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  • 99
    Thermo Fisher qubit ssdna kit
    Qubit Ssdna Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 62 article reviews
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    qubit ssdna kit - by Bioz Stars, 2020-03
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    99
    Zymo Research ssdna clean concentrator
    Ssdna Clean Concentrator, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ssdna clean concentrator/product/Zymo Research
    Average 99 stars, based on 12 article reviews
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    ssdna clean concentrator - by Bioz Stars, 2020-03
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    99
    Millipore ssdna
    Generation of antibody profiles by U937 cells and by IgM and <t>IgG</t> specific secondary antibodies. Following incubation with sera from normal and SLE patient donors cell adherence or bound IgM and IgG were determined on printed spots of C1q, dsDNA, Ro and <t>ssDNA.</t> Each marker represents median values of the sixplicates. Mann-Whitney U test was performed to assess statistical significance of differences. Values of p
    Ssdna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 581 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher ssdna
    mRNA or <t>ssDNA</t> but not dsDNA transfections lead to stress granule assembly in puromycin-treated cells. ( A ) 1 μg of 2Luc mRNA synthesized in vitro was transfected in NRK cells using lipofectamine in the presence of 2.5 μg/ml puromycin (see ‘Materials and Methods’ section). Anti-HuR and anti-YB-1 labeling show the formation of stress granules 3 h after <t>transfection.</t> ( B ) NRK cells were transfected using lipofectamine (Lipo) with 1 μg of α-globin mRNA, M13 ssDNA, or linearized pUC19 dsDNA in the presence or absence of puromycin for 3 h. Benzonase treatment was performed before the formation of lipoplexes. The statistical analysis was obtained on three different samples. Results are mean ± SD ( n = 3). Both mRNA and ssDNA lead to a significant formation of stress granules in puromycin-treated cells. Anti-YB-1 labeling shows the formation of stress granules 3 h after transfection.
    Ssdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1279 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    GE Healthcare ssdna
    Mutational analysis of <t>ssDNA-RNA</t> Δ3′ annealing in the presence of NC. The NC-mediated annealing assays were performed as described under ”Experimental Procedures.“ The samples were analyzed by 2% agarose gel electrophoresis
    Ssdna, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 99/100, based on 166 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Immuno-Biological Laboratories Co Ltd ssdna
    Degeneration of the OPL and ONL in the peripheral retina of E50K mice. ( A ) Immunostaining of the retina sections with <t>synaptophysin,</t> rhodopsin and <t>ssDNA,</t> specific markers for neuronal presynaptic vesicles, rod photoreceptors and apoptosis cells, respectively. Synapse disruption (arrow), rod photoreceptor cells degeneration and apoptosis cells were observed in the OPL and/or ONL in the peripheral retina of E50K mice. Scale bar: 20 μm. ( B ) Percentage of apoptotic cells in the ONL ( n = 6, ** P
    Ssdna, supplied by Immuno-Biological Laboratories Co Ltd, used in various techniques. Bioz Stars score: 89/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega ssdna
    DprA antagonizes the inhibitory effect of RecU on DNA strand exchange. Top left, scheme of reactions performed on the left part of the gel (lanes 2–9). The css (+ strand in black) and the homologous lds (– in gray) substrates were preincubated with SsbA, DprA, RecU, and ATP (5 min, 37°C), after which RecA was added. Top right, scheme of the reactions performed on the right part of the gel (lanes 11–18). Here, DNA substrates were preincubated with SsbA, DprA, RecA, and ATP (5 min, 37°C), followed by RecU. The predicted intermediates ( jm ) and final products ( nc ) are illustrated. Homologous <t>ssDNA</t> (10 μM) and <t>dsDNA</t> (20 μM) were preincubated with SsbA, DprA and with variable concentrations of RecU (lanes 3–9; doubling from 6.2 to 400 nM) or a fixed RecA concentration (lanes 11–18) in buffer B containing 5 mM ATP (5 min, 37°C). A fixed RecA concentration (lanes 2–9) or variable amounts of RecU (lanes 12–18) were then added and the reaction was incubated (60 min, 37°C). Lane 1, DNA substrate controls (C); lanes 2 and 11, RecU was omitted, and in lane 10, the reaction was terminated after preincubation (5 min) without RecU. Reactions were resolved after deproteinization by 0.8% agarose gel electrophoresis. Band positions for css, lds, cds, jm , and nc are indicated. Bottom, recombination intermediates ( jm ) and products ( nc ) are expressed as the percentage in respect to the total substrate added. Results are shown as the mean ± 5% SEM of ≥3 independent experiments.
    Ssdna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 214 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Eurofins ssdna
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Ssdna, supplied by Eurofins, used in various techniques. Bioz Stars score: 90/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Promega quantifluor ssdna system
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Quantifluor Ssdna System, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Abcam sperm ssdna
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Sperm Ssdna, supplied by Abcam, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher quant it oligreen ssdna
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Quant It Oligreen Ssdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher qubit ssdna assay
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Qubit Ssdna Assay, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Bio Basic Canada complementary ssdna
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Complementary Ssdna, supplied by Bio Basic Canada, used in various techniques. Bioz Stars score: 89/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    TaKaRa ssdna template
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Ssdna Template, supplied by TaKaRa, used in various techniques. Bioz Stars score: 78/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Eurofins antiparallel ssdnas
    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt <t>RRM</t> domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to <t>ssDNA:</t> Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.
    Antiparallel Ssdnas, supplied by Eurofins, used in various techniques. Bioz Stars score: 79/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Oxford Nanopore ssdna diameter
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    Ssdna Diameter, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher oligreen ssdna quantitation kit
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    Oligreen Ssdna Quantitation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Fisher Scientific m13mp18 ssdna
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    M13mp18 Ssdna, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    TriLink ssdna substrates
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    Ssdna Substrates, supplied by TriLink, used in various techniques. Bioz Stars score: 81/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    Promega quantifluor ssdna
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    Quantifluor Ssdna, supplied by Promega, used in various techniques. Bioz Stars score: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Midland Certified Reagent ssdna oligomers
    <t>ssDNA</t> translocation through a <t>nanopore</t> on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.
    Ssdna Oligomers, supplied by Midland Certified Reagent, used in various techniques. Bioz Stars score: 77/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    GE Healthcare m13 ssdna
    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded <t>M13</t> was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer <t>ssDNA</t> oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.
    M13 Ssdna, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 78/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Millipore m13 ssdna
    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded <t>M13</t> was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer <t>ssDNA</t> oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.
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    78
    Bayou Biolabs m13mp18 ssdna
    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded <t>M13</t> was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer <t>ssDNA</t> oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.
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    GE Healthcare m13mp18 ssdna
    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded <t>M13</t> was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer <t>ssDNA</t> oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.
    M13mp18 Ssdna, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 78/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Thermo Fisher m13mp19 ssdna
    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded <t>M13</t> was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer <t>ssDNA</t> oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.
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    78
    Agilent technologies ssdna pool
    Custom <t>DNA</t> and RNA pool generation from microarray. A) Agilent microarrays contain <t>ssDNA</t> probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
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    78
    MWG-Biotech ssdna fragments
    Custom <t>DNA</t> and RNA pool generation from microarray. A) Agilent microarrays contain <t>ssDNA</t> probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
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    Thermo Fisher ϕx174 ssdna
    Custom <t>DNA</t> and RNA pool generation from microarray. A) Agilent microarrays contain <t>ssDNA</t> probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
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    Thermo Fisher fluorescent ssdna
    Custom <t>DNA</t> and RNA pool generation from microarray. A) Agilent microarrays contain <t>ssDNA</t> probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
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    Roche cellular ssdna
    Custom <t>DNA</t> and RNA pool generation from microarray. A) Agilent microarrays contain <t>ssDNA</t> probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).
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    Image Search Results


