edc  (Jena Bioscience)


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  • 93
    Name:
    5 Ethynyl 2 deoxycytidine
    Description:

    Catalog Number:
    CLK-N003-10
    Price:
    108.0
    Category:
    Click Chemistry
    Size:
    10 mg
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    Structured Review

    Jena Bioscience edc

    https://www.bioz.com/result/edc/product/Jena Bioscience
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    edc - by Bioz Stars, 2021-06
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    Crystallization Assay:

    Article Title: Structural basis for gene regulation by a B12-dependent photoreceptor
    Article Snippet: CarH:DNA complexes for crystallization were generated by mixing protein and DNA at the desired ratio and incubating the mixture for 1 h on ice in the dark prior to crystallization experiments. .. Preparation of DNA segments for crystallization HPLC-purified single-stranded DNA oligonucleotides without heavy atom labels (Integrated DNA technologies) or containing a single 5-iodo-deoxycytidine (Jena Bioscience) were dissolved to 1 mM in CarH buffer. ..

    High Performance Liquid Chromatography:

    Article Title: Structural basis for gene regulation by a B12-dependent photoreceptor
    Article Snippet: CarH:DNA complexes for crystallization were generated by mixing protein and DNA at the desired ratio and incubating the mixture for 1 h on ice in the dark prior to crystallization experiments. .. Preparation of DNA segments for crystallization HPLC-purified single-stranded DNA oligonucleotides without heavy atom labels (Integrated DNA technologies) or containing a single 5-iodo-deoxycytidine (Jena Bioscience) were dissolved to 1 mM in CarH buffer. ..

    Diffusion-based Assay:

    Article Title: Structural basis for gene regulation by a B12-dependent photoreceptor
    Article Snippet: Crystals were transferred in 3 steps of increasing PEG 400 concentration into a cryogenic solution containing the precipitant supplemented with 15 % (w/v) PEG 400, incubated in that solution for 20 s, and then flash-frozen in liquid nitrogen. .. CarH bound to both AdoCbl and a 26-bp DNA segment containing 5-iodo-deoxycytidine ( ) in position −25 of the sense strand ( ) was crystallized by the hanging drop vapor diffusion technique at 25 °C. ..

    Produced:

    Article Title: The E3 ubiquitin ligase Mind bomb 1 enhances nuclear import of viral DNA by inactivating a virion linchpin protein that suppresses exposure of virion pathogen-associated molecular patterns
    Article Snippet: Capsid-labeled viruses were generated as described , . .. Genome-labeled AdV was produced by growing the virus in A549 cells in the presence of 2.5 μM EdC (5-ethynyl-2’-deoxycytidine, Jena Biosciences) as described . .. AdV-C5-ΔV, AdV-C5-V-KR, AdV-C5-V-KRrev, AdV-C5-V-K178R, AdV-C5-V-K188R, and AdV-C5-V-K178/188R were generated by recombineering from the pKSB2 bacmid which contains the entire AdV-C5 wt300 genome , .

