Paci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "RNA aptamer inhibitors of a restriction endonuclease"
Article Title: RNA aptamer inhibitors of a restriction endonuclease
Journal: Nucleic Acids Research
Figure Legend Snippet: In vitro selection process. ( A ) RNA aptamer library format, random region and tetraloop highlighted in black. ( B ) Fraction of RNA recovered from selections against BamHI (blue circles), KpnI (green triangles) and PacI (red squares), as a function of selection round.
Techniques Used: In Vitro, Selection
2) Product Images from "Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments"
Article Title: Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments
Journal: Nucleic Acids Research
Figure Legend Snippet: Sequential USER cloning of multiple inserts. Inclusion of 25 bp of the PacI cassette sequence in the reverse primer used to amplify a DNA fragment prior to USER cloning results in regeneration of the PacI cassette downstream of the inserted fragment. For smaller fragments the entire insert can be assembled from chemically synthesized oligonucleotides. Subsequent digestion of the construct with PacI and Nt.BbvCI allows insertion of another fragment into the vector by USER cloning. Sequentially inserted DNA fragments will have a minimum of 13 bp sequence between them. Nt.BbvCI recognition sites are marked in tan, PacI recognition sites are marked in light blue. Yellow and green mark the single base differences between the generated 3′ overhangs.
Techniques Used: Clone Assay, Sequencing, Synthesized, Construct, Plasmid Preparation, Generated
Figure Legend Snippet: Overview of the USER cloning technique. A PacI cassette containing USER vector (upper left corner) is digested with PacI and Nt.BbvCI to generate 8 nt single-stranded 3′ overhangs. A PCR fragment amplified with compatible uracil-containing primers by the PfuTurbo ® C x Hotstart DNA polymerase is mixed with USER™ enzyme mix (removing uracils, pink) and the linearized vector. The mixture is incubated 20 min at 37°C and 20 min at 25°C, and the hybridized product is ready to be transformed into E.coli without prior ligation. Nt.BbvCI recognition sites are marked in tan, PacI recognition sites are marked in light blue. Yellow and green mark single base differences between the generated 3′ overhangs, which are responsible for the directional insertion of the PCR fragment.
Techniques Used: Clone Assay, Plasmid Preparation, Polymerase Chain Reaction, Amplification, Incubation, Transformation Assay, Ligation, Generated
3) Product Images from "Pathogenicity and Immunogenicity of Recombinant Rabies Viruses Expressing the Lagos Bat Virus Matrix and Glycoprotein: Perspectives for a Pan-Lyssavirus Vaccine"
Article Title: Pathogenicity and Immunogenicity of Recombinant Rabies Viruses Expressing the Lagos Bat Virus Matrix and Glycoprotein: Perspectives for a Pan-Lyssavirus Vaccine
Journal: Tropical Medicine and Infectious Disease
Figure Legend Snippet: Schematic representation of the construction of recombinant viruses. Restriction enzyme sites are indicated ( XmaI , PacI , AvrII , KpnI . BsiWI , AsiSI , NheI and AscI ). GAS represents the SPBN G gene with two amino acid substitutions (Asn 194 to Ser and Arg 333 to Glu). The following abbreviations were used: N, nucleoprotein; M, matrix protein; G, glycoprotein; L, RNA-dependent RNA polymerase. LBVM and LBVG represent the LBV M and G gene respectively.
Techniques Used: Recombinant
4) Product Images from "RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences"
Article Title: RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences
Journal: Methods in enzymology
Figure Legend Snippet: The RNA-ID reporter and its derivatives. (A) In the RNA-ID vector, expression of two reporters GFP and RFP is driven by the bidirectional GAL1,10 promoter. The GFP reporter is a fusion protein encoding a 3C protease site, an HA epitope, His6, (marked by dark box) followed by superfolder GFP. Putative regulatory sequences are inserted into the PacI, BbrPI sites (GFP) or into the SwaI site (RFP) using LIC cloning. The GFP lacks a start codon, allowing insertion of sequences upstream or within the coding sequence. (B) The Renilla luciferase-GFP fusion protein allows for analysis of the upstream nascent polypeptide and uses the same restriction sites for cloning. (C) In the GLN4 -GFP fusion protein, varying lengths of GLN4 can be PCR amplified to allow for the insertion of sequences at different locations relative to the start codon.
