of the paused complex and release the radiolabeled RNA transcript from the strepavidin beads as the template was elongated were measured by gel electrophoresis. In the absence of NTP substrates, release of the transcript from the beads was also demonstrated. The ability of Mfd to act on the RNA transcript by both elongation and release was tested in the presence of GreB, another DNA repair enzyme with cleavage activity, as well as by protein interference of both an engineered RE site and sigma 70. (2492)

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Nucl. Acids Res. 30, 5017-5028. The 3´ untranslated region of human vimentin mRNA interacts with protein complexes containing eEF-1g and HAX-1 2002

Al-Maghrebi, M., Brule, H., Padkina, M., Allen, C., Holmes, W.M. and Zehner, Z.E.

Notes: One hundred and fifty picomoles of a synthetic, biotinylated oligonucleotide were hybridized to an in vitro-transcribed Vimentin 3' untranslated region (3´ UTR) and captured with Streptavidin MagneSphere® Paramagnetic Particles. The captured Vimentin 3´ UTRs were then washed and added to HeLa whole cell extracts. Proteins that bound to the  constructs were eluted with room temperature or boiling water and analyzed by SDS-PAGE and Western blotting. Recipes for a binding buffer and wash buffer are included. Details on washing and eluting protein from the Streptavidin MagneSphere® Paramagnetic Particles are also provided. (2656)

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Genes Dev. 14, 1156-1166. CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex. 2000

Masternak, K., Muhlethaler-Mottet, A., Villard, J., Zufferey, M., Steimle, V. and Reith, W.

Notes: Streptavidin MagneSphere® Paramagnetic Particles were used for a pulldown assay to isolate protein-promoter DNA complexes from an extract. The DNA used was a promoter DNA which was 5' end-labeled with biotin. (2152)

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J. Biol. Chem. 274, 26369-26377. Antiproliferative activity of G-rich oligonucleotides correlates with protein binding. 1999

Bates, P.J., Kahlon, J.B., Thomas, S.D., Trent, J.O. and Miller, D.M.

Notes: In this paper, Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to capture biotinylated oligo-protein complexes. The HeLa Nuclear Extract, Gel Shift Assay Grade, was used for EMSAs and Southwestern blotting. (1468)

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J. Biol. Chem. 274, 6667-6677. Competition between thyroid hormone receptor-associated protein (TRAP) 220 and transcriptional intermediary factor (TIF) 2 for binding to nuclear receptors. Implications for the recruitment of TRAP and p160 coactivator complexes. 1999

Treuter, E., Johansson, L., Thomsen, J. S. Warnmark, A., Leers, J., Pelto Huikko, M., Sjoberg, M., Wright, A. P., Spyrou, G., Gustafsson, J. A.

Notes: The authors used the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) in their studies on DNA dependent protein-protein interactions. Approximately 50μg of COS-1 cell extract transiently expressing TRAP was incubated with 1μg of double-stranded bintinylated DR4 oligonucleotides. The complex was immobilized on SA-PMP's and used to analyze binding of [35S]-labeled in vitro translated proteins. After washing, the radiolabeled proteins were eluted and analysed on SDS-PAGE gels by fluorography and by detection with TRAP220 specific antibodies. (0233)

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Mol. Cell 3, 371-378. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II 1999

Dye, M.J. and Proudfoot, N.J.

Notes: The MagneSphere® Paramagnetic Particles (SA-PMPs) were used to select for specific nuclear run-on transcripts that hybridize to a specific biotinylated probe. The captured material was eluted in water and hybridized to probes on membranes. The procedure details preparation of the SA-PMPs prior to capture of the labeled run-on transcripts. (1210)

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Mol. Cell 4, 573-584. The balance between two isoforms of the Drosophila RNA-binding protein How controls tendon cell differentiation. 1999

Nabel-Rosen, H., Dorevitch, N., Reuveny, A., Volk, T.

Notes: The Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to capture RNA:RNA binding protein complexes formed with biotinylated RNA and tissue extracts. The captured complexes were boiled in SDS sample buffer, electrophoresed and blotted for detection. The results of the capture were also confirmed by in vitro translation of the protein of interest with the TNT® Coupled Reticulocyte Lysate System and doing the same capture. (0639)

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Proc. Natl. Acad. Sci. USA 95, 7463-7468. A chloroplast processing enzyme functions as the general stromal processing peptidase. 1998

Richter, S. and Lamppa, G.K.