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  • 93
    Jena Bioscience 5 iodo deoxycytidine
    CarH DNA binding, conformational changes upon binding, and comparison to BmrR. ( a ) 2 F o – F c omit electron density for DNA-bound CarH, calculated after performing full refinement of the model with DNA omitted and contoured at 1.0 σ. DNA is shown with carbons in yellow and recognition helix of a CarH DNA-binding domain with carbons in cyan. ( b , c ) Validation of DNA-binding mode using heavy-atom derivatized DNA segments. CarH was crystallized with a DNA segment containing <t>5-iodo-deoxycytidine</t> in position −25 of the sense strand. Shown is the resulting anomalous difference density (purple mesh), contoured at 6 σ, for both CarH:DNA complexes in the asymmetric unit, with peaks directly adjacent to the C5 atom of deoxycytidine in position −25. ( d ) Chemical structure of 5-iodo-deoxycytidine. ( e ) Comparison of CarH before and after DNA binding, revealing rearrangement of DNA-binding domains. CarH before DNA binding is shown with helix bundles and Cbl-binding domains in gray and DNA-binding domains in pink. CarH bound to DNA is shown with helix bundles and Cbl-binding domains in green and DNA-binding domains in cyan. The fourth DNA-binding domain of DNA-bound CarH is disordered and not modelled. DNA is shown in yellow. AdoCbl is shown with Cbl carbons in pink and 5′-dAdo group carbons in cyan. ( f ) Contacts between residues in neighboring DNA-binding domains, colored by domain. Each interface between two DNA-binding domains buries 280 Å 2 of surface from solvent on each DNA-binding domain. Interactions of Arg72 to Tyr7 and Glu11 are indicated by black dashed lines. Coloring as in ( e ). ( g , h ) Models of individual CarH head-to-tail dimers bound to DNA. ( g ) Head-to-tail dimer contributing the middle of the three DNA-binding domains, colored by domain with DNA-binding domain in cyan, helix bundles in yellow, and Cbl-binding domains in green. The DNA-binding domain of the second protomer (right) is disordered and not modeled. DNA and AdoCbl are shown as in ( e ). ( h ) Head-to-tail dimer contributing the flanking DNA-binding domains. Helix bundles and Cbl-binding domains are shown in gray, remaining coloring as in ( e ). ( i ) BmrR bound to DNA (PDB ID code 1EXJ 38 ). A BmrR dimer is shown in ribbon representation in orange and red. DNA is shown in yellow. BmrR binds as a dimer to a palindromic sequence and distorts the DNA double strand from its ideal conformation.
    5 Iodo Deoxycytidine, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/5 iodo deoxycytidine/product/Jena Bioscience
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    5 iodo deoxycytidine - by Bioz Stars, 2021-06
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    CarH DNA binding, conformational changes upon binding, and comparison to BmrR. ( a ) 2 F o – F c omit electron density for DNA-bound CarH, calculated after performing full refinement of the model with DNA omitted and contoured at 1.0 σ. DNA is shown with carbons in yellow and recognition helix of a CarH DNA-binding domain with carbons in cyan. ( b , c ) Validation of DNA-binding mode using heavy-atom derivatized DNA segments. CarH was crystallized with a DNA segment containing 5-iodo-deoxycytidine in position −25 of the sense strand. Shown is the resulting anomalous difference density (purple mesh), contoured at 6 σ, for both CarH:DNA complexes in the asymmetric unit, with peaks directly adjacent to the C5 atom of deoxycytidine in position −25. ( d ) Chemical structure of 5-iodo-deoxycytidine. ( e ) Comparison of CarH before and after DNA binding, revealing rearrangement of DNA-binding domains. CarH before DNA binding is shown with helix bundles and Cbl-binding domains in gray and DNA-binding domains in pink. CarH bound to DNA is shown with helix bundles and Cbl-binding domains in green and DNA-binding domains in cyan. The fourth DNA-binding domain of DNA-bound CarH is disordered and not modelled. DNA is shown in yellow. AdoCbl is shown with Cbl carbons in pink and 5′-dAdo group carbons in cyan. ( f ) Contacts between residues in neighboring DNA-binding domains, colored by domain. Each interface between two DNA-binding domains buries 280 Å 2 of surface from solvent on each DNA-binding domain. Interactions of Arg72 to Tyr7 and Glu11 are indicated by black dashed lines. Coloring as in ( e ). ( g , h ) Models of individual CarH head-to-tail dimers bound to DNA. ( g ) Head-to-tail dimer contributing the middle of the three DNA-binding domains, colored by domain with DNA-binding domain in cyan, helix bundles in yellow, and Cbl-binding domains in green. The DNA-binding domain of the second protomer (right) is disordered and not modeled. DNA and AdoCbl are shown as in ( e ). ( h ) Head-to-tail dimer contributing the flanking DNA-binding domains. Helix bundles and Cbl-binding domains are shown in gray, remaining coloring as in ( e ). ( i ) BmrR bound to DNA (PDB ID code 1EXJ 38 ). A BmrR dimer is shown in ribbon representation in orange and red. DNA is shown in yellow. BmrR binds as a dimer to a palindromic sequence and distorts the DNA double strand from its ideal conformation.

