Structured Review

Eurofins dna sequences
Telomere <t>DNA</t> G-quadruplex unfolding by arginine to alanine mutants of <t>UP1+RGG</t> monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.
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Images

1) Product Images from "RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain"

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

Journal: Nucleic Acids Research

doi: 10.1093/nar/gky854

Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

Techniques Used: Spectroscopy, Protein Concentration, Titration

Interaction of RGG-box with the single stranded and G-quadruplex DNA monitored through NMR spectroscopy. ( A ) 2D 15 N– 1 H HSQC spectrum of the free RGG-box (black) and in complex with Tel22ss at 1:6 protein to DNA molar ratio (red). No significant chemical shift perturbations were observed for this interaction. Single stranded Tel22ss is shown as a cartoon. ( B ) 2D 15 N– 1 H HSQC spectrum of the RGG-box (black) and in complex with Tel22 at 1:6 protein to DNA molar ratio (red). Specific chemical shift perturbations were observed for several residues (marked with green arrows). A representative cartoon of monomeric G-quadruplex form of Tel22 is shown (only one conformation in K + ion is shown). ( C ) A subset of residues of RGG-box that show specific chemical shift perturbation upon addition of Tel22 is shown. The RGG-box and Tel22 complex was in fast exchange (weak binding) as we observed continuous movement of resonance peaks upon addition of increasing amount of the Tel22 DNA. Three steps of titration at different protein to DNA ratios are shown: black at 1:0, green at 1: 1, and red at 1:6. ( D ) The titration curves showing chemical shift change plotted as a function of increasing DNA:protein ratio for 14 interacting residues of the RGG-box is shown.
Figure Legend Snippet: Interaction of RGG-box with the single stranded and G-quadruplex DNA monitored through NMR spectroscopy. ( A ) 2D 15 N– 1 H HSQC spectrum of the free RGG-box (black) and in complex with Tel22ss at 1:6 protein to DNA molar ratio (red). No significant chemical shift perturbations were observed for this interaction. Single stranded Tel22ss is shown as a cartoon. ( B ) 2D 15 N– 1 H HSQC spectrum of the RGG-box (black) and in complex with Tel22 at 1:6 protein to DNA molar ratio (red). Specific chemical shift perturbations were observed for several residues (marked with green arrows). A representative cartoon of monomeric G-quadruplex form of Tel22 is shown (only one conformation in K + ion is shown). ( C ) A subset of residues of RGG-box that show specific chemical shift perturbation upon addition of Tel22 is shown. The RGG-box and Tel22 complex was in fast exchange (weak binding) as we observed continuous movement of resonance peaks upon addition of increasing amount of the Tel22 DNA. Three steps of titration at different protein to DNA ratios are shown: black at 1:0, green at 1: 1, and red at 1:6. ( D ) The titration curves showing chemical shift change plotted as a function of increasing DNA:protein ratio for 14 interacting residues of the RGG-box is shown.

Techniques Used: Nuclear Magnetic Resonance, Spectroscopy, Binding Assay, Titration

Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

Techniques Used: Spectroscopy, Protein Concentration, Titration

Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

Techniques Used: Nuclear Magnetic Resonance, Fluorescence, Spectroscopy, Titration, Labeling

Interaction of UP1+RGG and UP1 with the single stranded and G-quadruplex DNA monitored through ITC. Raw and fitted isotherms are shown and the equilibrium K d s obtained upon fitting of the raw data is mentioned in each panel. ( A, B ) Interaction of UP1 with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( C, D ) Interaction of UP1+RGG with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( E, F ) Interaction of UP1 with the Na + and K + forms of Tel22 G-quadruplex DNA respectively. ( G, H ) Interaction of UP1+RGG with the Na + and K + forms of Tel22 G-quadruplex DNA respectively.
Figure Legend Snippet: Interaction of UP1+RGG and UP1 with the single stranded and G-quadruplex DNA monitored through ITC. Raw and fitted isotherms are shown and the equilibrium K d s obtained upon fitting of the raw data is mentioned in each panel. ( A, B ) Interaction of UP1 with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( C, D ) Interaction of UP1+RGG with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( E, F ) Interaction of UP1 with the Na + and K + forms of Tel22 G-quadruplex DNA respectively. ( G, H ) Interaction of UP1+RGG with the Na + and K + forms of Tel22 G-quadruplex DNA respectively.

