Structured Review

Stratagene exonuclease iii
VPS35 , VPS30, and <t>VPS29</t> are highly conserved in eukaryotes. ( A ) Schematic view of homology between Vps35p and proteins found in the C. elegans and M. musculus proteomes. The numbers between the proteins are percent identities between Vps35p and the other two proteins. In the lower section, the two most highly conserved domains (designated domains I and <t>III)</t> are aligned to show the regions of greatest homology between the yeast, mouse, nematode, and also human homologues. The black boxes indicate completely conserved residues. ( B ) Alignments between Vps29p and homologues present in the proteomes of C. elegans and H. sapiens , and also alignments between Vps30p and homologues present in the proteomes of C. elegans and H. sapiens . Black shaded regions indicate areas that are completely conserved.
Exonuclease Iii, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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exonuclease iii - by Bioz Stars, 2020-11
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Images

1) Product Images from "Endosome to Golgi Retrieval of the Vacuolar Protein Sorting Receptor, Vps10p, Requires the Function of the VPS29, VPS30, and VPS35 Gene Products"

Article Title: Endosome to Golgi Retrieval of the Vacuolar Protein Sorting Receptor, Vps10p, Requires the Function of the VPS29, VPS30, and VPS35 Gene Products

Journal: The Journal of Cell Biology

doi:

VPS35 , VPS30, and VPS29 are highly conserved in eukaryotes. ( A ) Schematic view of homology between Vps35p and proteins found in the C. elegans and M. musculus proteomes. The numbers between the proteins are percent identities between Vps35p and the other two proteins. In the lower section, the two most highly conserved domains (designated domains I and III) are aligned to show the regions of greatest homology between the yeast, mouse, nematode, and also human homologues. The black boxes indicate completely conserved residues. ( B ) Alignments between Vps29p and homologues present in the proteomes of C. elegans and H. sapiens , and also alignments between Vps30p and homologues present in the proteomes of C. elegans and H. sapiens . Black shaded regions indicate areas that are completely conserved.
Figure Legend Snippet: VPS35 , VPS30, and VPS29 are highly conserved in eukaryotes. ( A ) Schematic view of homology between Vps35p and proteins found in the C. elegans and M. musculus proteomes. The numbers between the proteins are percent identities between Vps35p and the other two proteins. In the lower section, the two most highly conserved domains (designated domains I and III) are aligned to show the regions of greatest homology between the yeast, mouse, nematode, and also human homologues. The black boxes indicate completely conserved residues. ( B ) Alignments between Vps29p and homologues present in the proteomes of C. elegans and H. sapiens , and also alignments between Vps30p and homologues present in the proteomes of C. elegans and H. sapiens . Black shaded regions indicate areas that are completely conserved.

Techniques Used:

Related Articles

Sequencing:

Article Title: Endosome to Golgi Retrieval of the Vacuolar Protein Sorting Receptor, Vps10p, Requires the Function of the VPS29, VPS30, and VPS35 Gene Products
Article Snippet: .. Constructs for sequencing the VPS29 gene were made by treating pEMY29-1 with exonuclease III and mung bean nuclease as described in the Stratagene BlueScript manual. ..

Article Title: Sequence analysis of human coronavirus 229E mRNAs 4 and 5: evidence for polymorphism and homology with myelin basic protein.
Article Snippet: .. cDNA sequencing and sequence analysis Stepwise unidirectional deletions at both ends of the largest cDNA clone were created with exonuclease III, mung bean nuclease and deoxythionucleotide derivatives (Stratagene). .. The sequencing of both strands was performed by the plasmid sequencing technique (Hattori and Sakaki, 19861, with T7 DNA polymerase (Pharmacia) .

Clone Assay:

Article Title: u-shaped encodes a zinc finger protein that regulates the proneural genes achaete and scute during the formation of bristles in Drosophila
Article Snippet: .. A cDNA insert of 4.7 kb ( Kpn I– Hin dIII fragment) was cloned in pBluescript II SK+ (Stratagene) and directional deletions were generated using the exonuclease III (Stratagene kit). .. Sequence data were collected for both strands using the M13 universal primer as well as internal synthetic oligonucleotides.

Generated:

Article Title: Multiple Orientation-Dependent, Synergistically Interacting, Similar Domains in the Ribosomal DNA Replication Origin of the Fission Yeast, Schizosaccharomyces pombe
Article Snippet: .. Unidirectional sequential deletions from both ends of the insert were generated with exonuclease III as described previously ( ) with modifications suggested by Stratagene (protocol for the pBluescriptII exonuclease III-mung bean DNA sequencing system; Stratagene). .. For deletions starting at the Bam HI site, plasmid pRS406:rDNA-2.3k was digested with Bam HI, to generate recessed 3′ ends susceptible to exonuclease III attack, and also with Sac I, to generate exonuclease III-resistant protruding 3′ ends.

