ndei New England Biolabs Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs ndei
    <t>DNA</t> site requirements for cleavage by LlaGI. ( A and B ) Plasmid substrates with no sites, one-site or two indirectly-repeated sites were incubated with either saturating BamHI (B) or LlaGI (L) for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. ( C and D ) Plasmid substrates with two directly-repeated sites (pHT-12) or two indirectly-repeated sites (pHH-12) were cleaved with either AlwNI (A) or <t>NdeI</t> (N) to produce the linear DNA indicated. Sequences of the LlaGI sites are in Figure 3 . The parental plasmids and linear DNA were then incubated with saturating LlaGI for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. See main text for full details. Under these assay conditions, an additional slowly-migrating band was observed which we assign to a LlaGI-DNA bandshift. Gels labelled as in Figure 3 .
    Ndei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6328 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ndei/product/New England Biolabs
    Average 99 stars, based on 6328 article reviews
    Price from $9.99 to $1999.99
    ndei - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher t4 dna ligase
    <t>DNA</t> site requirements for cleavage by LlaGI. ( A and B ) Plasmid substrates with no sites, one-site or two indirectly-repeated sites were incubated with either saturating BamHI (B) or LlaGI (L) for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. ( C and D ) Plasmid substrates with two directly-repeated sites (pHT-12) or two indirectly-repeated sites (pHH-12) were cleaved with either AlwNI (A) or <t>NdeI</t> (N) to produce the linear DNA indicated. Sequences of the LlaGI sites are in Figure 3 . The parental plasmids and linear DNA were then incubated with saturating LlaGI for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. See main text for full details. Under these assay conditions, an additional slowly-migrating band was observed which we assign to a LlaGI-DNA bandshift. Gels labelled as in Figure 3 .
    T4 Dna Ligase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25057 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 dna ligase/product/Thermo Fisher
    Average 99 stars, based on 25057 article reviews
    Price from $9.99 to $1999.99
    t4 dna ligase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs t4 dna ligase
    Interaction of HMO2 with plasmid DNA. ( A , B ) Agarose gel retardation of 100 ng plasmid DNA titrated with HMO2. (A) Reactions with supercoiled pGEM5. Lane 1, DNA only, lanes 2–7 with 1.0–6.0 μM HMO2. (B) Reactions with linearized pGEM5. Lane 1, DNA only, lanes 2–6 with 1.0–5.0 μM HMO2. ( C ) HMO2 supercoils relaxed DNA. Lane 1, 100 ng supercoiled pUC18 DNA. Lane 2, nicked pUC18. Lane 3, nicked pUC18 and <t>T4</t> DNA ligase. Lanes 4–8, nicked DNA and T4 DNA ligase with 100, 500, 1000, 2000 and 3000 nM HMO2.
    T4 Dna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 49958 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 dna ligase/product/New England Biolabs
    Average 99 stars, based on 49958 article reviews
    Price from $9.99 to $1999.99
    t4 dna ligase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs xhoi
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Xhoi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 9984 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xhoi/product/New England Biolabs
    Average 99 stars, based on 9984 article reviews
    Price from $9.99 to $1999.99
    xhoi - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs bamhi
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Bamhi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11236 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bamhi/product/New England Biolabs
    Average 99 stars, based on 11236 article reviews
    Price from $9.99 to $1999.99
    bamhi - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs hindiii
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Hindiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8137 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hindiii/product/New England Biolabs
    Average 99 stars, based on 8137 article reviews
    Price from $9.99 to $1999.99
    hindiii - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs ecori
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Ecori, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10938 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori/product/New England Biolabs
    Average 99 stars, based on 10938 article reviews
    Price from $9.99 to $1999.99
    ecori - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Millipore ndei
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Ndei, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 13502 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ndei/product/Millipore
    Average 99 stars, based on 13502 article reviews
    Price from $9.99 to $1999.99
    ndei - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs phusion dna polymerase
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Phusion Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 14836 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phusion dna polymerase/product/New England Biolabs
    Average 99 stars, based on 14836 article reviews
    Price from $9.99 to $1999.99
    phusion dna polymerase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Qiagen qiaquick gel extraction kit
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Qiaquick Gel Extraction Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 113321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qiaquick gel extraction kit/product/Qiagen
    Average 99 stars, based on 113321 article reviews
    Price from $9.99 to $1999.99
    qiaquick gel extraction kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs q5 site directed mutagenesis kit
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Q5 Site Directed Mutagenesis Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11828 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q5 site directed mutagenesis kit/product/New England Biolabs
    Average 99 stars, based on 11828 article reviews
    Price from $9.99 to $1999.99
    q5 site directed mutagenesis kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs q5 high fidelity dna polymerase
    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An <t>NdeI</t> restriction site (CATATG) has been added to the N-terminal end of the sequence, and an <t>XhoI</t> restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)
    Q5 High Fidelity Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 9046 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q5 high fidelity dna polymerase/product/New England Biolabs
    Average 99 stars, based on 9046 article reviews
    Price from $9.99 to $1999.99
    q5 high fidelity dna polymerase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs bamhi hf
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Bamhi Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1377 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bamhi hf/product/New England Biolabs
    Average 99 stars, based on 1377 article reviews
    Price from $9.99 to $1999.99
    bamhi hf - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher ndei
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Ndei, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2380 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ndei/product/Thermo Fisher
    Average 99 stars, based on 2380 article reviews
    Price from $9.99 to $1999.99
    ndei - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs t4 polynucleotide kinase
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    T4 Polynucleotide Kinase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 29387 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 polynucleotide kinase/product/New England Biolabs
    Average 99 stars, based on 29387 article reviews
    Price from $9.99 to $1999.99
    t4 polynucleotide kinase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs antarctic phosphatase
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Antarctic Phosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6925 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/antarctic phosphatase/product/New England Biolabs
    Average 99 stars, based on 6925 article reviews
    Price from $9.99 to $1999.99
    antarctic phosphatase - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    98
    New England Biolabs sapi
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Sapi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 98/100, based on 728 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sapi/product/New England Biolabs
    Average 98 stars, based on 728 article reviews
    Price from $9.99 to $1999.99
    sapi - by Bioz Stars, 2020-09
    98/100 stars
      Buy from Supplier

