exonuclease iii Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs exonuclease iii exoiii
    Structural characterization of AQ-157TG rNCPs. ( A ) Exonuclease <t>III</t> footprinting of AQ-157TG rNCPs (lane 1) and free AQ-157TG (lane 2). The restriction of <t>ExoIII</t> activity to the ∼10 bp proximal to AQ in the AQ-157TG rNCPs is evident. ( B ) Autoradiogram of hydroxyl radical footprinting on AQ-157TG rNCPs (lanes 1 and 2) and free AQ-157TG (lane 3). ( C ) Partial scan of the footprint in B of both free AQ-157TG (bottom) and AQ-157TG rNCPs (top). The 10 bp periodic cutting in the rNCPs is apparent.
    Exonuclease Iii Exoiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii exoiii/product/New England Biolabs
    Average 99 stars, based on 45 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii exoiii - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    94
    Thermo Fisher exonuclease iii
    Evidence of a covalently linked 5′ TP. (A) <t>DNA-protein</t> complex (lane 1), complex treated with exonuclease <t>III</t> for 15 min (lane 2), complex treated with exonuclease III for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with exonuclease III for 15 min (lane 5), and PK-DNA treated with exonuclease III for 30 min (lane 6). (B) DNA-protein complex (lane 1), complex treated with λ exonuclease for 15 min (lane 2), complex treated with λ exonuclease for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with λ exonuclease for 30 min (lane 5), PK-DNA treated with 0.5 M piperidine (lane 6), PK-DNA treated with piperidine and λ exonuclease for 30 min (lane 7). The amounts used are indicated in Materials and Methods.
    Exonuclease Iii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 294 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Thermo Fisher
    Average 94 stars, based on 294 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    94/100 stars
      Buy from Supplier

    93
    TaKaRa exonuclease iii
    Analysis of terminal restriction fragments from replicated linear DNAs. (A and B) The bound fraction of pSVO11-bead replication products was purified and treated with either λ exonuclease or exonuclease <t>III.</t> To know the exonuclease digestion rates, we treated a separately prepared 199-bp terminal fragment with these exonucleases and found that under the employed conditions, approximately 100 nt is digested from the ends, albeit relatively asymmetrically (data not shown). After the digestion, a half aliquot of the <t>DNA</t> was further treated with Dra I, which produces 199- and 497-bp fragments from the left and right arms of the DNA, respectively (A). Samples were run in a 6% denaturing acrylamide gel, dried, and autoradiographed. Heavily and lightly exposed autoradiographs of the same gel are shown. Control pSVO11 DNA was digested with Bsr FI, and the two ends were filled-in with dNTPs. The resultant blunt-ended linear pSVO11 was first treated with either λ exonuclease or exonuclease III, followed by Dra I digestion. The products were first dephosphorylated by alkaline phosphatase at their 5′ ends and then labeled by T4 polynucleotide kinase and [γ- 32 P]ATP. Dra I digests DNA at a TTT/AAA site, leaving blunt ends. Therefore, the two 199-nt and 497-nt fragment strands have the same nucleotide lengths (arrows). However, because of the effect of different base compositions on migration rates, two distinct 199-nt single-stranded DNA bands are visible in lane 1. The upper and lower bands (marked by open and filled circles, respectively) of the 199-nt doublet were completely digested by λ exonuclease and exonuclease III, respectively (lanes 2 to 5). The 199- and 197-nt bands were detected in pSV011-band replication products. These two bands were resistant to λ exonuclease (lanes 9 and 11). In contrast, the 199-nt band was completely digested, and the 497-nt band was significantly trimmed by exonuclease III (lanes 13 and 15; shorter-sized 497-nt bands are indicated by a bracket). These results indicate that the observed 497- and 199-nt bands were derived solely from a strand whose 3′ ends correspond to nascent radiolabeled DNA ends. Several extra bands were observed in lane 7. We do not know the precise origin of these signals. However, because they are both λ exonuclease and exonuclease III sensitive, it is likely they represent unligated lagging strand DNA molecules derived from internal template regions. It seemed that λ exonuclease had reached the Dra I site on the template (cold) strand of some molecules, because the signal intensity of the 199-nt band decreased after the λ exonuclease treatment.
    Exonuclease Iii, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 175 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/TaKaRa
    Average 93 stars, based on 175 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    93/100 stars
      Buy from Supplier