Techniques Used:

2) Product Images from "The Effect of DNA-Dispersed Single-Walled Carbon Nanotubes on the Polymerase Chain Reaction"

Article Title: The Effect of DNA-Dispersed Single-Walled Carbon Nanotubes on the Polymerase Chain Reaction

Journal: PLoS ONE

doi: 10.1371/journal.pone.0094117

Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set one. For each panel, top left is agarose gel image with lanes and quantitized boxes shown, top center is intensity line graph, top right is NS1 synthesized fluorescence intensity plot of DNA:SWCNT samples (y-axis is excitation wavelength, x-axis is emission wavelength), bottom left is fluorescence efficiency at each excitation wavelength in NS1 analysis (higher numbers correlate with greater dispersion). Lanes in agarose gel images and intensity line graph: 1. 25 bp ladder (black) 2. unloaded empty well (dark blue) 3. negative control with no SWCNT or PCR template (red) 4. positive control with only PCR template and no SWCNT (green) 5. 0.01 mg/mL DNA:SWCNT (purple) 6. 0.1 mg/mL (neon blue) 7. 1 mg/mL (orange) 8. 5 mg/mL (light blue) 9. 10 mg/mL (pink)10. 100 bp ladder (black). a) TG15:Mix; b) TG15:(6,5); c) Salmon:Mix; d)Salmon:(6,5). (By convention, naming of DNA:SWCNT complexes is as follows: “DNA sequence: type of SWCNT”.)
Figure Legend Snippet: Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set one. For each panel, top left is agarose gel image with lanes and quantitized boxes shown, top center is intensity line graph, top right is NS1 synthesized fluorescence intensity plot of DNA:SWCNT samples (y-axis is excitation wavelength, x-axis is emission wavelength), bottom left is fluorescence efficiency at each excitation wavelength in NS1 analysis (higher numbers correlate with greater dispersion). Lanes in agarose gel images and intensity line graph: 1. 25 bp ladder (black) 2. unloaded empty well (dark blue) 3. negative control with no SWCNT or PCR template (red) 4. positive control with only PCR template and no SWCNT (green) 5. 0.01 mg/mL DNA:SWCNT (purple) 6. 0.1 mg/mL (neon blue) 7. 1 mg/mL (orange) 8. 5 mg/mL (light blue) 9. 10 mg/mL (pink)10. 100 bp ladder (black). a) TG15:Mix; b) TG15:(6,5); c) Salmon:Mix; d)Salmon:(6,5). (By convention, naming of DNA:SWCNT complexes is as follows: “DNA sequence: type of SWCNT”.)

Techniques Used: Agarose Gel Electrophoresis, Synthesized, Fluorescence, Negative Control, Polymerase Chain Reaction, Positive Control, Sequencing

Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set two. All parts of each figure panel are the same as in Figure 1 . a) E2 MRE:Mix; b) E2 MRE:(6,5); c) E2 MRE:Mix, No free template MRE; d) E2 MRE:(6,5), No free template MRE.
Figure Legend Snippet: Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set two. All parts of each figure panel are the same as in Figure 1 . a) E2 MRE:Mix; b) E2 MRE:(6,5); c) E2 MRE:Mix, No free template MRE; d) E2 MRE:(6,5), No free template MRE.

Techniques Used: Agarose Gel Electrophoresis

3) Product Images from "RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain"

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

Journal: Nucleic Acids Research

doi: 10.1093/nar/gky854

Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

Techniques Used: Spectroscopy, Protein Concentration, Titration

Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

Techniques Used: Spectroscopy, Protein Concentration, Titration

Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.
Figure Legend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

Techniques Used: Nuclear Magnetic Resonance, Fluorescence, Spectroscopy, Titration, Labeling

4) Product Images from "Assembly of Designer TAL Effectors by Golden Gate Cloning"