Article Title: Identification of a Suppressor of the Dictyostelium Profilin-minus Phenotype as a CD36/LIMP-II Homologue
Article Snippet: .. An EcoRI fragment of 2.5 kb and shorter fragments of 2.0 and 1.1 kb generated by treatment with exonuclease III (Erase-a-Base; Stratagene) were subcloned in pUC19 ( ). .. The fragments were sequenced with the chain termination dideoxy method ( ) using uni, reverse, and sequence specific primers.

Article Title: u-shaped encodes a zinc finger protein that regulates the proneural genes achaete and scute during the formation of bristles in Drosophila
Article Snippet: .. A cDNA insert of 4.7 kb ( Kpn I– Hin dIII fragment) was cloned in pBluescript II SK+ (Stratagene) and directional deletions were generated using the exonuclease III (Stratagene kit). .. Sequence data were collected for both strands using the M13 universal primer as well as internal synthetic oligonucleotides.

DNA Sequencing:

Article Title: Multiple Orientation-Dependent, Synergistically Interacting, Similar Domains in the Ribosomal DNA Replication Origin of the Fission Yeast, Schizosaccharomyces pombe
Article Snippet: .. Unidirectional sequential deletions from both ends of the insert were generated with exonuclease III as described previously ( ) with modifications suggested by Stratagene (protocol for the pBluescriptII exonuclease III-mung bean DNA sequencing system; Stratagene). .. For deletions starting at the Bam HI site, plasmid pRS406:rDNA-2.3k was digested with Bam HI, to generate recessed 3′ ends susceptible to exonuclease III attack, and also with Sac I, to generate exonuclease III-resistant protruding 3′ ends.

Construct:

Article Title: Endosome to Golgi Retrieval of the Vacuolar Protein Sorting Receptor, Vps10p, Requires the Function of the VPS29, VPS30, and VPS35 Gene Products
Article Snippet: .. Constructs for sequencing the VPS29 gene were made by treating pEMY29-1 with exonuclease III and mung bean nuclease as described in the Stratagene BlueScript manual. ..

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  • 85
    Stratagene exonuclease iii truncation mutagenesis
    Yeast 2-hybrid analysis of interaction between the PP2A A subunit and an exonuclease <t>III–generated</t> C-terminal truncation series of <t>HSF2.</t> Yeast strain pJ694A cotransformed with pGAD-A subunit and either pGBD-HSF2 full-length (1–517), pGBD-HSF2 (1–363), pGBD-HSF2 (1–354), pGBD-HSF2 (1–348), pGBD-HSF2 (1–343), or pGBD-HSF2 (1–339) were streaked on –TL, –TLH, or –TLA plates. Relative growth of each pairing on the selective plates was then scored
    Exonuclease Iii Truncation Mutagenesis, supplied by Stratagene, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii truncation mutagenesis/product/Stratagene
    Average 85 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii truncation mutagenesis - by Bioz Stars, 2020-11
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      Buy from Supplier

    80
    Stratagene exonuclease iii mung bean nuclease deletion kit
    Analysis of polysomal mRNA. Data from spermidine- and arginine-grown cultures are shown on the left and right, respectively, and the tops of the gradients are to the right. (A) A 254 profile of 10 to 40% sucrose gradients. (B) Northern blot analysis of <t>spe-1</t> mRNA from the aga strain (IC3). (C) Northern blot analysis of spe-1 mRNA from transformant DMH3, lacking the 5′-UTR sequences between the Afl <t>III</t> and Nru I sites. (D) Northern blot analysis of tub mRNA of strain IC3 shown in panel B ( tub mRNA from DMH3 was similar). Polysomal fractions are aligned below their approximate positions in the gradient.
    Exonuclease Iii Mung Bean Nuclease Deletion Kit, supplied by Stratagene, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii mung bean nuclease deletion kit/product/Stratagene
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii mung bean nuclease deletion kit - by Bioz Stars, 2020-11
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    85
    Stratagene exo iii deletions
    Analysis of polysomal mRNA. Data from spermidine- and arginine-grown cultures are shown on the left and right, respectively, and the tops of the gradients are to the right. (A) A 254 profile of 10 to 40% sucrose gradients. (B) Northern blot analysis of <t>spe-1</t> mRNA from the aga strain (IC3). (C) Northern blot analysis of spe-1 mRNA from transformant DMH3, lacking the 5′-UTR sequences between the Afl <t>III</t> and Nru I sites. (D) Northern blot analysis of tub mRNA of strain IC3 shown in panel B ( tub mRNA from DMH3 was similar). Polysomal fractions are aligned below their approximate positions in the gradient.
    Exo Iii Deletions, supplied by Stratagene, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exo iii deletions/product/Stratagene
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    exo iii deletions - by Bioz Stars, 2020-11
    85/100 stars
      Buy from Supplier