    93
    Promega exonuclease iii
    Deletion of the 20q-TERRA locus decreases telomere length and protection in U2OS cells. ( a ) Q-FISH images obtained from metaphases spreads from U2OS cells WT and KO for the Chr20q-TERRA locus (clones A4, B4 and C4). (Left graphs) Frequency graphs of telomere length (a.u.) distribution measured in WT and in the 20q-KO cells (clones A4, B4 and C4) from <t>three</t> independent experiments. The mean telomere length and the number of telomeres and metaphases analyzed is shown. The red lines are arbitrary lines placed in the exact same position in each frequency graph to visualize differences between the 20q-KO clones and the WT controls (right graphs) The mean telomere length, the percentage of short telomeres and the quantification of signal-free ends per metaphase are also represented. Short telomeres are considered those in the 10% percentile of the total telomere length distribution. Total number of metaphases used for the statistical analysis is indicated. Scale bar, 10 μm and (zoom) 1 μm. ( b ) WT and 20q-KO cells were analyzed for T-SCE events with G-rich (green) and C-rich (red) PNA probes. The fraction of chromosome ends with T-SCE obtained from three different experiments was quantified and graphed as the mean values±s.e.m., n =30 metaphases. The number of metaphases analyzed is shown. Only events in which interchange of both colours were quantified (see examples of no-T-SCE and T-SCE). The quantification was carried out by counting the number of events in the same chromosome or in different chromosomes and then normalizing it by the total number of chromosomes observed in each metaphase. Scale bar, 1 μm. ( c ) Quantification of <t>DNA-containing</t> double minute chromosomes (TDMs) in WT and 20q-KO cells from three different experiments (mean values±s.e.m., n =30 metaphases). An example of TDMs is shown. One-way Anova with Dunnett's post test was used for all statistical analysis (* P
    Exonuclease Iii, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 596 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Promega
    Average 93 stars, based on 596 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    93/100 stars
      Buy from Supplier