    99
    New England Biolabs xbai
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Xbai, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6141 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xbai/product/New England Biolabs
    Average 99 stars, based on 6141 article reviews
    Price from $9.99 to $1999.99
    xbai - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs quick ligation kit
    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for <t>BamHI</t> and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. <t>DNA</t> was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.
    Quick Ligation Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4509 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/quick ligation kit/product/New England Biolabs
    Average 99 stars, based on 4509 article reviews
    Price from $9.99 to $1999.99
    quick ligation kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    Image Search Results


    DNA site requirements for cleavage by LlaGI. ( A and B ) Plasmid substrates with no sites, one-site or two indirectly-repeated sites were incubated with either saturating BamHI (B) or LlaGI (L) for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. ( C and D ) Plasmid substrates with two directly-repeated sites (pHT-12) or two indirectly-repeated sites (pHH-12) were cleaved with either AlwNI (A) or NdeI (N) to produce the linear DNA indicated. Sequences of the LlaGI sites are in Figure 3 . The parental plasmids and linear DNA were then incubated with saturating LlaGI for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. See main text for full details. Under these assay conditions, an additional slowly-migrating band was observed which we assign to a LlaGI-DNA bandshift. Gels labelled as in Figure 3 .

    Journal: Nucleic Acids Research

    Article Title: DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI

    doi: 10.1093/nar/gkp790

    Figure Lengend Snippet: DNA site requirements for cleavage by LlaGI. ( A and B ) Plasmid substrates with no sites, one-site or two indirectly-repeated sites were incubated with either saturating BamHI (B) or LlaGI (L) for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. ( C and D ) Plasmid substrates with two directly-repeated sites (pHT-12) or two indirectly-repeated sites (pHH-12) were cleaved with either AlwNI (A) or NdeI (N) to produce the linear DNA indicated. Sequences of the LlaGI sites are in Figure 3 . The parental plasmids and linear DNA were then incubated with saturating LlaGI for 1 h. Substrates and products were separated by agarose gel electrophoresis as indicated. See main text for full details. Under these assay conditions, an additional slowly-migrating band was observed which we assign to a LlaGI-DNA bandshift. Gels labelled as in Figure 3 .

    Article Snippet: Linear DNA substrates were generated by incubating 4 nM plasmid DNA with 1 U/μl of AlwNI or 2 U/μl of NdeI in NEBuffer 2 (New England Biolabs, MA, USA).