    Image Search Results


    Yeast 2-hybrid analysis of interaction between the PP2A A subunit and an exonuclease III–generated C-terminal truncation series of HSF2. Yeast strain pJ694A cotransformed with pGAD-A subunit and either pGBD-HSF2 full-length (1–517), pGBD-HSF2 (1–363), pGBD-HSF2 (1–354), pGBD-HSF2 (1–348), pGBD-HSF2 (1–343), or pGBD-HSF2 (1–339) were streaked on –TL, –TLH, or –TLA plates. Relative growth of each pairing on the selective plates was then scored

    Journal: Cell Stress & Chaperones

    Article Title: Identification of the PP2A-interacting region of heat shock transcription factor 2

    doi: 10.1379/CSC-249R.1

    Figure Lengend Snippet: Yeast 2-hybrid analysis of interaction between the PP2A A subunit and an exonuclease III–generated C-terminal truncation series of HSF2. Yeast strain pJ694A cotransformed with pGAD-A subunit and either pGBD-HSF2 full-length (1–517), pGBD-HSF2 (1–363), pGBD-HSF2 (1–354), pGBD-HSF2 (1–348), pGBD-HSF2 (1–343), or pGBD-HSF2 (1–339) were streaked on –TL, –TLH, or –TLA plates. Relative growth of each pairing on the selective plates was then scored

    Article Snippet: The exonuclease III truncation mutagenesis of HSF2 was performed with a Stratagene Exo III–Mung bean nuclease kit (Stratagene, La Jolla, CA, USA) according to the manufacturer's instructions, following the strategy described previously ( ).

    Techniques: Generated

    VPS35 , VPS30, and VPS29 are highly conserved in eukaryotes. ( A ) Schematic view of homology between Vps35p and proteins found in the C. elegans and M. musculus proteomes. The numbers between the proteins are percent identities between Vps35p and the other two proteins. In the lower section, the two most highly conserved domains (designated domains I and III) are aligned to show the regions of greatest homology between the yeast, mouse, nematode, and also human homologues. The black boxes indicate completely conserved residues. ( B ) Alignments between Vps29p and homologues present in the proteomes of C. elegans and H. sapiens , and also alignments between Vps30p and homologues present in the proteomes of C. elegans and H. sapiens . Black shaded regions indicate areas that are completely conserved.

    Journal: The Journal of Cell Biology

    Article Title: Endosome to Golgi Retrieval of the Vacuolar Protein Sorting Receptor, Vps10p, Requires the Function of the VPS29, VPS30, and VPS35 Gene Products

    doi:

    Figure Lengend Snippet: VPS35 , VPS30, and VPS29 are highly conserved in eukaryotes. ( A ) Schematic view of homology between Vps35p and proteins found in the C. elegans and M. musculus proteomes. The numbers between the proteins are percent identities between Vps35p and the other two proteins. In the lower section, the two most highly conserved domains (designated domains I and III) are aligned to show the regions of greatest homology between the yeast, mouse, nematode, and also human homologues. The black boxes indicate completely conserved residues. ( B ) Alignments between Vps29p and homologues present in the proteomes of C. elegans and H. sapiens , and also alignments between Vps30p and homologues present in the proteomes of C. elegans and H. sapiens . Black shaded regions indicate areas that are completely conserved.

    Article Snippet: Constructs for sequencing the VPS29 gene were made by treating pEMY29-1 with exonuclease III and mung bean nuclease as described in the Stratagene BlueScript manual.

    Techniques:

    Analysis of polysomal mRNA. Data from spermidine- and arginine-grown cultures are shown on the left and right, respectively, and the tops of the gradients are to the right. (A) A 254 profile of 10 to 40% sucrose gradients. (B) Northern blot analysis of spe-1 mRNA from the aga strain (IC3). (C) Northern blot analysis of spe-1 mRNA from transformant DMH3, lacking the 5′-UTR sequences between the Afl III and Nru I sites. (D) Northern blot analysis of tub mRNA of strain IC3 shown in panel B ( tub mRNA from DMH3 was similar). Polysomal fractions are aligned below their approximate positions in the gradient.