    92
    GE Healthcare exonuclease iii
    Deletion of the 20q-TERRA locus decreases telomere length and protection in U2OS cells. ( a ) Q-FISH images obtained from metaphases spreads from U2OS cells WT and KO for the Chr20q-TERRA locus (clones A4, B4 and C4). (Left graphs) Frequency graphs of telomere length (a.u.) distribution measured in WT and in the 20q-KO cells (clones A4, B4 and C4) from <t>three</t> independent experiments. The mean telomere length and the number of telomeres and metaphases analyzed is shown. The red lines are arbitrary lines placed in the exact same position in each frequency graph to visualize differences between the 20q-KO clones and the WT controls (right graphs) The mean telomere length, the percentage of short telomeres and the quantification of signal-free ends per metaphase are also represented. Short telomeres are considered those in the 10% percentile of the total telomere length distribution. Total number of metaphases used for the statistical analysis is indicated. Scale bar, 10 μm and (zoom) 1 μm. ( b ) WT and 20q-KO cells were analyzed for T-SCE events with G-rich (green) and C-rich (red) PNA probes. The fraction of chromosome ends with T-SCE obtained from three different experiments was quantified and graphed as the mean values±s.e.m., n =30 metaphases. The number of metaphases analyzed is shown. Only events in which interchange of both colours were quantified (see examples of no-T-SCE and T-SCE). The quantification was carried out by counting the number of events in the same chromosome or in different chromosomes and then normalizing it by the total number of chromosomes observed in each metaphase. Scale bar, 1 μm. ( c ) Quantification of <t>DNA-containing</t> double minute chromosomes (TDMs) in WT and 20q-KO cells from three different experiments (mean values±s.e.m., n =30 metaphases). An example of TDMs is shown. One-way Anova with Dunnett's post test was used for all statistical analysis (* P
    Exonuclease Iii, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/GE Healthcare
    Average 92 stars, based on 51 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    92
    Roche exonuclease iii
    Deletion of the 20q-TERRA locus decreases telomere length and protection in U2OS cells. ( a ) Q-FISH images obtained from metaphases spreads from U2OS cells WT and KO for the Chr20q-TERRA locus (clones A4, B4 and C4). (Left graphs) Frequency graphs of telomere length (a.u.) distribution measured in WT and in the 20q-KO cells (clones A4, B4 and C4) from <t>three</t> independent experiments. The mean telomere length and the number of telomeres and metaphases analyzed is shown. The red lines are arbitrary lines placed in the exact same position in each frequency graph to visualize differences between the 20q-KO clones and the WT controls (right graphs) The mean telomere length, the percentage of short telomeres and the quantification of signal-free ends per metaphase are also represented. Short telomeres are considered those in the 10% percentile of the total telomere length distribution. Total number of metaphases used for the statistical analysis is indicated. Scale bar, 10 μm and (zoom) 1 μm. ( b ) WT and 20q-KO cells were analyzed for T-SCE events with G-rich (green) and C-rich (red) PNA probes. The fraction of chromosome ends with T-SCE obtained from three different experiments was quantified and graphed as the mean values±s.e.m., n =30 metaphases. The number of metaphases analyzed is shown. Only events in which interchange of both colours were quantified (see examples of no-T-SCE and T-SCE). The quantification was carried out by counting the number of events in the same chromosome or in different chromosomes and then normalizing it by the total number of chromosomes observed in each metaphase. Scale bar, 1 μm. ( c ) Quantification of <t>DNA-containing</t> double minute chromosomes (TDMs) in WT and 20q-KO cells from three different experiments (mean values±s.e.m., n =30 metaphases). An example of TDMs is shown. One-way Anova with Dunnett's post test was used for all statistical analysis (* P
    Exonuclease Iii, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Roche
    Average 92 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    92
    Sangon Biotech exonuclease iii
    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by <t>DNase</t> I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo <t>III.</t>
    Exonuclease Iii, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Sangon Biotech
    Average 92 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    92
    Toyobo exonuclease iii
    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by <t>DNase</t> I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo <t>III.</t>
    Exonuclease Iii, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Toyobo
    Average 92 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    92
    Boehringer Mannheim exonuclease iii
    Enhancement of <t>UDGase</t> activity by exonuclease <t>III.</t> Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.
    Exonuclease Iii, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/Boehringer Mannheim
    Average 92 stars, based on 29 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    88
    Roche exonuclease iii exoiii
    Enhancement of <t>UDGase</t> activity by exonuclease <t>III.</t> Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.
    Exonuclease Iii Exoiii, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii exoiii/product/Roche
    Average 88 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii exoiii - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    88
    Promega exonuclease iii exoiii
    Enhancement of <t>UDGase</t> activity by exonuclease <t>III.</t> Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.
    Exonuclease Iii Exoiii, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii exoiii/product/Promega
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii exoiii - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    88
    Fisher Scientific exonuclease iii exoiii
    Enhancement of <t>UDGase</t> activity by exonuclease <t>III.</t> Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.
    Exonuclease Iii Exoiii, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii exoiii/product/Fisher Scientific
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii exoiii - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    85
    Promega exonuclease iii buffer
    Enhancement of <t>UDGase</t> activity by exonuclease <t>III.</t> Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.
    Exonuclease Iii Buffer, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii buffer/product/Promega
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii buffer - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

    88
    Promega exonuclease iii digestion
    Repression of <t>HIF-1β</t> promoter activity by IFN-γ. A , Cloned HIF-1β promoter and series of truncated promoter-luciferase reporter constructs generated using exonuclease <t>III</t> digestion. Relative positions of each clone and major TSSs
    Exonuclease Iii Digestion, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii digestion/product/Promega
    Average 88 stars, based on 95 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii digestion - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    Image Search Results


    Structural characterization of AQ-157TG rNCPs. ( A ) Exonuclease III footprinting of AQ-157TG rNCPs (lane 1) and free AQ-157TG (lane 2). The restriction of ExoIII activity to the ∼10 bp proximal to AQ in the AQ-157TG rNCPs is evident. ( B ) Autoradiogram of hydroxyl radical footprinting on AQ-157TG rNCPs (lanes 1 and 2) and free AQ-157TG (lane 3). ( C ) Partial scan of the footprint in B of both free AQ-157TG (bottom) and AQ-157TG rNCPs (top). The 10 bp periodic cutting in the rNCPs is apparent.