Article Title: Assembly of Designer TAL Effectors by Golden Gate Cloning

Journal: PLoS ONE

doi: 10.1371/journal.pone.0019722

General overview of the two-step cloning strategy for dTALEs assembly. (A) Golden Gate cloning principle applied for assembly of dTALEs. Plasmids encoding selected repeat modules (an example with only two modules, R1 and R2, is shown here due to space limitation) are mixed in one tube together with BsaI, T4 DNA ligase and the destination vector (containing a lacZα fragment for blue-white selection). Assembly of R1 and R2 using BsaI and ligase gives rise to a plasmid lacking the initial BsaI sites, but containing a block of assembled repeats flanked by two BpiI sites. The two BpiI sites allow release of the assembled repeats as one block for the second step of cloning. fs, fusion site. (B) Structure of AvrBs3. AvrBs3 contains a central region with 17 direct repeats (light grey boxes) flanked by a thymidine-specific repeat (repeat 0) and a half repeat (repeat 17.5, both flanking repeats shown as dark grey boxes). Two nuclear localization sequences (NLS, black bars) and a transcription activation domain (AD) are located in the C-terminal region. One representative 34 aa repeat is shown, with the RVD of the NI type highlighted in grey. (C) RVD types and their specificities. (D) Set of 68 repeat modules, with 4 modules with different specificities for each of the 17 repeat positions. Repeat modules are flanked by two BsaI sites with fusion sites selected from the codon-optimized sequence of AvrBs3 (see Supporting Information S1 ). Sets of five (for repeats 13–17) or six (for repeats 1–6 and 7–12) selected repeat modules are preassembled via BsaI into preassembly vectors (pL1-TA1 to 3). Preassembled repeat blocks are then combined in the final destination vector (pL2-TA) using a second BpiI-based Golden Gate cloning reaction. Construction of dTALE-1 is shown as an example.
Figure Legend Snippet: General overview of the two-step cloning strategy for dTALEs assembly. (A) Golden Gate cloning principle applied for assembly of dTALEs. Plasmids encoding selected repeat modules (an example with only two modules, R1 and R2, is shown here due to space limitation) are mixed in one tube together with BsaI, T4 DNA ligase and the destination vector (containing a lacZα fragment for blue-white selection). Assembly of R1 and R2 using BsaI and ligase gives rise to a plasmid lacking the initial BsaI sites, but containing a block of assembled repeats flanked by two BpiI sites. The two BpiI sites allow release of the assembled repeats as one block for the second step of cloning. fs, fusion site. (B) Structure of AvrBs3. AvrBs3 contains a central region with 17 direct repeats (light grey boxes) flanked by a thymidine-specific repeat (repeat 0) and a half repeat (repeat 17.5, both flanking repeats shown as dark grey boxes). Two nuclear localization sequences (NLS, black bars) and a transcription activation domain (AD) are located in the C-terminal region. One representative 34 aa repeat is shown, with the RVD of the NI type highlighted in grey. (C) RVD types and their specificities. (D) Set of 68 repeat modules, with 4 modules with different specificities for each of the 17 repeat positions. Repeat modules are flanked by two BsaI sites with fusion sites selected from the codon-optimized sequence of AvrBs3 (see Supporting Information S1 ). Sets of five (for repeats 13–17) or six (for repeats 1–6 and 7–12) selected repeat modules are preassembled via BsaI into preassembly vectors (pL1-TA1 to 3). Preassembled repeat blocks are then combined in the final destination vector (pL2-TA) using a second BpiI-based Golden Gate cloning reaction. Construction of dTALE-1 is shown as an example.

Techniques Used: Clone Assay, Plasmid Preparation, Selection, Blocking Assay, Activation Assay, Sequencing

5) Product Images from "AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells"

