sbfi (New England Biolabs)


Name:
SbfI
Description:
SbfI 2 500 units
Catalog Number:
r0642l
Price:
302
Category:
Restriction Enzymes
Size:
2 500 units
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Structured Review

SbfI 2 500 units
https://www.bioz.com/result/sbfi/product/New England Biolabs
Average 94 stars, based on 1 article reviews
Price from $9.99 to $1999.99
Images
1) Product Images from "Conserved CxnC Motifs in Kaposi’s Sarcoma-Associated Herpesvirus ORF66 Are Required for Viral Late Gene Expression and Are Essential for Its Interaction with ORF34"
Article Title: Conserved CxnC Motifs in Kaposi’s Sarcoma-Associated Herpesvirus ORF66 Are Required for Viral Late Gene Expression and Are Essential for Its Interaction with ORF34
Journal: Journal of Virology
doi: 10.1128/JVI.01299-19

Figure Legend Snippet: ORF66 is essential in KSHV and required for late gene transcription. (A) (Left) Diagram showing the genomic locus of ORF66 with surrounding genes ORF67 (which partially overlaps ORF66) and ORF65, depicting the location of introduced mutations. (Right) The mutations were confirmed by Sanger sequencing. (B) Digestion of the recombinant BACs with SbfI or RsrII demonstrates that the introduction of mutations did not introduce large-scale changes. (C) Infectious virion production was measured by supernatant transfer from reactivated iSLK cell lines followed by flow cytometry. Data are from three independent biological replicates, with statistics being calculated using an unpaired t test. ****, P
Techniques Used: Sequencing, Recombinant, Introduce, Flow Cytometry
2) Product Images from "Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34"
Article Title: Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34
Journal: bioRxiv
doi: 10.1101/728139

Figure Legend Snippet: ORF66 is essential in KSHV and required for late gene transcription A) Diagram showing the genomic locus of ORF66 with surrounding genes ORF67 (which partially overlaps ORF66) and ORF65, depicting the location of introduced mutations. Mutations were confirmed by Sanger sequencing (right). B) Digestion of the recombinant BACs with SbfI or RsrII demonstrates that introduction of mutations did not introduce large-scale changes. C) Infectious virion production was measured by supernatant transfer from reactivated iSLK cell lines followed by flow cytometry. Data are from three independent biological replicates with statistics calculated using an unpaired t-test, where (****) p
Techniques Used: Sequencing, Recombinant, Introduce, Flow Cytometry

Figure Legend Snippet: ORF24 does not bind to late gene promoters in the absence of ORF30 or ORF66 iSLK cell lines were created using the recombinant BAC16 system. HA tags were added to the endogenous copies of the N-terminus of ORF24 (HA24) or the C-terminus of ORF66 (66HA). In select BACs, ORF24, ORF30, or ORF66 were deleted by the introduction of a stop codon early in the ORF (24S, 30S, and 66S respectively). A) Digestion of the recombinant BACs with SbfI or RsrII demonstrates that recombination did not introduce large-scale changes. B) Infectious virion production was measured by supernatant transfer from reactivated iSLK cell lines followed by flow cytometry. Data are from three independent biological replicates with statistics calculated using an unpaired t-test, where (****) p
Techniques Used: Recombinant, Introduce, Flow Cytometry
3) Product Images from "Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)"
Article Title: Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)
Journal: The Journal of Biological Chemistry
doi: 10.1074/jbc.RA118.003302