Notes: Chloroplast processing enzyme (CPE), was expressed in E. coli as a biotinylated fusion protein, and biotinylation was demonstrated using Promega's SoftLink™ Soft Release Avidin Resin. The singly-biotinylated protein was immobilized onto Streptavidin MagneSphere® Paramagnetic Particles. The immobilized CPE was incubated with the [35S]Methionine-labeled preribulose-1,5-bisphosphate carboxylase/oxygenase activase (preRBCA) and the processed RBCA protein was detected by autoradiography. To further demonstrate the processing, unlabeled preRBCA was processed with the immobilized CPE and the resulting RBCA was analyzed by N-terminal sequencing. The labeled pRBCA was generated with the Rabbit Reticulocyte Lysate System. (0515)

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Plant Mol. Biol. Rep. 16, 341–349. A high throughput procedure for capturing microsatellites from complex plant genomes. 1998

Connell, J.P., Pammi, S., Iqbal, M.J., Huizinga, T., and Reddy, A.S.

Notes: This paper describes a quick method for analyzing plant microsatellites, also referred to as Simple Sequence Repeats (SSRs), using adaptor-ligated genomic DNA, PCR, and the Streptavidin MagneSphere® Paramagnetic Particles. Briefly, 200μg of Streptavidin MagneSphere® Paramagnetic Particles (pre-equilibrated with 6X SSC) were added to 100ng of a PCR product annealed to a biotinylated-repeat oligo. The captured fragments were washed, size-fractionated and used in PCR with AP-11 primers. (3050)

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Clin. Chem. 44, 2471-2479. Characterization and immunological determination of the complex between prostate-specific antigen and alpha2-macroglobulin 1998

Zhang, W.-M., Finne, P., Leinonen, J., Vesalainen, S., Nordling, S., Rannikko, S., Stenman, U.-H.

Notes: Biotinylated antibodies specific to prostate specific antigen (PSA) were coupled to the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs). Complexes of PSA and alpha2-macroglobulin were formed in vitro and reacted with the coated SA-PMPs. Less than 1% of the PSA was not bound by the alpha2-macroglobulin and thus >99% of PSA was sequestered by the alpha2-macroglobulin and unavailable for reaction with the antibodies. (0097)

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J. Immunol. 160, 4719-4729. Direct evidence that functionally impaired CD4+ T cells persist in vivo following induction of peripheral tolerance 1998

Pape, K.A., Merica, R., Mondino, A., Khoruts, A., Jenkins, M.K.

Notes: KJI-26+ cells were removed from lymph node cell suspensions by a panning method using the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs). The SA-PMPs were first coated with a biotinylated Anti-KJI-26 mAb and then added to the lymph node cells at 10 coated SA-PMPs/lymph node cell. The SA-PMPs were captured and the remaining lymph node cell suspension (KJI-26–) was counted and cultured. (0583)

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Genetics 150, 1125-1131. Mouse Brachyury the Second (T2) is a gene next to classical T and a candidate gene for tct. 1998

Rennebeck, G., Lader, E., Fujimoto, A., Lei, E.P., Artzt, K.

Notes: Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to capture biotinylated primer probe in a random access retrieval of genetic information by PCR (rargip) screening [ABE, K., (1992) Rapid isolation of desired sequences from lone linker PCR amplified cDNA mixtures: application to identification and recovery of expressed sequences in cloned genomic DNA. Mamm. Genome 2:252-259]. The pGEM®-T Vector System and PolyATract® mRNA Isolation System were also used. (0513)

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Biochemistry 37, 17754-17764. Novel peptides selected to bind vascular endothelial growth factor target the receptor-binding site. 1998

Fairbrother, W.J., Christinger, H.W., Cochran, A.G., Fuh, G., Keenan, C.J., Quan, C., Shriver, S.K., Tom, J.Y.K., Wells, J.A., Cunningham, B.C.

Notes: A phage-display library was used to screen for binding to biotinylated vascular endothelial cell growth factor (VEGF) immobilized to neutravidin coated plates. The biotinylated VEGF with NHS-SS-Biotin bond could be cleaved with DTT to release the bound phage. Phages were put through two rounds of selection by this method then through three to seven rounds of selection by binding to decreasing amounts of biotinylated VEGF in solution. The Steptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to captured phage eluted with DTT. (1186)

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Clin. Diagn. Lab. Immunol. 5, 636-644.. Selection of recombinant, library-derived antibody fragments against p24 for human immunodeficiency virus type 1 diagnostics. 1998

de Haard, H.J.W., Kazemier, B., Koolen, M.J.M., Nijholt, L.J., Meloen, R.H., van Gemen, B., Hoogenboom, H.R., Arends, J.-W.