Article Title: AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells

Journal: European Journal of Immunology

doi: 10.1002/eji.201344421

Sequence analysis of IgV and Sμ regions of two IgV-UM and two IgV-Mut CLL samples. (A) From four purified CLL samples, DNA was extracted and subjected to nested PCR to amplify and deep sequence the VDJ and Sμ regions from the rearranged allele. A schematic representation of the rearranged IgH locus is indicated, showing the VDJ gene, the Iμ exon, the Sμ region, and the first constant exon of the IgM heavy chain (CH1μ). Primer-binding sites are indicated (gray: first round PCR and black: second round PCR). The graphs show the set of subclonal VDJ and Sμ sequences (seq#) appearing within the individual samples with a frequency above 0.1%. The particular VDJ usage is indicated below each sample name. Dots within graphs display the position of bases that do not match with the dominant sequence. Base substitutions corresponding to germ line sequences in Sμ are indicated with x. IgV mutations of the dominant clone (D) are indicated as vertical bars along the x -axis for the two IgV-Mut samples. (All sequences are listed in Supporting Information Table 3 .) (B) The frequency of subclonal sequences was determined by dividing the number of sublonal sequences gained by next generation sequencing (NGS) by the number of total sequences. The number above each pie chart gives the percentage of all subclonal variations of the respective sequence (only sequences with a frequency > 0.1% were counted). The mean percentage of base variants/sequence for all IgV versus Sμ regions and the resulting p -value are indicated on the bottom of the graph. Data are compiled from one NGS experiment on four samples (#1–4). (C) Replacement mutations at VDJ genes of all subclonal variations shown in (A) were determined according to the genetic letter code. Nonsense mutations are marked with an asterisk. (D) The mutation spectrum for all VDJ and Sμ mutations depicted in (A) is shown. Nucleotides are listed on the axes and the numbers in each box represent the number of the respective mutation.
Figure Legend Snippet: Sequence analysis of IgV and Sμ regions of two IgV-UM and two IgV-Mut CLL samples. (A) From four purified CLL samples, DNA was extracted and subjected to nested PCR to amplify and deep sequence the VDJ and Sμ regions from the rearranged allele. A schematic representation of the rearranged IgH locus is indicated, showing the VDJ gene, the Iμ exon, the Sμ region, and the first constant exon of the IgM heavy chain (CH1μ). Primer-binding sites are indicated (gray: first round PCR and black: second round PCR). The graphs show the set of subclonal VDJ and Sμ sequences (seq#) appearing within the individual samples with a frequency above 0.1%. The particular VDJ usage is indicated below each sample name. Dots within graphs display the position of bases that do not match with the dominant sequence. Base substitutions corresponding to germ line sequences in Sμ are indicated with x. IgV mutations of the dominant clone (D) are indicated as vertical bars along the x -axis for the two IgV-Mut samples. (All sequences are listed in Supporting Information Table 3 .) (B) The frequency of subclonal sequences was determined by dividing the number of sublonal sequences gained by next generation sequencing (NGS) by the number of total sequences. The number above each pie chart gives the percentage of all subclonal variations of the respective sequence (only sequences with a frequency > 0.1% were counted). The mean percentage of base variants/sequence for all IgV versus Sμ regions and the resulting p -value are indicated on the bottom of the graph. Data are compiled from one NGS experiment on four samples (#1–4). (C) Replacement mutations at VDJ genes of all subclonal variations shown in (A) were determined according to the genetic letter code. Nonsense mutations are marked with an asterisk. (D) The mutation spectrum for all VDJ and Sμ mutations depicted in (A) is shown. Nucleotides are listed on the axes and the numbers in each box represent the number of the respective mutation.

Techniques Used: Sequencing, Purification, Nested PCR, Binding Assay, Polymerase Chain Reaction, Next-Generation Sequencing, Mutagenesis