    Journal: Nature

    Article Title: Structural basis for gene regulation by a B12-dependent photoreceptor

    doi: 10.1038/nature14950

    Figure Lengend Snippet: CarH DNA binding, conformational changes upon binding, and comparison to BmrR. ( a ) 2 F o – F c omit electron density for DNA-bound CarH, calculated after performing full refinement of the model with DNA omitted and contoured at 1.0 σ. DNA is shown with carbons in yellow and recognition helix of a CarH DNA-binding domain with carbons in cyan. ( b , c ) Validation of DNA-binding mode using heavy-atom derivatized DNA segments. CarH was crystallized with a DNA segment containing 5-iodo-deoxycytidine in position −25 of the sense strand. Shown is the resulting anomalous difference density (purple mesh), contoured at 6 σ, for both CarH:DNA complexes in the asymmetric unit, with peaks directly adjacent to the C5 atom of deoxycytidine in position −25. ( d ) Chemical structure of 5-iodo-deoxycytidine. ( e ) Comparison of CarH before and after DNA binding, revealing rearrangement of DNA-binding domains. CarH before DNA binding is shown with helix bundles and Cbl-binding domains in gray and DNA-binding domains in pink. CarH bound to DNA is shown with helix bundles and Cbl-binding domains in green and DNA-binding domains in cyan. The fourth DNA-binding domain of DNA-bound CarH is disordered and not modelled. DNA is shown in yellow. AdoCbl is shown with Cbl carbons in pink and 5′-dAdo group carbons in cyan. ( f ) Contacts between residues in neighboring DNA-binding domains, colored by domain. Each interface between two DNA-binding domains buries 280 Å 2 of surface from solvent on each DNA-binding domain. Interactions of Arg72 to Tyr7 and Glu11 are indicated by black dashed lines. Coloring as in ( e ). ( g , h ) Models of individual CarH head-to-tail dimers bound to DNA. ( g ) Head-to-tail dimer contributing the middle of the three DNA-binding domains, colored by domain with DNA-binding domain in cyan, helix bundles in yellow, and Cbl-binding domains in green. The DNA-binding domain of the second protomer (right) is disordered and not modeled. DNA and AdoCbl are shown as in ( e ). ( h ) Head-to-tail dimer contributing the flanking DNA-binding domains. Helix bundles and Cbl-binding domains are shown in gray, remaining coloring as in ( e ). ( i ) BmrR bound to DNA (PDB ID code 1EXJ 38 ). A BmrR dimer is shown in ribbon representation in orange and red. DNA is shown in yellow. BmrR binds as a dimer to a palindromic sequence and distorts the DNA double strand from its ideal conformation.

    Article Snippet: Preparation of DNA segments for crystallization HPLC-purified single-stranded DNA oligonucleotides without heavy atom labels (Integrated DNA technologies) or containing a single 5-iodo-deoxycytidine (Jena Bioscience) were dissolved to 1 mM in CarH buffer.

    Techniques: Binding Assay, Sequencing

    Identification and validation of CarH operator sequence by EMSAs and footprinting. ( a ) Location of CarH operator in the intergenic region between carH and the carotenogenic crtB of the T. thermophilus genome. Structural and biochemical data are mapped onto the sequence. Three 11-bp CarH binding sites are shown in cyan font and the promoter −35 element is highlighted with a red box. Nucleotides protected from hydroxyl radical cleavage are indicated with bullets. The ∼42-nucleotide DNase I footprint on the sense strand is shown above the sequence and that of the antisense strand has been omitted for clarity. Nucleotide numbering on the sense strand is relative to the carH transcription start site (underlined, +1) 10 . To identify suitable DNA constructs for crystallization, operator sequences were systematically trimmed around a ∼40-bp segment, as indicated by the black bars, and binding was assessed by EMSAs (shown in b ). The sequences of two 26-bp DNA segments used for co-crystallization are also shown. The blunt-ended 26-bp segment was used for determination of the CarH:DNA structure. The second 26-bp segment contained 1-nucleotide 3′-overhangs and 5-iodo-deoxycytidine in position −25 (red) and was used to validate the mode of DNA binding. ( b ) Binding of CarH (800 nM) to DNA segments of different lengths after incubation with AdoCbl (4 μM) in the dark. Substantial DNA-binding was observed for a probe as small as 30-bp. ( c ) DNase I and hydroxyl radical footprints of CarH on a 130-bp operator DNA segment. Disappearance of bands in the presence of CarH indicates protection from cleavage. Protected regions are marked on the side and were mapped onto the operator sequence using G+A chemical sequencing experiments performed in parallel. ( d , e ) CarH binding to 40-bp operators carrying mutations. ( d ) Sequences of tested operator variants. WT operator sequence shown at the top and bottom, with repeat sequences that CarH recognizes shown in cyan. 6-bp stretch contacted by CarH recognition helix is boxed. Mutations are as follows: Mut1-7: single (1-3), pairwise (4-6), and triple (7) mutations of AC to GT (Positions 8/9); Mut8-14: single (8-10), double (11-13), and triple (14) mutations of (A/C)T to GC (Positions 4/5); Mut15-18: pairwise (15-17) and triple (18) mutations of (A/G)A) to TT (Positions 1/2). ( e ) EMSAs with WT CarH (800 nM) and each of the 40-bp operator variants after incubation with AdoCbl (4 μM) in the dark. Note that two additional lower mobility complexes are observed, most apparent with the WT operator and its variants with comparable binding. The origin of these complexes is unknown, but they likely arise from oligomeric equilibria and residual amounts of light-exposed protein in the sample.