    Techniques: Plasmid Preparation, Incubation, Agarose Gel Electrophoresis

    (A). Comparison of in vitro chaperone activity of α-crystallin and purified sHsp18 . Enzymes (2 U) were heat inactivated ( Sma I at 37°C for 90 min and Nde I at 45°C for 90 min) in the presence or absence of molecular chaperones (0.2 μg) and assayed for the cleavage of 1 μg of plasmid DNA. Lanes represent, λ Hind III marker (lane 1), digested plasmid (lane 2), uncut plasmid (lane 3), plasmid digested with- heat inactivated Sma I (lane 4), heat inactivated Nde I (lane 5), heat inactivated Sma I in the presence of sHsp18 (lane 6), heat inactivated Sma I in the presence of α-crystallin (lane 7), heat inactivated Nde I in the presence of sHsp18 (lane 8) and heat inactivated Nde I in the presence of α-crystallin (lane 9). (B). sHsp18 can act as a molecular chaperone in wide range of physiological temperatures. 0.2 μg sHsp18 or BSA was incubated with 2 U of Sma I at different temperatures for 90 min, and the cleavage of plasmid DNA was assayed at 25°C for 3 hrs. Lanes represent, λ Hind III marker (lane 1), uncut plasmid (lane 2), plasmid digested with Sma I as control (lane 3), plasmid incubated with heat inactivated Sma I without and with sHsp18 at 30°C (lanes 4–5); at 35°C (lanes 6–7), at 40°C (lanes 8–9), at 45°C (lanes 11–12), plasmid incubated with Sma I with BSA at 35°C, 40°C and 45°C (lanes 12–14). (C). Preheating of molecular chaperones does not affect chaperone activity. Lanes represent, λ Hind III marker (lane 1), undigested plasmid (lane 2), plasmid digested with- Sma I (lane 3), Sma I with preheated sHsp18 at 100°C for 5 min (lane 4) and with preheated α-crystallin at 100°C for 5 min (lane 5).

    Journal: BMC Microbiology

    Article Title: Functional characterization of a small heat shock protein from Mycobacterium leprae

    doi: 10.1186/1471-2180-8-208

    Figure Lengend Snippet: (A). Comparison of in vitro chaperone activity of α-crystallin and purified sHsp18 . Enzymes (2 U) were heat inactivated ( Sma I at 37°C for 90 min and Nde I at 45°C for 90 min) in the presence or absence of molecular chaperones (0.2 μg) and assayed for the cleavage of 1 μg of plasmid DNA. Lanes represent, λ Hind III marker (lane 1), digested plasmid (lane 2), uncut plasmid (lane 3), plasmid digested with- heat inactivated Sma I (lane 4), heat inactivated Nde I (lane 5), heat inactivated Sma I in the presence of sHsp18 (lane 6), heat inactivated Sma I in the presence of α-crystallin (lane 7), heat inactivated Nde I in the presence of sHsp18 (lane 8) and heat inactivated Nde I in the presence of α-crystallin (lane 9). (B). sHsp18 can act as a molecular chaperone in wide range of physiological temperatures. 0.2 μg sHsp18 or BSA was incubated with 2 U of Sma I at different temperatures for 90 min, and the cleavage of plasmid DNA was assayed at 25°C for 3 hrs. Lanes represent, λ Hind III marker (lane 1), uncut plasmid (lane 2), plasmid digested with Sma I as control (lane 3), plasmid incubated with heat inactivated Sma I without and with sHsp18 at 30°C (lanes 4–5); at 35°C (lanes 6–7), at 40°C (lanes 8–9), at 45°C (lanes 11–12), plasmid incubated with Sma I with BSA at 35°C, 40°C and 45°C (lanes 12–14). (C). Preheating of molecular chaperones does not affect chaperone activity. Lanes represent, λ Hind III marker (lane 1), undigested plasmid (lane 2), plasmid digested with- Sma I (lane 3), Sma I with preheated sHsp18 at 100°C for 5 min (lane 4) and with preheated α-crystallin at 100°C for 5 min (lane 5).

    Article Snippet: In this assay, restriction enzymes Sma I and Nde I (New England Biolabs, Beverly, MA) were used, according to the manufacturer's recommendations.

