fluorophore (New England Biolabs)


Name:
SNAP Surface 549
Description:
SNAP Surface 549 50 nmol
Catalog Number:
s9112s
Price:
344
Category:
Fluorochromes
Size:
50 nmol
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Structured Review

SNAP Surface 549 50 nmol
https://www.bioz.com/result/fluorophore/product/New England Biolabs
Average 94 stars, based on 1 article reviews
Price from $9.99 to $1999.99
Images
1) Product Images from "Evolution and Characterization of a Benzylguanine-binding RNA Aptamer"
Article Title: Evolution and Characterization of a Benzylguanine-binding RNA Aptamer
Journal: Chemical communications (Cambridge, England)
doi: 10.1039/c5cc07605f

Figure Legend Snippet: Cartoon of a bG-binding RNA aptamer and results from SELEX. (A) A bG-binding RNA aptamer can be used to target small molecule derivatives of bG to RNAs of interest. R represents a functional group such as a fluorophore or biotin. (B) Quantification of the fraction of RNA retained on bG agarose following each round of SELEX.
Techniques Used: Binding Assay, Functional Assay

Figure Legend Snippet: FP competition assay for monitoring specificity of JX1 for bG. (A) Cartoon showing how an effective competitor of Atto488-bG for JX1 binding prevents binding of the RNA to the fluorophore results in low FP. (B) Results from the competition assay for selected guanine-containing molecules. High ΔFP values result from Atto488-bG binding to JX1 and lack of inhibition from the competitor. Each bar graph represents the average from three separate experiments and error bars represent ± S.D. N.D., Not Determined.
Techniques Used: Competitive Binding Assay, Binding Assay, Inhibition
2) Product Images from "Dynamics and consequences of spliceosome E complex formation"
Article Title: Dynamics and consequences of spliceosome E complex formation
Journal: eLife
doi: 10.7554/eLife.27592

Figure Legend Snippet: Counting statistics for the number of steps observed during loss of fluorescence from either U1-double DHFR or BBP-SNAP f binding events in three-color CoSMoS experiments. ( A ) Number of steps observed during loss of U1 fluorescence. Each U1 molecule contains two fluorophores, which can result in either 1 or two steps. 91% of U1 binding events are consistent with presence of only a single U1 molecule on the pre-mRNA. ( B ) Number of steps observed during loss of BBP fluorescence. Each BBP molecule contains a single fluorophore. 88% of BBP binding events are consistent with presence of only a single BBP molecule on the pre-mRNA.
Techniques Used: Fluorescence, Binding Assay

Figure Legend Snippet: Single molecule analysis of BBP-SNAP f binding dynamics. ( A ) Cartoon of a two-color CoSMoS experiment for observing BBP binding dynamics. BBP was labeled with a single green-excited fluorophore while RNA was immobilized to the slide surface and contained a single, red-excited Cy5 fluorophore. ( B ) Graphic representation of capped RNAs with variable BS and ΨBS used in these experiments and their corresponding label number. RNA sequences are given in Supplementary file 1 . ( C ) Bar graph comparing the relative number of BBP binding events observed on each RNA depicted in panel ( B ). ( D ) Rastergram depicting BBP binding events on RNAs containing both a BS and ΨBS (RNA 3). ( E ) Rastergram depicting BBP binding events on RNAs containing only the BS (RNA 9). ( F ) Rastergram depicting BBP binding events on RNAs containing only the ΨBS (RNA 10). ( G ) Probability density histogram of dwell times for BBP on RNAs with variable BS and ΨBS. Lines represent fits of the distributions of dwell times to equations containing one or two exponential terms. ( H–J ) Bar graph comparison of the fit parameters (τ 1 , panel H; τ 2 , panel I; the τ 2 amplitude A 2 , panel J) obtained from analysis of the dwell time distributions of BBP binding events on RNAs 3, 9, and 10. Details of the fit parameters for data shown in ( H–J ) can be found in Supplementary file 3 . Error bars in ( C, G ) represent the error in counting statistics as given by the variance of a binomial distribution. Bars in ( H–J ) represent the fit parameters ± S.D.
Techniques Used: Binding Assay, Labeling