Techniques Used: Plasmid Preparation, Expressing, Clone Assay, Sequencing, Luciferase, Polymerase Chain Reaction, Amplification
5) Product Images from "Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state"
Article Title: Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
Journal: Nature biotechnology
Figure Legend Snippet: Symmetric barcoding and amplification of chromatin fragments A) Barcode adapters (top) are 64 bp double-stranded oligonucleotides with universal primers, barcode sequences and restriction sites, whose symmetric design allows ligation on either side. Schematic (bottom left) depicts possible outcomes of ligation in drops, including symmetrically labeled nucleosomes, asymmetrically labeled nucleosomes, and adapter concatemers. Concatemers are removed by digestion of PacI sites formed by adapter juxtaposition (bottom center), allowing selective PCR amplification of symmetrically adapted chromatin fragments (bottom right). See also Supplementary Figure 2 . B) Gel electrophoresis for DNA products at successive assay stages: left : DNA ladder; MNase : DNA fragments purified after capture, lysis and MNase digestion of single cells in drops confirm efficient digestion to mononucleosomes (∼1 million drops collected); Concat : Illumina library prepared from adaptor-ligated chromatin fragments without PacI digestion reveals overwhelming concatemer bias. Library : Illumina library prepared from adaptor-ligated chromatin fragments digested with PacI, reveals appropriate MNase digestion pattern, shifted by the size of barcode and Illumina adapters. C) Pie charts depict numbers of uniquely aligned sequencing read that satisfy successive filtering criteria (values reflect data from 100 single cells, averaged over 82 trials). We select reads that have barcode sequences on both ends (top) with matching sequence (middle). We then apply a Poisson model to identify barcodes that represent single cells (bottom). D) Heatmap depicts homogeneity of barcode selection. Barcodes (rows) are colored according to their relative prevalence (rank order) across 37 experiments (columns). The absence of bias towards particular barcodes (light or dark horizontal stripes) indicates the homogeneity of the barcode library. The mean normalized rank over all barcodes (right) is close to 0.5, consistent with balanced representation. E) Stability of the barcode library emulsion over time. The fraction of reads with matching barcodes on both ends is plotted as a function of time from encapsulation of the barcode library. F) The microfluidics system was applied to barcode a mixed suspension of human and mouse cells. For each barcode, plot depicts the number of reads aligning to the mouse genome (y-axis) versus the number of reads aligning to the human genome (x-axis). The data suggest that a vast majority of barcodes is unique to a single cell.
Techniques Used: Amplification, Ligation, Labeling, Polymerase Chain Reaction, Nucleic Acid Electrophoresis, Purification, Lysis, Sequencing, Selection
6) Product Images from "Identification and Characterization of a Phase-Variable Element That Regulates the Autotransporter UpaE in Uropathogenic Escherichia coli"
Article Title: Identification and Characterization of a Phase-Variable Element That Regulates the Autotransporter UpaE in Uropathogenic Escherichia coli
Figure Legend Snippet: Assessment of each recombinase’s ability to catalyze inversion of ipuS in vitro . Ethidium bromide-stained electrophoretic gels of PacI-digested PCR products are shown. Lanes 1 and 2 contain digested PCR products from CFT073 ipuS phase locked-ON (WAM5064) and -OFF (WAM5065) strains generated by 5-way recombinase deletion. Lanes 3 and 4 contain digested PCR products from vector-only controls (WAM5070, WAM5079, WAM5074, and WAM5083). Lanes 5 to 10 contain PCR products from the locked-OFF strain WAM5065 (top panel) or locked-ON strain WAM5064 (bottom panel) after transforming each with a recombinant plasmid containing the indicated recombinase. Both the full-length and truncated forms of ipuA were tested for activity (lanes 9 and 10).
Techniques Used: In Vitro, Staining, Polymerase Chain Reaction, Generated, Plasmid Preparation, Recombinant, Activity Assay