Abstract:
:An immunofluorescence assay was developed to identify proteins specifically binding to oligonucleoside phosphorodithioate (ODN) aptamers from a bead-bound ODN library. Accordingly, NF-kappaB p50 protein was incubated with either bead-bound NF-kappaB consensus sequence or a bead-bound ODN combinatorial library and adsorption was then assessed using a specific primary antibody and a secondary antibody conjugated with Alexa 488 fluorescent dye. This assay avoids any problems related to fluorescently labeling target proteins. The method is straightforward and readily applicable to other transcription factors and proteins, and the feasibility of its application for high-throughput screening of large aptamer bead-based libraries by flow cytometry is demonstrated.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yang X,Li X,Prow TW,Reece LM,Bassett SE,Luxon BA,Herzog NK,Aronson J,Shope RE,Leary JF,Gorenstein DGdoi
10.1093/nar/gng054keywords:
subject
Has Abstractpub_date
2003-05-15 00:00:00pages
e54issue
10eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::Interaction detection methods have led to the discovery of thousands of interactions between proteins, and discerning relevance within large-scale data sets is important to present-day biology. Here, a spectral method derived from graph theory was introduced to uncover hidden topological structures (i.e. quasi-cliques...
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abstract::Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...
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abstract::SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. S...
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journal_title:Nucleic acids research
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abstract::From a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties. The planning of such an in vitro selection experiment requires some consideration regarding how much DNA template or RNA transcript should be used initially. The ...
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abstract::CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavag...
journal_title:Nucleic acids research
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abstract::The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...
journal_title:Nucleic acids research
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更新日期:1982-09-25 00:00:00
abstract::We have previously shown that hedamycin, a GC-rich DNA-binding antitumor agent, downregulates survivin transcription (Wu et al. (2005) Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence selective DNA-binding antitumor agent, hedamycin: evidence of survivin downregulation associated wit...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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doi:10.1093/nar/gki536
更新日期:2005-05-10 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...
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abstract::A mass culture of human diploid fibroblasts, and eight clones isolated from that mass culture, were examined for methylation patterns in several regions of DNA. Plasmid-inserted cDNA sequences were used as probes for alpha-hCG, beta-globin, A gamma- and G gamma-globin, and beta- and gamma-actin gene regions. Each prob...
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abstract::Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...
journal_title:Nucleic acids research
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更新日期:2020-09-18 00:00:00
abstract::In metazoan cells, only a limited number of mini chromosome maintenance (MCM) complexes are fired during S phase, while the majority remain dormant. Several methods have been used to map replication origins, but such methods cannot identify dormant origins. Herein, we determined MCM7-binding sites in human cells using...
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更新日期:2018-07-27 00:00:00
abstract::Mitochondrial transcription factor A (TFAM) stimulates transcription from mitochondrial DNA (mtDNA) promoters in vitro and in organello. To investigate whether changes of TFAM levels also modulate transcription and replication in situ, the protein was transiently overexpressed in cultured cells. Mitochondrial mRNAs we...
journal_title:Nucleic acids research
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abstract::This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping mitochondrial DNA (mtDNA) of 34 119 bp contains 58 densely packed genes (all without introns) and five unique open reading frames ...
journal_title:Nucleic acids research
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更新日期:2000-07-01 00:00:00
abstract::Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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abstract::The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, cha...
journal_title:Nucleic acids research
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abstract::Release of phosphorothioate antisense oligonucleotides (PS-ASOs) from late endosomes (LEs) is a rate-limiting step and a poorly defined process for productive intracellular ASO drug delivery. Here, we examined the role of Golgi-endosome transport, specifically M6PR shuttling mediated by GCC2, in PS-ASO trafficking and...
journal_title:Nucleic acids research
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更新日期:2020-02-20 00:00:00