    Journal: Nucleic Acids Research

    Article Title: Attenuation of DNA charge transport by compaction into a nucleosome core particle

    doi: 10.1093/nar/gkl030

    Figure Lengend Snippet: Structural characterization of AQ-157TG rNCPs. ( A ) Exonuclease III footprinting of AQ-157TG rNCPs (lane 1) and free AQ-157TG (lane 2). The restriction of ExoIII activity to the ∼10 bp proximal to AQ in the AQ-157TG rNCPs is evident. ( B ) Autoradiogram of hydroxyl radical footprinting on AQ-157TG rNCPs (lanes 1 and 2) and free AQ-157TG (lane 3). ( C ) Partial scan of the footprint in B of both free AQ-157TG (bottom) and AQ-157TG rNCPs (top). The 10 bp periodic cutting in the rNCPs is apparent.

    Article Snippet: T4 Polynucleotide Kinase (PNK), T4 DNA Ligase (T4 Lig) and Exonuclease III (ExoIII) were purchased from New England Biolabs.

    Techniques: Footprinting, Activity Assay

    Proliferation-inducing capacity of pPCR102-2 and derivatives in HUVECs. HUVECs were transiently transfected with either pPCR102-2 ( A ), pND-A8 ( B ), pND-A2 ( C ) or pPI1-His ( D ) in order to assess their proliferation-inducing potential. Forty-eight hours post transfection, the cell populations were transduced with a GFP-encoding oncoretroviral vector, which exclusively targets proliferating cells. Forty-eight hours post-transduction, GFP-mediated fluorescence was quantified by FACS. Fluorescence values were calculated by multiplying the number of GFP-expressing cells by the average intensity of GFP expression. The relative fluorescence units were obtained by comparison with GFP-mediated fluorescence control populations (cntrl) transfected with isogenic pcDNA3.1/V5-His-TOPO. Corresponding FACS histograms are also shown. All values are representative of at least three independent experiments. FS, forward scatter; FL, fluoresence.

    Journal: Nucleic Acids Research

    Article Title: Identification of a novel proliferation-inducing determinant using lentiviral expression cloning

    doi: 10.1093/nar/gng115

    Figure Lengend Snippet: Proliferation-inducing capacity of pPCR102-2 and derivatives in HUVECs. HUVECs were transiently transfected with either pPCR102-2 ( A ), pND-A8 ( B ), pND-A2 ( C ) or pPI1-His ( D ) in order to assess their proliferation-inducing potential. Forty-eight hours post transfection, the cell populations were transduced with a GFP-encoding oncoretroviral vector, which exclusively targets proliferating cells. Forty-eight hours post-transduction, GFP-mediated fluorescence was quantified by FACS. Fluorescence values were calculated by multiplying the number of GFP-expressing cells by the average intensity of GFP expression. The relative fluorescence units were obtained by comparison with GFP-mediated fluorescence control populations (cntrl) transfected with isogenic pcDNA3.1/V5-His-TOPO. Corresponding FACS histograms are also shown. All values are representative of at least three independent experiments. FS, forward scatter; FL, fluoresence.

    Article Snippet: All PCR reactions were conducted using DyNAzyme.EXT polymerase (Finnzymes, Oulu, Finland). pND-A2 and pND-A8 represent nested deletions of pPCR102-2 which were performed by restricting pPCR102-2 with KpnI and BamHI followed by Exonuclease III (NEB, Beverly, MA) mediated digestion at 37°C for 1, 2 and 3 min, respectively.

    Techniques: Transfection, Transduction, Plasmid Preparation, Fluorescence, FACS, Expressing

    Evidence of a covalently linked 5′ TP. (A) DNA-protein complex (lane 1), complex treated with exonuclease III for 15 min (lane 2), complex treated with exonuclease III for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with exonuclease III for 15 min (lane 5), and PK-DNA treated with exonuclease III for 30 min (lane 6). (B) DNA-protein complex (lane 1), complex treated with λ exonuclease for 15 min (lane 2), complex treated with λ exonuclease for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with λ exonuclease for 30 min (lane 5), PK-DNA treated with 0.5 M piperidine (lane 6), PK-DNA treated with piperidine and λ exonuclease for 30 min (lane 7). The amounts used are indicated in Materials and Methods.