Figure Legend Snippet: Single molecule analysis of U1 binding after ablation of the 5' end of the snRNA. ( A ) Cartoon of a two-color CoSMoS experiment for observing U1 binding dynamics. U1 was labeled with two green-excited fluorophores while the RNA was immobilized to the slide surface and contained a single, red-excited Cy5 fluorophore. ( B ) Confirmation of U1 ablation by primer extension. Primer extension of the U2 snRNA is included as a loading control. Quantification of the band intensities indicate that ≥96% of the U1 snRNA was cleaved by RNase H. ( C ) Bar graph comparing the relative number of U1 binding events observed on RNAs 3 or 7, in the presence or absence of CA and/or the RNase H ablation oligo. ( D–F ) Bar graph comparison of the fit parameters (τ 1 , panel D; τ 2 , panel E; the τ 2 amplitude A 2 , panel F) obtained from analysis of the dwell time distributions of U1 binding events. Details of the fit parameters for data shown in ( D–F ) can be found in Supplementary file 2 . Error bars in ( C ) represent the error in counting statistics as given by the variance of a binomial distribution. Bars in ( D–F ) represent the fit parameters ± S.D.
Techniques Used: Binding Assay, Labeling
Related Articles
Labeling:Article Title: Dynamics and consequences of spliceosome E complex formation Article Snippet: Preparation and labeling of yeast whole-cell splicing extracts Yeast whole cell extract (WCE) was prepared as previously described ( ). .. SNAPf -tagged proteins were labeled by incubation of the lysate for 30 min at room temperature with the Article Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Article Snippet: Oligonucleotides (IDT Ultramers) for PCR had 50 nt of homology to the target gene C-terminal coding region and 20 nt of homology to the fusion cassette. .. In-frame fusion protein expression and stability was confirmed by immunoblotting for the target protein (e.g., ), and in the case of SNAP fusions, by SDS-PAGE after labeling with Article Title: Pathway of actin filament branch formation by Arp2/3 complex revealed by single-molecule imaging Article Snippet: Arp2/3-SNAP was purified from an S. cerevisiae strain in which the ARC18 locus was modified to produce an Arc18-SNAP fusion protein. .. The complex was labeled in vitro with the Article Title: Single molecule analysis reveals reversible and irreversible steps during spliceosome activation Article Snippet: The lysate buffer was exchanged into 50 mM HEPES/KOH pH 7.9, 50 mM KCl, 10% (v/v) glycerol, and 1 mM DTT by gel filtration using a previously published protocol , aliquoted (42 µL), frozen in liquid N2 , and stored at -80°C. .. In cases where SNAP-tagged proteins were labeled, the lysate was incubated for 30 min at room temperature with the Incubation:Article Title: Dynamics and consequences of spliceosome E complex formation Article Snippet: Preparation and labeling of yeast whole-cell splicing extracts Yeast whole cell extract (WCE) was prepared as previously described ( ). .. SNAPf -tagged proteins were labeled by incubation of the lysate for 30 min at room temperature with the Article Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Article Snippet: For SNAP fusion strains, the protocol was modified in that nuclear protein pellets were resuspended in 1–2 mL of buffer C′ (20 mM HEPES, pH 7.6, 10 mM MgSO4 , 1 mM EGTA, 10% glycerol, 3 mM DTT, and 1 μg ml−1 each of aprotinin, leupeptin, pepstatin A, and antipain). (In pilot experiments, the 20% glycerol concentration and PMSF used in ( ) were found to reduce SNAP labeling.) .. To fluorescently label extracts with SNAP fusion proteins, Article Title: Single molecule analysis reveals reversible and irreversible steps during spliceosome activation Article Snippet: The lysate buffer was exchanged into 50 mM HEPES/KOH pH 7.9, 50 mM KCl, 10% (v/v) glycerol, and 