    Generation of antibody profiles by U937 cells and by IgM and IgG specific secondary antibodies. Following incubation with sera from normal and SLE patient donors cell adherence or bound IgM and IgG were determined on printed spots of C1q, dsDNA, Ro and ssDNA. Each marker represents median values of the sixplicates. Mann-Whitney U test was performed to assess statistical significance of differences. Values of p

    Journal: PLoS ONE

    Article Title: Application of Fluorescent Monocytes for Probing Immune Complexes on Antigen Microarrays

    doi: 10.1371/journal.pone.0072401

    Figure Lengend Snippet: Generation of antibody profiles by U937 cells and by IgM and IgG specific secondary antibodies. Following incubation with sera from normal and SLE patient donors cell adherence or bound IgM and IgG were determined on printed spots of C1q, dsDNA, Ro and ssDNA. Each marker represents median values of the sixplicates. Mann-Whitney U test was performed to assess statistical significance of differences. Values of p

    Article Snippet: To generate immune profiles of SLE patients and healthy donors by U937, anti-human IgG and anti-human IgM, Ro (SSA) (Arotec; 0.374 mg/ml), dsDNA and ssDNA (Sigma; 0.2 mg/ml), human IgG (hIgG) (Sigma; 0.5 mg/ml), C1q (Sigma; 1 mg/ml) and pG (Sigma; 0.25 mg/ml) all diluted in PBS were printed in sixplicates onto 16 pad FAST slides.