    Journal: Journal of Bacteriology

    Article Title: Genomic Sequence of C1, the First Streptococcal Phage

    doi: 10.1128/JB.185.11.3325-3332.2003

    Figure Lengend Snippet: Evidence of a covalently linked 5′ TP. (A) DNA-protein complex (lane 1), complex treated with exonuclease III for 15 min (lane 2), complex treated with exonuclease III for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with exonuclease III for 15 min (lane 5), and PK-DNA treated with exonuclease III for 30 min (lane 6). (B) DNA-protein complex (lane 1), complex treated with λ exonuclease for 15 min (lane 2), complex treated with λ exonuclease for 30 min (lane 3), PK-DNA (lane 4), PK-DNA treated with λ exonuclease for 30 min (lane 5), PK-DNA treated with 0.5 M piperidine (lane 6), PK-DNA treated with piperidine and λ exonuclease for 30 min (lane 7). The amounts used are indicated in Materials and Methods.

    Article Snippet: Aliquots (10 μg each) of the DNA-protein complex or protease K-digested DNA (PK-DNA) were treated with either 2 μl (130 U) of exonuclease III or 2 μl (11 U) of lambda exonuclease (both from Gibco/BRL) at 37°C according to the manufacturer's instructions.

    Techniques:

    Analysis of terminal restriction fragments from replicated linear DNAs. (A and B) The bound fraction of pSVO11-bead replication products was purified and treated with either λ exonuclease or exonuclease III. To know the exonuclease digestion rates, we treated a separately prepared 199-bp terminal fragment with these exonucleases and found that under the employed conditions, approximately 100 nt is digested from the ends, albeit relatively asymmetrically (data not shown). After the digestion, a half aliquot of the DNA was further treated with Dra I, which produces 199- and 497-bp fragments from the left and right arms of the DNA, respectively (A). Samples were run in a 6% denaturing acrylamide gel, dried, and autoradiographed. Heavily and lightly exposed autoradiographs of the same gel are shown. Control pSVO11 DNA was digested with Bsr FI, and the two ends were filled-in with dNTPs. The resultant blunt-ended linear pSVO11 was first treated with either λ exonuclease or exonuclease III, followed by Dra I digestion. The products were first dephosphorylated by alkaline phosphatase at their 5′ ends and then labeled by T4 polynucleotide kinase and [γ- 32 P]ATP. Dra I digests DNA at a TTT/AAA site, leaving blunt ends. Therefore, the two 199-nt and 497-nt fragment strands have the same nucleotide lengths (arrows). However, because of the effect of different base compositions on migration rates, two distinct 199-nt single-stranded DNA bands are visible in lane 1. The upper and lower bands (marked by open and filled circles, respectively) of the 199-nt doublet were completely digested by λ exonuclease and exonuclease III, respectively (lanes 2 to 5). The 199- and 197-nt bands were detected in pSV011-band replication products. These two bands were resistant to λ exonuclease (lanes 9 and 11). In contrast, the 199-nt band was completely digested, and the 497-nt band was significantly trimmed by exonuclease III (lanes 13 and 15; shorter-sized 497-nt bands are indicated by a bracket). These results indicate that the observed 497- and 199-nt bands were derived solely from a strand whose 3′ ends correspond to nascent radiolabeled DNA ends. Several extra bands were observed in lane 7. We do not know the precise origin of these signals. However, because they are both λ exonuclease and exonuclease III sensitive, it is likely they represent unligated lagging strand DNA molecules derived from internal template regions. It seemed that λ exonuclease had reached the Dra I site on the template (cold) strand of some molecules, because the signal intensity of the 199-nt band decreased after the λ exonuclease treatment.

