fluorophore (New England Biolabs)
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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
New England Biolabs
fluorophore
SNAP Surface 549 50 nmol
https://www.bioz.com/result/fluorophore/product/New England Biolabs
Average 98 stars, based on 1 article reviews
Price from $9.99 to $1999.99
SNAP Surface 549 50 nmol
https://www.bioz.com/result/fluorophore/product/New England Biolabs
Average 98 stars, based on 1 article reviews
Price from $9.99 to $1999.99
fluorophore - by Bioz Stars,
2021-06
98/100 stars
Images
1) 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
2) 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
Related Articles
Labeling: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: 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 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 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 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: USP42 protects ZNRF3/RNF43 from R‐spondin‐dependent clearance and inhibits Wnt signalling Article Snippet: For SNAP labelling, HEK293T cells were seeded on Poly‐Lysine coated coverslips in 12‐well plates and transfected with 200 ng empty vector, 100 ng SNAP‐tagged Frizzled, 100 ng GFP‐USP42 and 100 ng of ZNRF3‐HA plasmids. .. 24 h after transfection, cells were incubated in 1 µM 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 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 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 Transfection:Article Title: USP42 protects ZNRF3/RNF43 from R‐spondin‐dependent clearance and inhibits Wnt signalling Article Snippet: For SNAP labelling, HEK293T cells were seeded on Poly‐Lysine coated coverslips in 12‐well plates and transfected with 200 ng empty vector, 100 ng SNAP‐tagged Frizzled, 100 ng GFP‐USP42 and 100 ng of ZNRF3‐HA plasmids. .. 24 h after transfection, cells were incubated in 1 µM |
![Tagged yeast strains have growth rates, nuclear extract protein expression levels, and transcription activities similar to wild-type. (A) Western blot showing that the concentrations of Rpb1 SNAP in Rpb1 SNAP /Spt5 DHFR strain (YSB3403; see Table S5 ) (lane 2) and Rpb1 in parental strain (WT; YF702) are similar. TATA binding protein (TBP) was used as a loading control. Rpb1 was detected by monoclonal antibody 8WG16 ( 66 ) and TBP by a polyclonal anti-TBP antibody ( 67 ). (B) Western blot showing that the concentration of Spt5 DHFR in Rpb1 SNAP /Spt5 DHFR strain is similar to that of Spt5 in the parental strain. The anti-Spt5 antibody ( 68 ) was provided by Grant Hartzog. (C and D) RNA produced in bulk from plasmid transcription by Rpb1 SNAP /Spt5 DHFR (C) and Hek2 SNAP /Spt5 DHFR (D) nuclear extracts in comparison with extracts from corresponding parental strains (WT; see Table S5 ). Where indicated, extracts were labeled with 0.5 μM SNAP-Surface 549 and subsequently depleted of unreacted dye. Bulk in vitro transcription reactions were performed with 400 μM each ATP, CTP, and UTP supplemented with [α- 32 P]- UTP, separated by urea polyacrylamide gel electrophoresis, and visualized by autoradiography. The lower two bands in each lane are the transcripts from the two major transcription start sites of the template. The same volume of nuclear extract preparation was used in each reaction (10 μL in C and 8 μL in D); all extract preparations were 30-40 mg/mL protein. (E) Growth rates (mean ± S.E.; N = 5) of tagged strains relative to the corresponding parental (WT) strain. Colors denote correspondence between parental (YF702, blue; YF4, green) and tagged strains.](https://www.biorxiv.org/content/biorxiv/early/2020/06/02/2020.06.01.127969/F5.large.jpg)