    Techniques: Incubation, Marker, MANN-WHITNEY

    mRNA or ssDNA but not dsDNA transfections lead to stress granule assembly in puromycin-treated cells. ( A ) 1 μg of 2Luc mRNA synthesized in vitro was transfected in NRK cells using lipofectamine in the presence of 2.5 μg/ml puromycin (see ‘Materials and Methods’ section). Anti-HuR and anti-YB-1 labeling show the formation of stress granules 3 h after transfection. ( B ) NRK cells were transfected using lipofectamine (Lipo) with 1 μg of α-globin mRNA, M13 ssDNA, or linearized pUC19 dsDNA in the presence or absence of puromycin for 3 h. Benzonase treatment was performed before the formation of lipoplexes. The statistical analysis was obtained on three different samples. Results are mean ± SD ( n = 3). Both mRNA and ssDNA lead to a significant formation of stress granules in puromycin-treated cells. Anti-YB-1 labeling shows the formation of stress granules 3 h after transfection.

    Journal: Nucleic Acids Research

    Article Title: Free mRNA in excess upon polysome dissociation is a scaffold for protein multimerization to form stress granules

    doi: 10.1093/nar/gku582

    Figure Lengend Snippet: mRNA or ssDNA but not dsDNA transfections lead to stress granule assembly in puromycin-treated cells. ( A ) 1 μg of 2Luc mRNA synthesized in vitro was transfected in NRK cells using lipofectamine in the presence of 2.5 μg/ml puromycin (see ‘Materials and Methods’ section). Anti-HuR and anti-YB-1 labeling show the formation of stress granules 3 h after transfection. ( B ) NRK cells were transfected using lipofectamine (Lipo) with 1 μg of α-globin mRNA, M13 ssDNA, or linearized pUC19 dsDNA in the presence or absence of puromycin for 3 h. Benzonase treatment was performed before the formation of lipoplexes. The statistical analysis was obtained on three different samples. Results are mean ± SD ( n = 3). Both mRNA and ssDNA lead to a significant formation of stress granules in puromycin-treated cells. Anti-YB-1 labeling shows the formation of stress granules 3 h after transfection.

    Article Snippet: mRNA and ssDNA, and dsDNA transfection One microgram of mRNA (α-globin, and 2Luc mRNAs, fluorescent or not), ssDNA (M13, Invitrogen) or dsDNA (pUC19, Invitrogen) were incubated with 1 μl lipofectamine™ 2000 (Invitrogen) for 20 min in 100 μl of DMEM.

    Techniques: Transfection, Synthesized, In Vitro, Labeling

    Mutational analysis of ssDNA-RNA Δ3′ annealing in the presence of NC. The NC-mediated annealing assays were performed as described under ”Experimental Procedures.“ The samples were analyzed by 2% agarose gel electrophoresis

    Journal: The Journal of Biological Chemistry

    Article Title: Structural Insights into the HIV-1 Minus-strand Strong-stop DNA *

    doi: 10.1074/jbc.M115.708099

    Figure Lengend Snippet: Mutational analysis of ssDNA-RNA Δ3′ annealing in the presence of NC. The NC-mediated annealing assays were performed as described under ”Experimental Procedures.“ The samples were analyzed by 2% agarose gel electrophoresis

    Article Snippet: The monomeric (m) and heteroduplex (hd) forms of ssDNA, and the high molecular weight DNA-RNA complexes (hmw) were quantified using a TyphoonTM TRIO (GE Healthcare) and ImageQuant software.