    Journal: Molecular and Cellular Biology

    Article Title: Polyamine Regulation of Ornithine Decarboxylase Synthesis in Neurospora crassa

    doi:

    Figure Lengend Snippet: Analysis of polysomal mRNA. Data from spermidine- and arginine-grown cultures are shown on the left and right, respectively, and the tops of the gradients are to the right. (A) A 254 profile of 10 to 40% sucrose gradients. (B) Northern blot analysis of spe-1 mRNA from the aga strain (IC3). (C) Northern blot analysis of spe-1 mRNA from transformant DMH3, lacking the 5′-UTR sequences between the Afl III and Nru I sites. (D) Northern blot analysis of tub mRNA of strain IC3 shown in panel B ( tub mRNA from DMH3 was similar). Polysomal fractions are aligned below their approximate positions in the gradient.

    Article Snippet: This plasmid was used as starting material for 5′-to-3′ deletions from the spe-1 upstream Pst I site using an exonuclease III/mung bean nuclease deletion kit (Stratagene) as specified by the manufacturer.

    Techniques: Northern Blot

    Restriction map of the spe-1 gene and flanking sequences found in plasmids pPHL1 and pPH1. The boxed area represents the transcribed region, beginning with the right-pointing arrow. The coding sequence, interrupted by one intron, is shown in black. Abbreviations: MCS, multiple-cloning site; B, Bgl II; V, Eco V; C, Cla I; R, Eco RI; P, Pst I; S, Sac I; A, Afl III; N, Nru I; K, Kpn I; Sa, Sal I; H, Hin dIII.

    Journal: Molecular and Cellular Biology

    Article Title: Polyamine Regulation of Ornithine Decarboxylase Synthesis in Neurospora crassa

    doi:

    Figure Lengend Snippet: Restriction map of the spe-1 gene and flanking sequences found in plasmids pPHL1 and pPH1. The boxed area represents the transcribed region, beginning with the right-pointing arrow. The coding sequence, interrupted by one intron, is shown in black. Abbreviations: MCS, multiple-cloning site; B, Bgl II; V, Eco V; C, Cla I; R, Eco RI; P, Pst I; S, Sac I; A, Afl III; N, Nru I; K, Kpn I; Sa, Sal I; H, Hin dIII.

    Article Snippet: This plasmid was used as starting material for 5′-to-3′ deletions from the spe-1 upstream Pst I site using an exonuclease III/mung bean nuclease deletion kit (Stratagene) as specified by the manufacturer.

    Techniques: Sequencing, Clone Assay

    Role of the UAR on the regulation of spe-1 genes lacking the Afl III- Nru I segment of the 5′-UTR. (A) Schematic of spe-1 genes lacking 5′-UTR sequences in which the spe-1 UAR is either present (DMH3) or absent (DMH4). The positions of the Afl III and Nru I sites of the 5′-UTR are indicated. (B) Northern blot analysis of repressed (SPD) and derepressed (ARG) cultures of the transformants. Northern blots were hybridized with probes derived from spe-1 cDNA or the coding region of the tub gene.

    Journal: Molecular and Cellular Biology

    Article Title: Polyamine Regulation of Ornithine Decarboxylase Synthesis in Neurospora crassa

    doi:

    Figure Lengend Snippet: Role of the UAR on the regulation of spe-1 genes lacking the Afl III- Nru I segment of the 5′-UTR. (A) Schematic of spe-1 genes lacking 5′-UTR sequences in which the spe-1 UAR is either present (DMH3) or absent (DMH4). The positions of the Afl III and Nru I sites of the 5′-UTR are indicated. (B) Northern blot analysis of repressed (SPD) and derepressed (ARG) cultures of the transformants. Northern blots were hybridized with probes derived from spe-1 cDNA or the coding region of the tub gene.

    Article Snippet: This plasmid was used as starting material for 5′-to-3′ deletions from the spe-1 upstream Pst I site using an exonuclease III/mung bean nuclease deletion kit (Stratagene) as specified by the manufacturer.

    Techniques: Northern Blot, Derivative Assay

    Expression of various spe-1 and chimeric transcripts driven by the β-tubulin ( tub ) promoter of N. crassa . (A) Schematic diagram of tub :: spe-1 genes introduced into strain IC54, with functional regions of each gene listed across the top. The spe-1 sequences are represented by open boxes; and tub sequences are represented by shaded boxes. The positions of the Afl III and Nru I sites in the spe-1 5′-UTR are shown. (B) Northern blots of 10 μg of total RNA from repressed (SPD) or derepressed (ARG) cultures, probed with spe-1 cDNA or the coding region of tub DNA. The relative abundance of tub :: spe-1 mRNA in each transformant, normalized to tub mRNA and relative to that in DMH43/SPD, is given below the panel.