    Journal: Nature

    Article Title: Structural basis for gene regulation by a B12-dependent photoreceptor

    doi: 10.1038/nature14950

    Figure Lengend Snippet: Identification and validation of CarH operator sequence by EMSAs and footprinting. ( a ) Location of CarH operator in the intergenic region between carH and the carotenogenic crtB of the T. thermophilus genome. Structural and biochemical data are mapped onto the sequence. Three 11-bp CarH binding sites are shown in cyan font and the promoter −35 element is highlighted with a red box. Nucleotides protected from hydroxyl radical cleavage are indicated with bullets. The ∼42-nucleotide DNase I footprint on the sense strand is shown above the sequence and that of the antisense strand has been omitted for clarity. Nucleotide numbering on the sense strand is relative to the carH transcription start site (underlined, +1) 10 . To identify suitable DNA constructs for crystallization, operator sequences were systematically trimmed around a ∼40-bp segment, as indicated by the black bars, and binding was assessed by EMSAs (shown in b ). The sequences of two 26-bp DNA segments used for co-crystallization are also shown. The blunt-ended 26-bp segment was used for determination of the CarH:DNA structure. The second 26-bp segment contained 1-nucleotide 3′-overhangs and 5-iodo-deoxycytidine in position −25 (red) and was used to validate the mode of DNA binding. ( b ) Binding of CarH (800 nM) to DNA segments of different lengths after incubation with AdoCbl (4 μM) in the dark. Substantial DNA-binding was observed for a probe as small as 30-bp. ( c ) DNase I and hydroxyl radical footprints of CarH on a 130-bp operator DNA segment. Disappearance of bands in the presence of CarH indicates protection from cleavage. Protected regions are marked on the side and were mapped onto the operator sequence using G+A chemical sequencing experiments performed in parallel. ( d , e ) CarH binding to 40-bp operators carrying mutations. ( d ) Sequences of tested operator variants. WT operator sequence shown at the top and bottom, with repeat sequences that CarH recognizes shown in cyan. 6-bp stretch contacted by CarH recognition helix is boxed. Mutations are as follows: Mut1-7: single (1-3), pairwise (4-6), and triple (7) mutations of AC to GT (Positions 8/9); Mut8-14: single (8-10), double (11-13), and triple (14) mutations of (A/C)T to GC (Positions 4/5); Mut15-18: pairwise (15-17) and triple (18) mutations of (A/G)A) to TT (Positions 1/2). ( e ) EMSAs with WT CarH (800 nM) and each of the 40-bp operator variants after incubation with AdoCbl (4 μM) in the dark. Note that two additional lower mobility complexes are observed, most apparent with the WT operator and its variants with comparable binding. The origin of these complexes is unknown, but they likely arise from oligomeric equilibria and residual amounts of light-exposed protein in the sample.

    Article Snippet: Preparation of DNA segments for crystallization HPLC-purified single-stranded DNA oligonucleotides without heavy atom labels (Integrated DNA technologies) or containing a single 5-iodo-deoxycytidine (Jena Bioscience) were dissolved to 1 mM in CarH buffer.

    Techniques: Sequencing, Footprinting, Binding Assay, Construct, Crystallization Assay, Incubation