    Techniques: Agarose Gel Electrophoresis

    Degeneration of the OPL and ONL in the peripheral retina of E50K mice. ( A ) Immunostaining of the retina sections with synaptophysin, rhodopsin and ssDNA, specific markers for neuronal presynaptic vesicles, rod photoreceptors and apoptosis cells, respectively. Synapse disruption (arrow), rod photoreceptor cells degeneration and apoptosis cells were observed in the OPL and/or ONL in the peripheral retina of E50K mice. Scale bar: 20 μm. ( B ) Percentage of apoptotic cells in the ONL ( n = 6, ** P

    Journal: Human Molecular Genetics

    Article Title: Overexpression of optineurin E50K disrupts Rab8 interaction and leads to a progressive retinal degeneration in mice

    doi: 10.1093/hmg/ddq146

    Figure Lengend Snippet: Degeneration of the OPL and ONL in the peripheral retina of E50K mice. ( A ) Immunostaining of the retina sections with synaptophysin, rhodopsin and ssDNA, specific markers for neuronal presynaptic vesicles, rod photoreceptors and apoptosis cells, respectively. Synapse disruption (arrow), rod photoreceptor cells degeneration and apoptosis cells were observed in the OPL and/or ONL in the peripheral retina of E50K mice. Scale bar: 20 μm. ( B ) Percentage of apoptotic cells in the ONL ( n = 6, ** P

    Article Snippet: These sections were incubated with blocking solution for 1 h followed by overnight incubation with primary antibody against HA tag (1:500 dilution; Sigma-Aldrich, St Louis, MO, USA), OPTN (1:500 dilution; kind gift from Dr Mansoor Sarfarazi, University of Connecticut), tubulin β-III isoform (1:100 dilution; Millipore, Billerica, MA, USA), NeuN (1:100 dilution; Millipore), calretinin (1:500 dilution; Sigma), tyrosine hydroxylase (1:100 dilution; Millipore), PKC α (1:500 dilution; Millipore), rhodopsin (1:200 dilution; Santa Cruz, CA, USA), synaptophysin (1:500 dilution; Abcam, Cambridge, MA, USA) or ssDNA (1:500 dilution; Immuno-Biological Laboratories, Gunma, Japan) in phosphate-buffered saline (PBS) containing 1% BSA at 4°C.

    Techniques: Mouse Assay, Immunostaining

    DprA antagonizes the inhibitory effect of RecU on DNA strand exchange. Top left, scheme of reactions performed on the left part of the gel (lanes 2–9). The css (+ strand in black) and the homologous lds (– in gray) substrates were preincubated with SsbA, DprA, RecU, and ATP (5 min, 37°C), after which RecA was added. Top right, scheme of the reactions performed on the right part of the gel (lanes 11–18). Here, DNA substrates were preincubated with SsbA, DprA, RecA, and ATP (5 min, 37°C), followed by RecU. The predicted intermediates ( jm ) and final products ( nc ) are illustrated. Homologous ssDNA (10 μM) and dsDNA (20 μM) were preincubated with SsbA, DprA and with variable concentrations of RecU (lanes 3–9; doubling from 6.2 to 400 nM) or a fixed RecA concentration (lanes 11–18) in buffer B containing 5 mM ATP (5 min, 37°C). A fixed RecA concentration (lanes 2–9) or variable amounts of RecU (lanes 12–18) were then added and the reaction was incubated (60 min, 37°C). Lane 1, DNA substrate controls (C); lanes 2 and 11, RecU was omitted, and in lane 10, the reaction was terminated after preincubation (5 min) without RecU. Reactions were resolved after deproteinization by 0.8% agarose gel electrophoresis. Band positions for css, lds, cds, jm , and nc are indicated. Bottom, recombination intermediates ( jm ) and products ( nc ) are expressed as the percentage in respect to the total substrate added. Results are shown as the mean ± 5% SEM of ≥3 independent experiments.

    Journal: Frontiers in Microbiology

    Article Title: RecA Regulation by RecU and DprA During Bacillus subtilis Natural Plasmid Transformation

    doi: 10.3389/fmicb.2018.01514

    Figure Lengend Snippet: DprA antagonizes the inhibitory effect of RecU on DNA strand exchange. Top left, scheme of reactions performed on the left part of the gel (lanes 2–9). The css (+ strand in black) and the homologous lds (– in gray) substrates were preincubated with SsbA, DprA, RecU, and ATP (5 min, 37°C), after which RecA was added. Top right, scheme of the reactions performed on the right part of the gel (lanes 11–18). Here, DNA substrates were preincubated with SsbA, DprA, RecA, and ATP (5 min, 37°C), followed by RecU. The predicted intermediates ( jm ) and final products ( nc ) are illustrated. Homologous ssDNA (10 μM) and dsDNA (20 μM) were preincubated with SsbA, DprA and with variable concentrations of RecU (lanes 3–9; doubling from 6.2 to 400 nM) or a fixed RecA concentration (lanes 11–18) in buffer B containing 5 mM ATP (5 min, 37°C). A fixed RecA concentration (lanes 2–9) or variable amounts of RecU (lanes 12–18) were then added and the reaction was incubated (60 min, 37°C). Lane 1, DNA substrate controls (C); lanes 2 and 11, RecU was omitted, and in lane 10, the reaction was terminated after preincubation (5 min) without RecU. Reactions were resolved after deproteinization by 0.8% agarose gel electrophoresis. Band positions for css, lds, cds, jm , and nc are indicated. Bottom, recombination intermediates ( jm ) and products ( nc ) are expressed as the percentage in respect to the total substrate added. Results are shown as the mean ± 5% SEM of ≥3 independent experiments.