    Journal: Molecular and Cellular Biology

    Article Title: Polyamine Regulation of Ornithine Decarboxylase Synthesis in Neurospora crassa

    doi:

    Figure Lengend Snippet: Expression of various spe-1 and chimeric transcripts driven by the β-tubulin ( tub ) promoter of N. crassa . (A) Schematic diagram of tub :: spe-1 genes introduced into strain IC54, with functional regions of each gene listed across the top. The spe-1 sequences are represented by open boxes; and tub sequences are represented by shaded boxes. The positions of the Afl III and Nru I sites in the spe-1 5′-UTR are shown. (B) Northern blots of 10 μg of total RNA from repressed (SPD) or derepressed (ARG) cultures, probed with spe-1 cDNA or the coding region of tub DNA. The relative abundance of tub :: spe-1 mRNA in each transformant, normalized to tub mRNA and relative to that in DMH43/SPD, is given below the panel.

    Article Snippet: This plasmid was used as starting material for 5′-to-3′ deletions from the spe-1 upstream Pst I site using an exonuclease III/mung bean nuclease deletion kit (Stratagene) as specified by the manufacturer.

    Techniques: Expressing, Functional Assay, Northern Blot

    Effects of 5′-to-3′ deletions of the spe-1 upstream region on ODC activity and derepression of spe-1 mRNA. (A) Schematic representation of the wild-type (P2) and deleted spe-1 genes integrated at the his-3 locus of strain IC2794-5. Distances from the major transcription start site, indicated by the arrow, are given in base pairs. The relative positions of the Pst I (−1000), Sac I (−167), and Afl III (+97) sites are also shown. ODC activity (in units per milligram of protein) of the transformants grown with 1 mM spermidine (SPD) or 1 mM arginine (ARG) are given to the right. (B) Northern blots of total RNA (10 μg) from repressed (left) and derepressed (right) cultures of these transformants were probed with spe-1 cDNA ( spe-1 ) or a fragment of the β-tubulin gene ( tub ), the latter as a loading control. Lanes: 1, P2; 2, PΔ1; 3, PΔ2; 4, PΔ3; 5, PΔ4; 6, PΔ5; 7, S8; 8, PΔ6; 9, PΔ7. (C) Approximately 25 μg of total RNA from the derepressed transformants was analyzed by primer extension reactions with the MH12 primer to determine the 5′ ends of their spe-1 transcripts. The molecular size marker on the right is given in nucleotides. Lanes are labeled as in panel B.

    Journal: Molecular and Cellular Biology

    Article Title: Polyamine Regulation of Ornithine Decarboxylase Synthesis in Neurospora crassa

    doi:

    Figure Lengend Snippet: Effects of 5′-to-3′ deletions of the spe-1 upstream region on ODC activity and derepression of spe-1 mRNA. (A) Schematic representation of the wild-type (P2) and deleted spe-1 genes integrated at the his-3 locus of strain IC2794-5. Distances from the major transcription start site, indicated by the arrow, are given in base pairs. The relative positions of the Pst I (−1000), Sac I (−167), and Afl III (+97) sites are also shown. ODC activity (in units per milligram of protein) of the transformants grown with 1 mM spermidine (SPD) or 1 mM arginine (ARG) are given to the right. (B) Northern blots of total RNA (10 μg) from repressed (left) and derepressed (right) cultures of these transformants were probed with spe-1 cDNA ( spe-1 ) or a fragment of the β-tubulin gene ( tub ), the latter as a loading control. Lanes: 1, P2; 2, PΔ1; 3, PΔ2; 4, PΔ3; 5, PΔ4; 6, PΔ5; 7, S8; 8, PΔ6; 9, PΔ7. (C) Approximately 25 μg of total RNA from the derepressed transformants was analyzed by primer extension reactions with the MH12 primer to determine the 5′ ends of their spe-1 transcripts. The molecular size marker on the right is given in nucleotides. Lanes are labeled as in panel B.

    Article Snippet: This plasmid was used as starting material for 5′-to-3′ deletions from the spe-1 upstream Pst I site using an exonuclease III/mung bean nuclease deletion kit (Stratagene) as specified by the manufacturer.

    Techniques: Activity Assay, Northern Blot, Marker, Labeling