    Journal: Molecular and Cellular Biology

    Article Title: In Vitro Reconstitution of the End Replication Problem

    doi: 10.1128/MCB.21.17.5753-5766.2001

    Figure Lengend Snippet: Analysis of terminal restriction fragments from replicated linear DNAs. (A and B) The bound fraction of pSVO11-bead replication products was purified and treated with either λ exonuclease or exonuclease III. To know the exonuclease digestion rates, we treated a separately prepared 199-bp terminal fragment with these exonucleases and found that under the employed conditions, approximately 100 nt is digested from the ends, albeit relatively asymmetrically (data not shown). After the digestion, a half aliquot of the DNA was further treated with Dra I, which produces 199- and 497-bp fragments from the left and right arms of the DNA, respectively (A). Samples were run in a 6% denaturing acrylamide gel, dried, and autoradiographed. Heavily and lightly exposed autoradiographs of the same gel are shown. Control pSVO11 DNA was digested with Bsr FI, and the two ends were filled-in with dNTPs. The resultant blunt-ended linear pSVO11 was first treated with either λ exonuclease or exonuclease III, followed by Dra I digestion. The products were first dephosphorylated by alkaline phosphatase at their 5′ ends and then labeled by T4 polynucleotide kinase and [γ- 32 P]ATP. Dra I digests DNA at a TTT/AAA site, leaving blunt ends. Therefore, the two 199-nt and 497-nt fragment strands have the same nucleotide lengths (arrows). However, because of the effect of different base compositions on migration rates, two distinct 199-nt single-stranded DNA bands are visible in lane 1. The upper and lower bands (marked by open and filled circles, respectively) of the 199-nt doublet were completely digested by λ exonuclease and exonuclease III, respectively (lanes 2 to 5). The 199- and 197-nt bands were detected in pSV011-band replication products. These two bands were resistant to λ exonuclease (lanes 9 and 11). In contrast, the 199-nt band was completely digested, and the 497-nt band was significantly trimmed by exonuclease III (lanes 13 and 15; shorter-sized 497-nt bands are indicated by a bracket). These results indicate that the observed 497- and 199-nt bands were derived solely from a strand whose 3′ ends correspond to nascent radiolabeled DNA ends. Several extra bands were observed in lane 7. We do not know the precise origin of these signals. However, because they are both λ exonuclease and exonuclease III sensitive, it is likely they represent unligated lagging strand DNA molecules derived from internal template regions. It seemed that λ exonuclease had reached the Dra I site on the template (cold) strand of some molecules, because the signal intensity of the 199-nt band decreased after the λ exonuclease treatment.

    Article Snippet: The purified DNA was either treated with or without λ exonuclease (GIBCO), exonuclease III (Takara), and exonuclease I (New England BioLabs).

    Techniques: Purification, Acrylamide Gel Assay, Labeling, Migration, Derivative Assay

    Deletion of the 20q-TERRA locus decreases telomere length and protection in U2OS cells. ( a ) Q-FISH images obtained from metaphases spreads from U2OS cells WT and KO for the Chr20q-TERRA locus (clones A4, B4 and C4). (Left graphs) Frequency graphs of telomere length (a.u.) distribution measured in WT and in the 20q-KO cells (clones A4, B4 and C4) from three independent experiments. The mean telomere length and the number of telomeres and metaphases analyzed is shown. The red lines are arbitrary lines placed in the exact same position in each frequency graph to visualize differences between the 20q-KO clones and the WT controls (right graphs) The mean telomere length, the percentage of short telomeres and the quantification of signal-free ends per metaphase are also represented. Short telomeres are considered those in the 10% percentile of the total telomere length distribution. Total number of metaphases used for the statistical analysis is indicated. Scale bar, 10 μm and (zoom) 1 μm. ( b ) WT and 20q-KO cells were analyzed for T-SCE events with G-rich (green) and C-rich (red) PNA probes. The fraction of chromosome ends with T-SCE obtained from three different experiments was quantified and graphed as the mean values±s.e.m., n =30 metaphases. The number of metaphases analyzed is shown. Only events in which interchange of both colours were quantified (see examples of no-T-SCE and T-SCE). The quantification was carried out by counting the number of events in the same chromosome or in different chromosomes and then normalizing it by the total number of chromosomes observed in each metaphase. Scale bar, 1 μm. ( c ) Quantification of DNA-containing double minute chromosomes (TDMs) in WT and 20q-KO cells from three different experiments (mean values±s.e.m., n =30 metaphases). An example of TDMs is shown. One-way Anova with Dunnett's post test was used for all statistical analysis (* P