    Article Snippet: The 3,199-base pair (bp) pGEM3 Zf(+) was used as a source of dsDNA and ssDNA (Promega Biotech).

    Techniques: Concentration Assay, Incubation, Agarose Gel Electrophoresis

    Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt RRM domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to ssDNA: Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.

    Journal: Nucleic Acids Research

    Article Title: Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function

    doi: 10.1093/nar/gku468

    Figure Lengend Snippet: Nucleic acid binding mode. ( A ) Identification of CTG as binding surface for the Nt RRM domain. Overlay of natural abundance 1 H- 13 C-HSQC spectra showing C6-H6/C8-H8 and C1′-H1′ regions. Final spectrum corresponds to ssDNA: Nt RRM 1:0.3 molar ratio. Significant exchange induced peak broadening and interference from Nt RRM resonances towards the end of the titration prohibited tracking the ssDNA resonances to the final bound state. Arrows indicate the direction of the CSP. ( B ) Sections of F2 15 N/ 13 C-filtered 2D NOESY showing intense NOEs observed for G5 H1′. Two intermolecular NOEs involving this resonance could be identified, of which one (to Ile38δ1) could be unambiguously assigned, based on the corresponding peak in the 13 C-edited NOESY. The peak at 7.3 ppm is an ambiguously assigned intermolecular NOE involving the aromatic protons of F9, F49 and F51. ( C ) HADDOCK model of RNA–RRM complex. Selected residues from RNP motifs and residues that mediate intermolecular interactions are shown in ball-and-stick representation. Rotated view from Figure 3A , looking down on the β-sheet.

    Article Snippet: Titration experiments and data analysis Interaction between Nt RRM and ssDNA or RNA was studied using a 6-nt probe (5′-TTCTGG-3′ for DNA and 5′-UUCUGG-3′ for RNA; Eurofins MWG Operon) that was previously identified as a minimum binding sequence for homologue At GR-RBP7 ( ).

    Techniques: Binding Assay, CTG Assay, Titration

    Nt RRM interacts strongly and specifically with nucleic acids ( A ) NMR titration results for ssDNA (5′-TTCTGG-3′), showing an overlay of a section of the 15 N-HSQC spectra for each titration point. Colour coding of the spectra is indicated at the top, the free Nt RRM spectrum is in black, fully bound spectrum is in red. Molar ratio Nt RRM:ssDNA at the end of the titration is 1:1.50. Assignments of resonances of interest are indicated. ( B ) Interaction surface for ssDNA binding. CSP colour coded on the van der Waals surface. Grey is used for residues without data; residues with CSP larger than 10% trimmed mean + 2 σ are labelled. ( C ) Experimental (points) and fitted (lines) line shapes during the titration for two selected residues. Fits for all residues including error analysis are shown in Supplementary Figure S4. Best fit was obtained with K D of 4.2 μM and k off of 860 s −1 . Goodness-of-fit in terms \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\chi _{{\rm red}}^2$\end{document} \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\chi _{{\rm red}}^2$\end{document} is indicated for each titration point as well as for all points combined. The exchange regime α (2· k off /Δω) is also indicated; fast α > 10; intermediate 10

    Journal: Nucleic Acids Research

    Article Title: Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function

    doi: 10.1093/nar/gku468

    Figure Lengend Snippet: Nt RRM interacts strongly and specifically with nucleic acids ( A ) NMR titration results for ssDNA (5′-TTCTGG-3′), showing an overlay of a section of the 15 N-HSQC spectra for each titration point. Colour coding of the spectra is indicated at the top, the free Nt RRM spectrum is in black, fully bound spectrum is in red. Molar ratio Nt RRM:ssDNA at the end of the titration is 1:1.50. Assignments of resonances of interest are indicated. ( B ) Interaction surface for ssDNA binding. CSP colour coded on the van der Waals surface. Grey is used for residues without data; residues with CSP larger than 10% trimmed mean + 2 σ are labelled. ( C ) Experimental (points) and fitted (lines) line shapes during the titration for two selected residues. Fits for all residues including error analysis are shown in Supplementary Figure S4. Best fit was obtained with K D of 4.2 μM and k off of 860 s −1 . Goodness-of-fit in terms \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\chi _{{\rm red}}^2$\end{document} \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\chi _{{\rm red}}^2$\end{document} is indicated for each titration point as well as for all points combined. The exchange regime α (2· k off /Δω) is also indicated; fast α > 10; intermediate 10