1 mM DTT by gel filtration using a previously published protocol , aliquoted (42 µL), frozen in liquid N2 , and stored at -80°C. .. In cases where SNAP-tagged proteins were labeled, the lysate was incubated for 30 min at room temperature with the Filtration:Article Title: Dynamics and consequences of spliceosome E complex formation Article Snippet: Preparation and labeling of yeast whole-cell splicing extracts Yeast whole cell extract (WCE) was prepared as previously described ( ). .. SNAPf -tagged proteins were labeled by incubation of the lysate for 30 min at room temperature with the Article Title: Single molecule analysis reveals reversible and irreversible steps during spliceosome activation Article Snippet: The lysate buffer was exchanged into 50 mM HEPES/KOH pH 7.9, 50 mM KCl, 10% (v/v) glycerol, and 1 mM DTT by gel filtration using a previously published protocol , aliquoted (42 µL), frozen in liquid N2 , and stored at -80°C. .. In cases where SNAP-tagged proteins were labeled, the lysate was incubated for 30 min at room temperature with the Concentration Assay:Article Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Article Snippet: For SNAP fusion strains, the protocol was modified in that nuclear protein pellets were resuspended in 1–2 mL of buffer C′ (20 mM HEPES, pH 7.6, 10 mM MgSO4 , 1 mM EGTA, 10% glycerol, 3 mM DTT, and 1 μg ml−1 each of aprotinin, leupeptin, pepstatin A, and antipain). (In pilot experiments, the 20% glycerol concentration and PMSF used in ( ) were found to reduce SNAP labeling.) .. To fluorescently label extracts with SNAP fusion proteins, Expressing:Article Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Article Snippet: Oligonucleotides (IDT Ultramers) for PCR had 50 nt of homology to the target gene C-terminal coding region and 20 nt of homology to the fusion cassette. .. In-frame fusion protein expression and stability was confirmed by immunoblotting for the target protein (e.g., ), and in the case of SNAP fusions, by SDS-PAGE after labeling with SDS Page:Article Title: Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription Article Snippet: Oligonucleotides (IDT Ultramers) for PCR had 50 nt of homology to the target gene C-terminal coding region and 20 nt of homology to the fusion cassette. .. In-frame fusion protein expression and stability was confirmed by immunoblotting for the target protein (e.g., ), and in the case of SNAP fusions, by SDS-PAGE after labeling with In Vitro:Article Title: Pathway of actin filament branch formation by Arp2/3 complex revealed by single-molecule imaging Article Snippet: Arp2/3-SNAP was purified from an S. cerevisiae strain in which the ARC18 locus was modified to produce an Arc18-SNAP fusion protein. .. The complex was labeled in vitro with the Article Title: A ligand-based system for receptor-specific delivery of proteins Article Snippet: .. In-vitro labelling For keratinocyte labelling, IL-31K138A SNAP, NGFR121W SNAP or SNAP were coupled with an excess of Microscopy:Article Title: Disconnect between signalling potency and in vivo efficacy of pharmacokinetically optimised biased glucagon-like peptide-1 receptor agonists Article Snippet: Briefly, HEK293-SNAP-GLP-1R cells were transfected with PKA activation FRET biosensor AKAR4-NES (a gift from Dr. Jin Zhang, Addgene plasmid #61620) for 36 h, and FRET signal was recorded before and after ligand addition and expressed ratiometrically after normalisation to well baseline. .. 2.8 Confocal microscopyHEK293-SNAP-GLP-1R cells seeded on coverslips were labelled with FP Assay:Article Title: Evolution and Characterization of a Benzylguanine-binding RNA Aptamer Article Snippet: .. To test how well JX1 binds bG derivatives other than Atto488-bG we carried out the FP assay with a bG derivative containing a structurally and spectrally different |