Notes: The Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to select single-chain Fv (scFv) fragments capable of binding the major HIV-1 capsid protein, p24. The library was constructed and expressed scFv fragments were screened for their interaction with biotinylated p24. The scFv were either reacted with biotinylated p24 in solution then captured with SA-PMPs for analysis or reacted with the biotinylated p24 already captured on the SA-PMPs. The panning method resulted in a 100 fold enrichment for the soluble interaction then capture and a 10,000-fold enrichment with precaptured complexes. (1260)

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EMBO J. 16, 6849-6859. Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-crosslinking. 1997

Jenkins, T.M., Esposito, D., Engelman, A., Craigie, R.

Notes: Both specific and nonspecific oligonucleotide were synthesized with a 3´-biotin tag. The peptides were used to purify binding proteins via the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs). Many details of the binding and the washing of the particles are provided. (0975)

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EMBO J. 16, 1427-1435. Ligand-independent activation of the oestrogen receptor by mutation of a conserved tyrosine. 1997

White, R. , Sjoberg, M. , Kalkhoven, E. , Parker, M. G.

Notes: Wildtype mouse oestrogen receptors and various tyrosine-replacement mutants were reacted with a biotinylated oestrogen response element and immobilized on the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs). The immobilized complexes were then assayed for the ability to interact with in vitro translated RIP140 and SRC-1 protein in the presence or absence of 17β-estradiol. The capture proteins were analyzed by SDS-PAGE and fluorography. In vitro translations were performed with the TNT® Coupled Reticulocyte Lysate System. (0181)

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J. Biol. Chem. 272, 26727-26733. Sequence of cDNAs encoding components of vascular actin single-stranded DNA-binding factor 2 establish identity to Purα and Purβ. 1997

Kelm, R. J., Jr., Elder, P. K., Strauch, A.R., Getz, M.J.

Notes: Single-stranded 3´-end biotinylated oligonucleotides were captured on the Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) and incubated with heparin-agarose affinity-purified nuclear proteins. The reaction was performed under the conditions used for electrophoretic gel shifts. Proteins were eluted in 1X nonreducing SDS-PAGE sample buffer at 65°C for 3 minutes and analyzed by Southwestern blotting with 32P-labeled oligonucleotides. The ssDNA-affinity capture worked with the oligonucleotides prebound to the particles or after allowing the interactions to occur in solution prior to capture. The pCI Mammalian Expression Vector was used to express the proteins Purα (321 amino acids) and Purβ (324 amino acids) in mouse embryo-derived AKR-2B fibroblasts. Cell extracts were prepared and assayed by Southwestern blotting. The same proteins were in vitro translated with the TNT® Coupled Reticulocyte Lysate System and assayed as well. (0929)

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J. Biol. Chem. 272(42), 26727-26733. Sequence of cDNAs encoding components of vascular actin single-stranded DNA-binding factor 2 establish identity to Pura and Purb. 1997

Kelm, R.J. Jr., Elder, P.K., Strauch, A.R. and Getz, M.J.

Notes: Single-stranded 3'-end biotinylated oligonucleotides were captured on the paramagnetic particles and incubated with heparin-agarose affinity-purified nuclear proteins. The reaction was performed under the conditions used for electrophoretic gel shifts. Proteins were eluted in 1X non-reducing SDS-PAGE sample buffer at 65°C for 3 min and analyzed by Southwestern blotting with 32P-labeled oligonucleotides. The ssDNA-affinity capture apparently worked with the oligonucleotides prebound to the particles or after allowing the interactions to occur in solution prior to capture. (1666)

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Cell 86(3), 485-493. Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. 1996

Ring, B.Z., Yarnell, W.S. and Roberts, J.W.

Notes: Stopped transcription complexes were formed on DNA templates attached to the paramagnetic particles. (1668)

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J. Cell Sci. 109(Pt 1), 73-81. Isolation of the Schizosaccharomyces pombe RAD54 homologue, rhp54+, a gene involved in the repair of radiation damage and replication fidelity. 1996

Muris, D.F.R., Vreeken, K., Carr, A.M., Murray, J.M., Smit, C., Lohman, P.H.M. and Pastink, A.

Notes: The particles were used for further purification of 5'-RACE products. 5'RACE products were amplified with the 5'RACE anchor plasmid and a biotinylated primer. The products were purified with the particles and the non-biotinylated strand was eluted and used as a template for nested amplification of the 5'RACE product. (1667)

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