    Article Snippet: Titration experiments and data analysis Interaction between Nt RRM and ssDNA or RNA was studied using a 6-nt probe (5′-TTCTGG-3′ for DNA and 5′-UUCUGG-3′ for RNA; Eurofins MWG Operon) that was previously identified as a minimum binding sequence for homologue At GR-RBP7 ( ).

    Techniques: Nuclear Magnetic Resonance, Titration, Binding Assay

    Full-length Nt GR-RBP1 and isolated Nt RRM share similar nucleic acid binding mode. ( A ) Overlay of Nt GRP-RBP1 in absence (blue) and presence (red) of 1 M equivalent of 6-nt ssDNA. Significant chemical shift changes occur for resonances at the edges of the spectrum that are attributed to the Nt RRM domain (compare with Figure 2 ). ( B ) Detail of (A) including an overlay of isolated Nt RRM domain in absence (grey) and presence (black) of ssDNA. Selected residues are indicated. ( C ) Analysis of peak intensities ratios (top) and CSPs (bottom) upon addition of ssDNA. Grey solid lines indicate expected intensity ratio due to dilution (0.9). Residues with significant intensity increase upon ssDNA addition and those with CSPs more than 2 SD (red line) from the 10% trimmed mean (green broken line) are labelled, residues that deviate more than 1 SD (orange line) are highlighted in yellow. ( D ) Results of (C) plotted on the structure of Nt RRM. Colour coding: grey—no data due to missing assignment; cyan—no significant change in intensity or peak position; orange—significantly reduced peak intensity; magenta—significant CSP; red—significant CSP and reduced intensity. ( E ) Detail of (A) focusing on the glycine region of the spectrum with unassigned peaks from GR. Arrows point to small changes in peak positions. Labelled peaks are from RRM domain in ssDNA bound state (shown in black).

    Journal: Nucleic Acids Research

    Article Title: Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function

    doi: 10.1093/nar/gku468

    Figure Lengend Snippet: Full-length Nt GR-RBP1 and isolated Nt RRM share similar nucleic acid binding mode. ( A ) Overlay of Nt GRP-RBP1 in absence (blue) and presence (red) of 1 M equivalent of 6-nt ssDNA. Significant chemical shift changes occur for resonances at the edges of the spectrum that are attributed to the Nt RRM domain (compare with Figure 2 ). ( B ) Detail of (A) including an overlay of isolated Nt RRM domain in absence (grey) and presence (black) of ssDNA. Selected residues are indicated. ( C ) Analysis of peak intensities ratios (top) and CSPs (bottom) upon addition of ssDNA. Grey solid lines indicate expected intensity ratio due to dilution (0.9). Residues with significant intensity increase upon ssDNA addition and those with CSPs more than 2 SD (red line) from the 10% trimmed mean (green broken line) are labelled, residues that deviate more than 1 SD (orange line) are highlighted in yellow. ( D ) Results of (C) plotted on the structure of Nt RRM. Colour coding: grey—no data due to missing assignment; cyan—no significant change in intensity or peak position; orange—significantly reduced peak intensity; magenta—significant CSP; red—significant CSP and reduced intensity. ( E ) Detail of (A) focusing on the glycine region of the spectrum with unassigned peaks from GR. Arrows point to small changes in peak positions. Labelled peaks are from RRM domain in ssDNA bound state (shown in black).

    Article Snippet: Titration experiments and data analysis Interaction between Nt RRM and ssDNA or RNA was studied using a 6-nt probe (5′-TTCTGG-3′ for DNA and 5′-UUCUGG-3′ for RNA; Eurofins MWG Operon) that was previously identified as a minimum binding sequence for homologue At GR-RBP7 ( ).