Figure Legend Snippet: Screening for sialidase activity from a hot spring metagenomic library. A , restriction fragment analysis of 12 randomly selected clones from the hot spring metagenomic library were isolated and digested with the rare-cutting endonuclease SbfI. Digested fosmids were separated overnight on a 1% agarose gel along with a λHindIII size marker and a linearized pSMART FOS empty vector control ( lane 14 ; contains one SbfI site). Each clone showed a unique banding pattern, with fragments whose combined sizes indicated the presence of an insert of at least 30–40 kb. B , E. coli cells harboring individual fosmid clones were assayed for sialidase activity with X-Neu5Ac incorporated into agar medium. A single positive clone forming a blue colony is denoted with an arrow. C , lysate from microcultures of E. coli cells harboring individual fosmid clones were assayed for sialidase activity with 4MU-α-Neu5Ac. A single positive clone is denoted with an arrow .
Techniques Used: Activity Assay, Clone Assay, Isolation, Agarose Gel Electrophoresis, Marker, Plasmid Preparation
4) Product Images from "A pentameric protein ring with novel architecture is required for herpesviral packaging"
Article Title: A pentameric protein ring with novel architecture is required for herpesviral packaging
Journal: bioRxiv
doi: 10.1101/2020.07.16.206755

Figure Legend Snippet: Construction and validation of mutant viruses. a , Schematic of the genomic locus of ORF68, with the location of introduced mutations depicted in detail below. Sanger sequencing traces for the mutants and corresponding mutant rescues are shown to the right. b , Digestion of recombinant BACs with RsrII and SbfI was used to assess whether large-scale recombination had occurred during mutagenesis. c , Western blot of whole cell lysate (25 μg) from ORF68.stop iSLK cell lines. GAPDH was used as a loading control. ORF6 is an early gene and K8.1 is a late gene. d , Viral DNA replication was measured by qPCR before and after reactivation. Data are from three independent biological replicates, with statistics being calculated using an unpaired t test. **, p
Techniques Used: Mutagenesis, Sequencing, Recombinant, Western Blot, Real-time Polymerase Chain Reaction
5) Product Images from "Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol"
Article Title: Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol
Journal: PLoS ONE
doi: 10.1371/journal.pone.0106713

Figure Legend Snippet: Sequencing depth for single copy ddRAD loci in relation to the corresponding sequence in the zebra finch reference genome. Categories from top to bottom include: loci mapping as expected to predicted SbfI-EcoRI restriction fragments≤328 bp in length; all loci beginning at a genomic location similar but not identical to the canonical SbfI recognition sequence (1–4 mismatches); subset of loci with one mismatch in position 1 or 8 of the SbfI recognition sequence; subset of loci with one mismatch in positions 2 through 7 of the SbfI recognition sequence; loci mapping to a genomic SbfI site without an EcoRI site within 328 bp; and loci mapping to a predicted SbfI-SbfI restriction fragment less than 328 bp in length.
Techniques Used: Sequencing

Figure Legend Snippet: Recovery and sequencing depth for predicted, single-copy ddRAD loci in the empirical zebra finch data. (A) Proportion of predicted loci recovered at three different minimum depth thresholds as a function of predicted fragment length. Each data point represents the proportion of ∼140–220 predicted loci recovered in a given 10 bp size range. Dashed vertical lines represent the upper and lower bounds of the size range isolated from the agarose gel. (B) Sequencing depth for recovered (depth ≥1), single-copy loci in the 32–500 bp size range (includes 5,232 of 5,783 predicted loci in the 38–328 bp size range). (C) The relationship between GC content and sequencing depth for zebra finch ddRAD loci. Data are shown for predicted, single-copy loci recovered at a depth ≥1 in three selected subsets of the overall size range ( n = 502, 466, and 445 loci in the 100–125, 200–225, and 300–325 bp size ranges, respectively). The predicted length and GC content of each locus are based on the full-length fragment in the reference genome, inclusive of the SbfI and EcoRI restriction sites on either end. Note that the y-axis is on a logarithmic scale in (B) and (C).
Techniques Used: Sequencing, Isolation, Agarose Gel Electrophoresis
6) Product Images from "Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)"
Article Title: Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)
Journal: The Journal of Biological Chemistry
doi: 10.1074/jbc.RA118.003302