    Techniques: In Vitro, Activity Assay, Purification, Plasmid Preparation, Marker, Activated Clotting Time Assay, Incubation

    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An NdeI restriction site (CATATG) has been added to the N-terminal end of the sequence, and an XhoI restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Engineering and Flow-Cytometric Analysis of Chimeric LAGLIDADG Homing Endonucleases from Homologous I-OnuI-Family Enzymes

    doi: 10.1007/978-1-62703-968-0_14

    Figure Lengend Snippet: Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An NdeI restriction site (CATATG) has been added to the N-terminal end of the sequence, and an XhoI restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)

    Article Snippet: Restriction enzymes NdeI, KpnI-HF, and XhoI with supplied buffers and 100× BSA solution (New England Biolabs).

    Techniques: Polymerase Cycling Assembly, Selection, Sequencing

    Interaction of HMO2 with plasmid DNA. ( A , B ) Agarose gel retardation of 100 ng plasmid DNA titrated with HMO2. (A) Reactions with supercoiled pGEM5. Lane 1, DNA only, lanes 2–7 with 1.0–6.0 μM HMO2. (B) Reactions with linearized pGEM5. Lane 1, DNA only, lanes 2–6 with 1.0–5.0 μM HMO2. ( C ) HMO2 supercoils relaxed DNA. Lane 1, 100 ng supercoiled pUC18 DNA. Lane 2, nicked pUC18. Lane 3, nicked pUC18 and T4 DNA ligase. Lanes 4–8, nicked DNA and T4 DNA ligase with 100, 500, 1000, 2000 and 3000 nM HMO2.

    Journal: Nucleic Acids Research

    Article Title: The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends

    doi: 10.1093/nar/gkp695

    Figure Lengend Snippet: Interaction of HMO2 with plasmid DNA. ( A , B ) Agarose gel retardation of 100 ng plasmid DNA titrated with HMO2. (A) Reactions with supercoiled pGEM5. Lane 1, DNA only, lanes 2–7 with 1.0–6.0 μM HMO2. (B) Reactions with linearized pGEM5. Lane 1, DNA only, lanes 2–6 with 1.0–5.0 μM HMO2. ( C ) HMO2 supercoils relaxed DNA. Lane 1, 100 ng supercoiled pUC18 DNA. Lane 2, nicked pUC18. Lane 3, nicked pUC18 and T4 DNA ligase. Lanes 4–8, nicked DNA and T4 DNA ligase with 100, 500, 1000, 2000 and 3000 nM HMO2.

    Article Snippet: One hundred nanograms of linearized pGEM5 was incubated with varying concentrations of HMO2 or HMO1 at room temperature for 1 h. To this reaction, 1 μl of 400 U/μl of T4 DNA ligase was added and incubated at room temperature for 1 h. Samples were treated with exonuclease III (100 U/μl) at room temperature for 1 h. Reactions were terminated by adding 2 μl stop buffer (5 mM EDTA, 1.1% glycerol and 0.2 mg/ml proteinase K).

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis

    HMO2 prevents ligation of DNA by T4 DNA ligase. ( A ) DNA with overhangs (5′-TA extensions). ( B ) DNA with blunt ends. Lanes 1, 100 ng of DNA (∼4 nM, corresponding to ∼8 nM DNA ends). Lane 2, DNA and T4 DNA ligase. Lanes 3–8, DNA, T4 DNA ligase with 100, 500, 1000, 2000, 3000 and 4000 nM HMO2. Lane 9, DNA, T4 DNA ligase, 4000 nM HMO2 and exonuclease III.

    Journal: Nucleic Acids Research

    Article Title: The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends

    doi: 10.1093/nar/gkp695

    Figure Lengend Snippet: HMO2 prevents ligation of DNA by T4 DNA ligase. ( A ) DNA with overhangs (5′-TA extensions). ( B ) DNA with blunt ends. Lanes 1, 100 ng of DNA (∼4 nM, corresponding to ∼8 nM DNA ends). Lane 2, DNA and T4 DNA ligase. Lanes 3–8, DNA, T4 DNA ligase with 100, 500, 1000, 2000, 3000 and 4000 nM HMO2. Lane 9, DNA, T4 DNA ligase, 4000 nM HMO2 and exonuclease III.

    Article Snippet: One hundred nanograms of linearized pGEM5 was incubated with varying concentrations of HMO2 or HMO1 at room temperature for 1 h. To this reaction, 1 μl of 400 U/μl of T4 DNA ligase was added and incubated at room temperature for 1 h. Samples were treated with exonuclease III (100 U/μl) at room temperature for 1 h. Reactions were terminated by adding 2 μl stop buffer (5 mM EDTA, 1.1% glycerol and 0.2 mg/ml proteinase K).