    Techniques: Isolation, Binding Assay

    Glycine-rich region stimulates higher-order complex formation and dsDNA unfolding ( A ) Representative DNA binding experiment by EMSA for the binding of 0, 0.7, 2, 7, 20 μM Nt RRM or Nt GR-RBP1 to a single or double ssDNA binding element (ssP1 or ss-dP1). Dashed lines indicate the positions of the wells and the free mobilities of ssP1 and ss-dP1, and serve to guide the eye. The arrows indicate lanes of interest with clear band shifts. Several lanes show a smeared, asymmetric band appearance caused by significant dissociation during electrophoresis. The selection box for quantification of the free DNA probe is indicated in white on the first lane. ( B ) 1D traces of the lanes with 20 μM Nt RRM or Nt GR-RBP1 added to ssP1 show a small but reproducible and concentration-dependent shifts in mobility. ( C ) Quantification of the fraction of bound ssDNA for the ss-dP1 probe at the indicated concentration of Nt GR-RBP1 and Nt RRM, the line represents the calculated binding curve based on three independent experiments. ( D ) UV melting curves of indicated oligonucleotides in presence of 3 M equivalents of Nt GR-RBP1, Nt RRM or BSA. Absorbance (at 260 nm) versus temperature curves in 20 mM KPi, 100 mM KCl, 1 mM BME at pH 7.0. Temperatures (°C) at the transition midpoint, T m , are indicated for the free DNA probes, with changes in T m listed in the presence of the three proteins.

    Journal: Nucleic Acids Research

    Article Title: Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function

    doi: 10.1093/nar/gku468

    Figure Lengend Snippet: Glycine-rich region stimulates higher-order complex formation and dsDNA unfolding ( A ) Representative DNA binding experiment by EMSA for the binding of 0, 0.7, 2, 7, 20 μM Nt RRM or Nt GR-RBP1 to a single or double ssDNA binding element (ssP1 or ss-dP1). Dashed lines indicate the positions of the wells and the free mobilities of ssP1 and ss-dP1, and serve to guide the eye. The arrows indicate lanes of interest with clear band shifts. Several lanes show a smeared, asymmetric band appearance caused by significant dissociation during electrophoresis. The selection box for quantification of the free DNA probe is indicated in white on the first lane. ( B ) 1D traces of the lanes with 20 μM Nt RRM or Nt GR-RBP1 added to ssP1 show a small but reproducible and concentration-dependent shifts in mobility. ( C ) Quantification of the fraction of bound ssDNA for the ss-dP1 probe at the indicated concentration of Nt GR-RBP1 and Nt RRM, the line represents the calculated binding curve based on three independent experiments. ( D ) UV melting curves of indicated oligonucleotides in presence of 3 M equivalents of Nt GR-RBP1, Nt RRM or BSA. Absorbance (at 260 nm) versus temperature curves in 20 mM KPi, 100 mM KCl, 1 mM BME at pH 7.0. Temperatures (°C) at the transition midpoint, T m , are indicated for the free DNA probes, with changes in T m listed in the presence of the three proteins.

    Article Snippet: Titration experiments and data analysis Interaction between Nt RRM and ssDNA or RNA was studied using a 6-nt probe (5′-TTCTGG-3′ for DNA and 5′-UUCUGG-3′ for RNA; Eurofins MWG Operon) that was previously identified as a minimum binding sequence for homologue At GR-RBP7 ( ).

    Techniques: Binding Assay, Electrophoresis, Selection, Concentration Assay

    ssDNA translocation through a nanopore on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.

    Journal: Scientific Reports

    Article Title: Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure

    doi: 10.1038/srep16640

    Figure Lengend Snippet: ssDNA translocation through a nanopore on the substrate coated with 100-nm silica beads. ( a ) Typical concatenated translocation events for 5.3 k-mer poly(dA) passing through a nanopore on a bare substrate (upper) and on a substrate coated with 100-nm silica beads (lower). The bare substrate had a 2.0-nm-diameter nanopore in a 20-nm-thickness membrane. The bead-coated substrate had a 3.0-nm-diameter nanopore in 12-nm-thickness membrane. The applied voltage was 1 V. The data was low-pass filtered at 100 kHz (bare substrate) or 5 kHz (bead-coated substrate). ( b ) Log-scaled histogram of dwell time for the same silica-bead-coated substrate (blue, N = 1167). The broken line is a fitted curve using a log-normal distribution.

    Article Snippet: The observed blockade currents for the bead-coated substrate (1.9 ± 0.4 nA) were in good agreement with the theoretically calculated value (i.e., 2.2 nA = baseline (10 nA) × (ssDNA diameter (1.4 nm))2 /(nanopore diameter (3.0 nm))2 ).