    Journal: Nature Communications

    Article Title: Telomeric RNAs are essential to maintain telomeres

    doi: 10.1038/ncomms12534

    Figure Lengend Snippet: Deletion of the 20q-TERRA locus decreases telomere length and protection in U2OS cells. ( a ) Q-FISH images obtained from metaphases spreads from U2OS cells WT and KO for the Chr20q-TERRA locus (clones A4, B4 and C4). (Left graphs) Frequency graphs of telomere length (a.u.) distribution measured in WT and in the 20q-KO cells (clones A4, B4 and C4) from three independent experiments. The mean telomere length and the number of telomeres and metaphases analyzed is shown. The red lines are arbitrary lines placed in the exact same position in each frequency graph to visualize differences between the 20q-KO clones and the WT controls (right graphs) The mean telomere length, the percentage of short telomeres and the quantification of signal-free ends per metaphase are also represented. Short telomeres are considered those in the 10% percentile of the total telomere length distribution. Total number of metaphases used for the statistical analysis is indicated. Scale bar, 10 μm and (zoom) 1 μm. ( b ) WT and 20q-KO cells were analyzed for T-SCE events with G-rich (green) and C-rich (red) PNA probes. The fraction of chromosome ends with T-SCE obtained from three different experiments was quantified and graphed as the mean values±s.e.m., n =30 metaphases. The number of metaphases analyzed is shown. Only events in which interchange of both colours were quantified (see examples of no-T-SCE and T-SCE). The quantification was carried out by counting the number of events in the same chromosome or in different chromosomes and then normalizing it by the total number of chromosomes observed in each metaphase. Scale bar, 1 μm. ( c ) Quantification of DNA-containing double minute chromosomes (TDMs) in WT and 20q-KO cells from three different experiments (mean values±s.e.m., n =30 metaphases). An example of TDMs is shown. One-way Anova with Dunnett's post test was used for all statistical analysis (* P

    Article Snippet: The slides were treated with 0.5 mg ml−1 RNase A for 10 min at 37 °C, stained with 0.5 μg ml−1 Hoechst 33258 (Sigma) in 2 × SSC (0.3 M NaCl, 0.03 M sodium citrate) for 15 min at room temperature and then exposed to 365 nm UV light (Stratalinker 1800 UV irradiator) for 25–30 min. Enzymatic digestion of the BrdU/BrdC-substituted DNA strands with 3 U μl−1 of Exonuclease III (Promega) in buffer supplied by the manufacturer (50 mM Tris–HCl, 5 mM MgCl2 and 5 mM dithiothreitol, pH 8) was allowed to proceed for 10 min at room temperature.

    Techniques: Fluorescence In Situ Hybridization, Clone Assay

    Deletion of the 20q-TERRA locus decreases telomere protection in U2OS cells. ( a ) Quantification of the total γH2AX signal per nucleus (mean values±s.e.m., n =number of cells) is shown. The total number of cells analyzed is indicated. ( b ) Quantification of the total 53BP1 spot signal per nucleus (mean values±s.e.m., n =number of cells is shown). The total number of cells analyzed is indicated. ( c ) Graphs showing the quantification of the co-localization (TIF) between TRF2 and either γH2AX or 53BP1 in WT cells and in all 20q-KO clones (mean values±s.e.m., n =3 independent experiments for γH2AX and n =number of cells for 53BP1) per cell is shown. The total number of nuclei analyzed is indicated. ( d ) Representative images of the average number of TIFs found on double inmunostain to detect the telomere protein TRF2 (green) and either the DNA damage markers phospho-Histone γH2AX or 53BP1 (red) in the U2OS cells WT or deleted for the 20q locus. Arrowheads indicate co-localization events. Scale bar, 10 μm. ( e ) Quantification of chromosomal end-to-end fusions in WT and in the 20q-KO cells from three independent experiments (mean values±s.e.m., n =metaphases). Examples of end-to-end fusions are shown as well. Scale bar, 1 μm. ( f ) Array-CGH analysis was performed on hybridization on the same membrane of DNA differentially labelled from WT and 20q-KO cells. The chromosomal gains and losses in 20q-KO cells normalized by WT cells are represented. The chromosomal gains are shown in green and in red the chromosomal losses. One-way Anova with Dunnett's post test was used for all statistical analysis except for the quantification of chromosomal fusions in which the Student's t -test was used (* P