    Techniques: Ligation

    HMO1 promotes DNA end-joining, but does not protect DNA from exonucleolytic cleavage. ( A ) HMO1 can promote end-joining of pGEM5 DNA with 2-nt 5′ overhang in presence of T4 DNA ligase. Lane 1, 100 ng DNA only. Lane 2, DNA and T4 DNA ligase. Lanes 3–5, DNA, T4 DNA ligase, and 500, 1000 and 2000 nM HMO1, respectively. ( B ) HMO1 is unable to protect DNA with 2-nt 5′ overhangs from exonuclease III. Lane 1, 100 ng DNA only. Lane 2, DNA and exonuclease III. Lane 3, DNA and 500 nM HMO1. Lanes 4–6, DNA, exonuclease III, and 500, 1000 and 2000 nM HMO1, respectively.

    Journal: Nucleic Acids Research

    Article Title: The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends

    doi: 10.1093/nar/gkp695

    Figure Lengend Snippet: HMO1 promotes DNA end-joining, but does not protect DNA from exonucleolytic cleavage. ( A ) HMO1 can promote end-joining of pGEM5 DNA with 2-nt 5′ overhang in presence of T4 DNA ligase. Lane 1, 100 ng DNA only. Lane 2, DNA and T4 DNA ligase. Lanes 3–5, DNA, T4 DNA ligase, and 500, 1000 and 2000 nM HMO1, respectively. ( B ) HMO1 is unable to protect DNA with 2-nt 5′ overhangs from exonuclease III. Lane 1, 100 ng DNA only. Lane 2, DNA and exonuclease III. Lane 3, DNA and 500 nM HMO1. Lanes 4–6, DNA, exonuclease III, and 500, 1000 and 2000 nM HMO1, respectively.

    Article Snippet: One hundred nanograms of linearized pGEM5 was incubated with varying concentrations of HMO2 or HMO1 at room temperature for 1 h. To this reaction, 1 μl of 400 U/μl of T4 DNA ligase was added and incubated at room temperature for 1 h. Samples were treated with exonuclease III (100 U/μl) at room temperature for 1 h. Reactions were terminated by adding 2 μl stop buffer (5 mM EDTA, 1.1% glycerol and 0.2 mg/ml proteinase K).

    Techniques:

    DNA protection by HMO2 depends on DNA length and sequence of DNA overhangs. ( A ) DNA with G+C-containing overhangs is not protected by HMO2. Lanes 1–4, DNA with 5′-CATG extensions (∼2 nM), lanes 5–8, DNA with 5′-TA extensions (∼4 nM). Lanes 1 and 5, DNA only. Lanes 2 and 6, DNA treated with exonuclease III for 1 h. Lanes 3 and 7, DNA and 2000 nM HMO2. Lanes 4 and 8, DNA with 2000 nM HMO2 incubated with exonuclease III for 1 h. Note in lane 8 the appearance of a product with lower mobility. Only the two largest fragments of BspHI-digested pET5a are shown in lanes 1–4. ( B ) Ligation of DNA with 5′-CATG extension (∼2 nM). Lane 1, DNA only. Lane 2, DNA and T4 DNA ligase. Lane 3, DNA, T4 DNA ligase and 2.5 µM HMO2. ( C ) Length dependence of DNA protection by HMO2. Lane 1, DNA with 4-nt 5′ overhangs. Lane 2, DNA treated with exonuclease III for 1 h. Lane 3, DNA and 2000 nM HMO2. Lane 4, DNA incubated with HMO2 and exonuclease III for 1 h. ( D ) HMO2 can end-join 105 bp DNA in presence of T4 DNA ligase. Lane 1, 100 fmol of 105 bp DNA. Lane 2, 105 bp DNA and T4 DNA ligase. Lanes 3–5, 105 bp DNA, T4 DNA ligase and 100, 250 and 500 nM HMO2. Lane 6, 105 bp DNA, T4 DNA ligase and 100 nM B. subtilis HU (HBsu). Lane 7, 105 bp DNA, T4 DNA ligase, 100 nM B. subtilis HU and exonuclease III. Lane 8, 105 bp DNA, T4 DNA ligase, 250 nM HMO2 and exonuclease III.