Figure Legend Snippet: Screening for sialidase activity from a hot spring metagenomic library. A , restriction fragment analysis of 12 randomly selected clones from the hot spring metagenomic library were isolated and digested with the rare-cutting endonuclease SbfI. Digested fosmids were separated overnight on a 1% agarose gel along with a λHindIII size marker and a linearized pSMART FOS empty vector control ( lane 14 ; contains one SbfI site). Each clone showed a unique banding pattern, with fragments whose combined sizes indicated the presence of an insert of at least 30–40 kb. B , E. coli cells harboring individual fosmid clones were assayed for sialidase activity with X-Neu5Ac incorporated into agar medium. A single positive clone forming a blue colony is denoted with an arrow. C , lysate from microcultures of E. coli cells harboring individual fosmid clones were assayed for sialidase activity with 4MU-α-Neu5Ac. A single positive clone is denoted with an arrow .
Techniques Used: Activity Assay, Clone Assay, Isolation, Agarose Gel Electrophoresis, Marker, Plasmid Preparation
7) Product Images from "Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)"
Article Title: Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)
Journal: The Journal of Biological Chemistry
doi: 10.1074/jbc.RA118.003302

Figure Legend Snippet: Screening for sialidase activity from a hot spring metagenomic library. A , restriction fragment analysis of 12 randomly selected clones from the hot spring metagenomic library were isolated and digested with the rare-cutting endonuclease SbfI. Digested fosmids were separated overnight on a 1% agarose gel along with a λHindIII size marker and a linearized pSMART FOS empty vector control ( lane 14 ; contains one SbfI site). Each clone showed a unique banding pattern, with fragments whose combined sizes indicated the presence of an insert of at least 30–40 kb. B , E. coli cells harboring individual fosmid clones were assayed for sialidase activity with X-Neu5Ac incorporated into agar medium. A single positive clone forming a blue colony is denoted with an arrow. C , lysate from microcultures of E. coli cells harboring individual fosmid clones were assayed for sialidase activity with 4MU-α-Neu5Ac. A single positive clone is denoted with an arrow .
Techniques Used: Activity Assay, Clone Assay, Isolation, Agarose Gel Electrophoresis, Marker, Plasmid Preparation
Related Articles
BAC Assay:Article Title: A pentameric protein ring with novel architecture is required for herpesviral packaging Article Snippet: Modified BACs were purified using a Nucleobond BAC 100 kit (Clontech). .. BAC quality was assessed by digestion with RsrII and Article Title: Conserved CxnC Motifs in Kaposi’s Sarcoma-Associated Herpesvirus ORF66 Are Required for Viral Late Gene Expression and Are Essential for Its Interaction with ORF34 Article Snippet: The modified BACs were purified using a Nucleobond BAC 100 kit (Clontech). .. BAC quality was assessed by digestion with RsrII and Article Title: Conserved CxnC motifs in Kaposi’s sarcoma-associated herpesvirus ORF66 are required for viral late gene expression and mediate its interaction with ORF34 Article Snippet: The modified BACs were purified using a Nucleobond BAC 100 kit (Clontech). .. BAC quality was assessed by digestion with RsrII and Plasmid Preparation:Article Title: Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156) Article Snippet: Fosmids were individually isolated from 12 randomly selected library clones using the FosmidMAXTM DNA purification kit (Lucigen Corporation). .. Each fosmid was digested with Isolation:Article Title: Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers Article Snippet: Therefore, even as sequencing technology continues to improve, RAD marker sequencing will remain a useful and cost-effective tool for most genetic mapping studies. .. Isolation of RAD markers for Illumina sequencing Genomic DNA (0.1–1 µg; from either individual or pooled samples) was digested for 15 min at 37°C in a 50 µL reaction with 20 units (U) of EcoR I or Sequencing:Article Title: Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers Article Snippet: Therefore, even as sequencing technology continues to improve, RAD marker sequencing will remain a useful and cost-effective tool for most genetic mapping studies. .. Isolation of RAD markers for Illumina sequencing Genomic DNA (0.1–1 µg; from either individual or pooled samples) was digested for 15 min at 37°C in a 50 µL reaction with 20 units (U) of EcoR I or |