    Journal: Nature Communications

    Article Title: Telomeric RNAs are essential to maintain telomeres

    doi: 10.1038/ncomms12534

    Figure Lengend Snippet: Deletion of the 20q-TERRA locus decreases telomere protection in U2OS cells. ( a ) Quantification of the total γH2AX signal per nucleus (mean values±s.e.m., n =number of cells) is shown. The total number of cells analyzed is indicated. ( b ) Quantification of the total 53BP1 spot signal per nucleus (mean values±s.e.m., n =number of cells is shown). The total number of cells analyzed is indicated. ( c ) Graphs showing the quantification of the co-localization (TIF) between TRF2 and either γH2AX or 53BP1 in WT cells and in all 20q-KO clones (mean values±s.e.m., n =3 independent experiments for γH2AX and n =number of cells for 53BP1) per cell is shown. The total number of nuclei analyzed is indicated. ( d ) Representative images of the average number of TIFs found on double inmunostain to detect the telomere protein TRF2 (green) and either the DNA damage markers phospho-Histone γH2AX or 53BP1 (red) in the U2OS cells WT or deleted for the 20q locus. Arrowheads indicate co-localization events. Scale bar, 10 μm. ( e ) Quantification of chromosomal end-to-end fusions in WT and in the 20q-KO cells from three independent experiments (mean values±s.e.m., n =metaphases). Examples of end-to-end fusions are shown as well. Scale bar, 1 μm. ( f ) Array-CGH analysis was performed on hybridization on the same membrane of DNA differentially labelled from WT and 20q-KO cells. The chromosomal gains and losses in 20q-KO cells normalized by WT cells are represented. The chromosomal gains are shown in green and in red the chromosomal losses. One-way Anova with Dunnett's post test was used for all statistical analysis except for the quantification of chromosomal fusions in which the Student's t -test was used (* P

    Article Snippet: The slides were treated with 0.5 mg ml−1 RNase A for 10 min at 37 °C, stained with 0.5 μg ml−1 Hoechst 33258 (Sigma) in 2 × SSC (0.3 M NaCl, 0.03 M sodium citrate) for 15 min at room temperature and then exposed to 365 nm UV light (Stratalinker 1800 UV irradiator) for 25–30 min. Enzymatic digestion of the BrdU/BrdC-substituted DNA strands with 3 U μl−1 of Exonuclease III (Promega) in buffer supplied by the manufacturer (50 mM Tris–HCl, 5 mM MgCl2 and 5 mM dithiothreitol, pH 8) was allowed to proceed for 10 min at room temperature.

    Techniques: Clone Assay, Hybridization

    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Journal: Theranostics

    Article Title: High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells

    doi: 10.7150/thno.23852

    Figure Lengend Snippet: Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Article Snippet: Human DNase I and exonuclease III originated from Sangon Biotechnology Co., Ltd (Shanghai, China).

    Techniques: Modification, Fluorescence

    Enhancement of UDGase activity by exonuclease III. Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.

    Journal: Nucleic Acids Research

    Article Title: Characterization of uracil-DNA glycosylase activity from Trypanosoma cruzi and its stimulation by AP endonuclease

    doi:

    Figure Lengend Snippet: Enhancement of UDGase activity by exonuclease III. Decrease in fluorescence observed in the presence of different concentrations of exonuclease III. Open squares, UDGase; closed squares, UDGase + 40 U; triangles, UDGase +80 U; open circles, UDGase +175 U; closed circles, LmAP.

    Article Snippet: Modulation of UDGase activity by exonuclease III (from E.coli ; Boehringer Mannheim) or LmAP was measured in the same mixture after adding from 40 to 175 U exonuclease III or a molar excess of up to 100-fold AP endonuclease.

    Techniques: Activity Assay, Fluorescence

    Repression of HIF-1β promoter activity by IFN-γ. A , Cloned HIF-1β promoter and series of truncated promoter-luciferase reporter constructs generated using exonuclease III digestion. Relative positions of each clone and major TSSs

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: IFN-? Attenuates Hypoxia-Inducible Factor (HIF) Activity in Intestinal Epithelial Cells through Transcriptional Repression of HIF-1?

    doi: 10.4049/jimmunol.1001442

    Figure Lengend Snippet: Repression of HIF-1β promoter activity by IFN-γ. A , Cloned HIF-1β promoter and series of truncated promoter-luciferase reporter constructs generated using exonuclease III digestion. Relative positions of each clone and major TSSs

    Article Snippet: Sequential truncations of the cloned HIF-1β promoter sequence were generated by exonuclease III digestion (Erase-a-Base; Promega).

    Techniques: Activity Assay, Clone Assay, Luciferase, Construct, Generated