    Journal: Nucleic Acids Research

    Article Title: The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends

    doi: 10.1093/nar/gkp695

    Figure Lengend Snippet: DNA protection by HMO2 depends on DNA length and sequence of DNA overhangs. ( A ) DNA with G+C-containing overhangs is not protected by HMO2. Lanes 1–4, DNA with 5′-CATG extensions (∼2 nM), lanes 5–8, DNA with 5′-TA extensions (∼4 nM). Lanes 1 and 5, DNA only. Lanes 2 and 6, DNA treated with exonuclease III for 1 h. Lanes 3 and 7, DNA and 2000 nM HMO2. Lanes 4 and 8, DNA with 2000 nM HMO2 incubated with exonuclease III for 1 h. Note in lane 8 the appearance of a product with lower mobility. Only the two largest fragments of BspHI-digested pET5a are shown in lanes 1–4. ( B ) Ligation of DNA with 5′-CATG extension (∼2 nM). Lane 1, DNA only. Lane 2, DNA and T4 DNA ligase. Lane 3, DNA, T4 DNA ligase and 2.5 µM HMO2. ( C ) Length dependence of DNA protection by HMO2. Lane 1, DNA with 4-nt 5′ overhangs. Lane 2, DNA treated with exonuclease III for 1 h. Lane 3, DNA and 2000 nM HMO2. Lane 4, DNA incubated with HMO2 and exonuclease III for 1 h. ( D ) HMO2 can end-join 105 bp DNA in presence of T4 DNA ligase. Lane 1, 100 fmol of 105 bp DNA. Lane 2, 105 bp DNA and T4 DNA ligase. Lanes 3–5, 105 bp DNA, T4 DNA ligase and 100, 250 and 500 nM HMO2. Lane 6, 105 bp DNA, T4 DNA ligase and 100 nM B. subtilis HU (HBsu). Lane 7, 105 bp DNA, T4 DNA ligase, 100 nM B. subtilis HU and exonuclease III. Lane 8, 105 bp DNA, T4 DNA ligase, 250 nM HMO2 and exonuclease III.

    Article Snippet: One hundred nanograms of linearized pGEM5 was incubated with varying concentrations of HMO2 or HMO1 at room temperature for 1 h. To this reaction, 1 μl of 400 U/μl of T4 DNA ligase was added and incubated at room temperature for 1 h. Samples were treated with exonuclease III (100 U/μl) at room temperature for 1 h. Reactions were terminated by adding 2 μl stop buffer (5 mM EDTA, 1.1% glycerol and 0.2 mg/ml proteinase K).

    Techniques: Sequencing, Incubation, Ligation

    Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An NdeI restriction site (CATATG) has been added to the N-terminal end of the sequence, and an XhoI restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Engineering and Flow-Cytometric Analysis of Chimeric LAGLIDADG Homing Endonucleases from Homologous I-OnuI-Family Enzymes

    doi: 10.1007/978-1-62703-968-0_14

    Figure Lengend Snippet: Example of assembly PCR primers and introduction of variation via degenerate codons. Each colored selection represents a single assembly primer; the sum of all primers is designed to produce the entire coding sequence shown. An NdeI restriction site (CATATG) has been added to the N-terminal end of the sequence, and an XhoI restriction site (CTCGAG) has been added to the C-terminal end. The magnified inset towards the C-terminal end of the sequence gives an example of introducing variation using the degenerate codon “RAA.” The “R” base designates the introduction of either a guanine (G) or adenine (A) base at that position, resulting in a translated protein sequence with either glutamic acid (E) or lysine (K)

    Article Snippet: Restriction enzymes NdeI, KpnI-HF, and XhoI with supplied buffers and 100× BSA solution (New England Biolabs).

    Techniques: Polymerase Cycling Assembly, Selection, Sequencing

    Polymerase Chain Reaction Amplification and Restriction Enzyme Analyses of Different Plasmids by NdeI and XhoI Restriction Enzymes and Comparison of Undigested and Digested Patterns of Plasmids With orf2.1 and orf2.2 on Agarose Gel Electrophoresis PCR amplification and restriction enzyme analyses of plasmids pBluescript II SK-ORF2.1, pET30a-ORF2.1, pET30a-ORF2.2, and pET30a+ without ORF2.1 by NdeI and XhoI restriction enzymes. Lane 1, the 1 kb DNA marker; Lane 2, the undigested plasmid pET30a+; Lane 3, the digested plasmid pET30a+; Lane 4, the undigested pBluescript II SK-ORF2.1; Lane 5, the digested pBluescript II SK-ORF2.1; Lane 6, the undigested plasmid pET30a-ORF2.1; Lane 7, the digested plasmid pET30a- ORF2.1; Lane 8, the amplified orf2.1 gene by PCR (with T7 promoter and T7 terminator primers); Lane 9, the undigested plasmid pET30a-ORF2.2; Lane 10, the digested plasmid pET30a-ORF2.2; Lane 11, the amplified orf2.2 gene by PCR (with T7 promoter and T7 terminator primers); Lane 13, the 1kb DNA marker; Lane 14, the amplified orf2.1 gene by PCR; and Lane 15, the amplified orf2.2 gene by PCR.