    Techniques: Translocation Assay

    Nanopore with nanometre-sized bead nanostructure. ( a ) Schematic of solid-state nanopore with nanometre-sized bead structure coated on the membrane. ( b ) Schematic showing interaction between ssDNA and the silica bead around a nanopore. ( c ) Typical top-view scanning electron microscope image of the bead-coated substrate. The dashed line shows the square area that is the thinnest part of the membrane. (The thickness of the membrane: 20 nm, the diameter of the beads: 50 nm, the width of the square area: 500 nm, the base length of ssDNA: 60-mer.).

    Journal: Scientific Reports

    Article Title: Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure

    doi: 10.1038/srep16640

    Figure Lengend Snippet: Nanopore with nanometre-sized bead nanostructure. ( a ) Schematic of solid-state nanopore with nanometre-sized bead structure coated on the membrane. ( b ) Schematic showing interaction between ssDNA and the silica bead around a nanopore. ( c ) Typical top-view scanning electron microscope image of the bead-coated substrate. The dashed line shows the square area that is the thinnest part of the membrane. (The thickness of the membrane: 20 nm, the diameter of the beads: 50 nm, the width of the square area: 500 nm, the base length of ssDNA: 60-mer.).

    Article Snippet: The observed blockade currents for the bead-coated substrate (1.9 ± 0.4 nA) were in good agreement with the theoretically calculated value (i.e., 2.2 nA = baseline (10 nA) × (ssDNA diameter (1.4 nm))2 /(nanopore diameter (3.0 nm))2 ).

    Techniques: Microscopy

    BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded M13 was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer ssDNA oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.

    Journal: Nucleic Acids Research

    Article Title: Molecular architecture of a multifunctional MCM complex

    doi: 10.1093/nar/gkr831

    Figure Lengend Snippet: BcMCM has intrinsic primase and polymerase activity. ( A ) Circular single-stranded M13 was used as template for BcMCM primase activity. BcMCM primase uses dNTPs more efficiently than NTPs and the reaction is favoured in the presence of manganese as cofactor. ( B ) A 60-mer ssDNA oligonucleotide (see scheme) was used as template with a putative priming site at the boxed sequence. The wild-type BcMCM displayed an intrinsic primase that preferentially uses dNTPs as substrates and manganese as metal activator. The primase activity is eliminated by the double mutation AxA in the catalytic site. In the monomeric Walker A mutant (K653A) and in the truncated version BcMCM 1–400 the primase activity was similar. Arrows indicate the main formation of a dinucleotide and a 4-mer products. ( C ) Using a conventional template/primer substrate (see scheme), BcMCM displayed an intrinsic DNA polymerization activity, which was absent in the mutant AxA. The polymerase activity is preferentially activated by manganese ions. The DNA synthesis of the hexameric BcMCM is similar to the monomeric Walker A mutant (K653A), thus DNA polymerase activity does not involve hexamerization. The DNA polymerase activity of BcMCM, as in the case of the primase activity, is normal in the truncated version BcMCM 1–400 . Therefore both the primase and polymerase activities do not require the helicase domain. The initial substrate and the complete product positions are depicted with two-headed arrows. The asterisk in the substrate sketch indicates the labelled primer.

    Article Snippet: Primase assays As a DNA template to assay primase activity, we first used M13 ssDNA (Amersham Bosciences-GE).

    Techniques: Activity Assay, Sequencing, Mutagenesis, DNA Synthesis

    Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Journal: Methods (San Diego, Calif.)

    Article Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

    doi: 10.1016/j.ymeth.2016.12.003

    Figure Lengend Snippet: Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Article Snippet: Assemble PCR reaction (scale as required): 61.5 μL H2 O, 7.5 μL 10× Platinum Taq PCR Buffer, 1 μL 10 mM dNTPs, 2 μL 50 mM MgOAc, 0.5 μL Forward Primer (5′-CTAATACGACTCACTATTAG, 100 pmol/μL, IDT), 0.5 μL Reverse Primer (5′-CCAGTCAGCACTGTATCCGCTCGCTCTTCA, 100 pmol/μL, IDT), 1 μL of diluted ssDNA pool, and 1 μL Platinum Taq DNA Polymerase High Fidelity (5U/μL).

    Techniques: Microarray, Sequencing, Labeling, Ligation, Polymerase Chain Reaction, Amplification, Purification, Staining, Agarose Gel Electrophoresis, Generated