    Journal: Jundishapur Journal of Microbiology

    Article Title: Codon-Optimized Expression and Purification of Truncated ORF2 Protein of Hepatitis E Virus in Escherichia coli

    doi: 10.5812/jjm.11261

    Figure Lengend Snippet: Polymerase Chain Reaction Amplification and Restriction Enzyme Analyses of Different Plasmids by NdeI and XhoI Restriction Enzymes and Comparison of Undigested and Digested Patterns of Plasmids With orf2.1 and orf2.2 on Agarose Gel Electrophoresis PCR amplification and restriction enzyme analyses of plasmids pBluescript II SK-ORF2.1, pET30a-ORF2.1, pET30a-ORF2.2, and pET30a+ without ORF2.1 by NdeI and XhoI restriction enzymes. Lane 1, the 1 kb DNA marker; Lane 2, the undigested plasmid pET30a+; Lane 3, the digested plasmid pET30a+; Lane 4, the undigested pBluescript II SK-ORF2.1; Lane 5, the digested pBluescript II SK-ORF2.1; Lane 6, the undigested plasmid pET30a-ORF2.1; Lane 7, the digested plasmid pET30a- ORF2.1; Lane 8, the amplified orf2.1 gene by PCR (with T7 promoter and T7 terminator primers); Lane 9, the undigested plasmid pET30a-ORF2.2; Lane 10, the digested plasmid pET30a-ORF2.2; Lane 11, the amplified orf2.2 gene by PCR (with T7 promoter and T7 terminator primers); Lane 13, the 1kb DNA marker; Lane 14, the amplified orf2.1 gene by PCR; and Lane 15, the amplified orf2.2 gene by PCR.

    Article Snippet: Subcloning and Plasmid Construction For subcloning the optimized orf2.1 gene into the expression vector pET-30a (+) (Novagen, Madison, WI, USA), the pBlue script II SK(+) vector carrying optimized orf2.1 gene (pBluescript II SK-ORF2.1) and the plasmid pET30a+ were both digested by NdeI and XhoI restriction enzymes (New England BioLab, USA).

    Techniques: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Marker, Plasmid Preparation

    Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for BamHI and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. DNA was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.

    Journal: bioRxiv

    Article Title: Age-dependent ribosomal DNA variations and their effect on cellular function in mammalian cells

    doi: 10.1101/2020.07.10.196840

    Figure Lengend Snippet: Detection of relative rDNA copy number in old and young mice (A) Position of the probe for Southern blot analysis in ( BC ) and recognition sites for BamHI and NdeI are shown. ( BC ) Detection of relative rDNA copy number. (Top panel) Southern analysis for rDNA copy number. DNA was digested with BamHI and NdeI. Upper bands (4 kb) come from rDNA units without BamHI-2 site and lower bands (2.4 kb) from rDNA units with BamHI-2 site. (Middle panel) Detection of SWI5 gene as a loading control. A single copy gene SWI5 was detected on the same filter used in the upper panel. (Bottom panel) Relative amount of rDNA copy number. The band intensities of rDNA were normalized by those of SWI5 and the values are relative to the average of rDNA values in the four young mice. The blue dots show the results from the upper band intensities of rDNA and the red dots are the results from the lower bands. ID# is the identification number of individual mice that were used to isolate the bone marrow cells ( Figure 1 ). p values are shown at the bottom of the panel. n.s. is “not significant”.

    Article Snippet: Southern blot analysis to detect rDNA For Southern blot analysis 150 ng of mouse DNA was digested with 10 units of BamHI-HF (NEB, and ), NdeI (NEB, and ) and SacII (NEB, ) overnight at 37°C.

    Techniques: Mouse Assay, Southern Blot