IgV and Sμ region mutations in unsorted versus CD86 + -sorted CLL cells. The diverse set of VDJ sequences (seq#) for (A) IgV-Mut #3 and (B) IgV-Mut #4, appearing with a frequency > 0.1%, is shown for unsorted and CD86 + -sorted CLL cells as described in Figure 1 . (For IgV-Mut #4, only sequences from CD86 + -sorted samples are shown as no subclonal variations were detected in unsorted samples.) The relative frequencies of the subclones are indicated as horizontal bars on the right of each graph. Data are compiled from one NGS experiment on pooled tagged amplicons derived from DNA of > 50 000 sorted cells. Sequences of subclonal VDJ mutations from CD86 + -sorted samples of (C) IgV-Mut #3 and (D) IgV-Mut #4 are shown in alignment with germ line V sequences (GL) and the respective dominant clone (D). Amino acid changes are shown underneath the alignment and are indicated in gray. Silent mutations are underlined. The resulting mutation spectrum is shown in (E). Nucleotides are listed on the axes and the numbers in each box represent the number of the respective mutation. (F) Genealogical relation of VDJ mutations from CD86 + -sorted IgV-Mut #4 is given. The frequency (frq) of the individual subclones is indicated. The branch support values are given within the diagram and the length of each branch is proportional to the number of varying bases (evolutionary distance).
Figure Legend Snippet: IgV and Sμ region mutations in unsorted versus CD86 + -sorted CLL cells. The diverse set of VDJ sequences (seq#) for (A) IgV-Mut #3 and (B) IgV-Mut #4, appearing with a frequency > 0.1%, is shown for unsorted and CD86 + -sorted CLL cells as described in Figure 1 . (For IgV-Mut #4, only sequences from CD86 + -sorted samples are shown as no subclonal variations were detected in unsorted samples.) The relative frequencies of the subclones are indicated as horizontal bars on the right of each graph. Data are compiled from one NGS experiment on pooled tagged amplicons derived from DNA of > 50 000 sorted cells. Sequences of subclonal VDJ mutations from CD86 + -sorted samples of (C) IgV-Mut #3 and (D) IgV-Mut #4 are shown in alignment with germ line V sequences (GL) and the respective dominant clone (D). Amino acid changes are shown underneath the alignment and are indicated in gray. Silent mutations are underlined. The resulting mutation spectrum is shown in (E). Nucleotides are listed on the axes and the numbers in each box represent the number of the respective mutation. (F) Genealogical relation of VDJ mutations from CD86 + -sorted IgV-Mut #4 is given. The frequency (frq) of the individual subclones is indicated. The branch support values are given within the diagram and the length of each branch is proportional to the number of varying bases (evolutionary distance).

Techniques Used: Next-Generation Sequencing, Derivative Assay, Mutagenesis

6) Product Images from "Oral delivery of Lactococcus lactis that secretes bioactive heme oxygenase-1 alleviates development of acute colitis in mice"

Article Title: Oral delivery of Lactococcus lactis that secretes bioactive heme oxygenase-1 alleviates development of acute colitis in mice

Journal: Microbial Cell Factories

doi: 10.1186/s12934-015-0378-2

Survival of NZ-HO in the mouse intestine. a Experimental schedule. b Homogenates of the entire colon (including luminal contents) were plated on GM17 cm agar. c , d Ten single colonies were randomly chosen for each sample from healthy ( c ) or colitis ( d ) mice and were subjected to colony-direct PCR with pNZ8148-specific ( upper images of each group) or L. lactis subsp. cremoris -specific ( lower images of each group) primer pairs. Bands indicated by blue (586 bp), salmon pink (1,403 bp), and black arrows (163 bp) were further analyzed by DNA sequencing and were consistent with the putative sequences. L : DNA ladder (bp). e Immunohistochemical staining/detection of His-tagged proteins in colonic tissue. Positive reactions were observed in the mucosal epithelial cells ( arrows ), in the crypt, and the lamina propria ( asterisks ) of the colon from gmNZ9000-treated mice. Bars 50 μm. Normal colon and Inflamed colon mean colons from healthy (mice that drank sterile water) or colitis (mice that drank DSS in the water) mice, respectively. Similar results were seen in two different mice. Representative images are shown
Figure Legend Snippet: Survival of NZ-HO in the mouse intestine. a Experimental schedule. b Homogenates of the entire colon (including luminal contents) were plated on GM17 cm agar. c , d Ten single colonies were randomly chosen for each sample from healthy ( c ) or colitis ( d ) mice and were subjected to colony-direct PCR with pNZ8148-specific ( upper images of each group) or L. lactis subsp. cremoris -specific ( lower images of each group) primer pairs. Bands indicated by blue (586 bp), salmon pink (1,403 bp), and black arrows (163 bp) were further analyzed by DNA sequencing and were consistent with the putative sequences. L : DNA ladder (bp). e Immunohistochemical staining/detection of His-tagged proteins in colonic tissue. Positive reactions were observed in the mucosal epithelial cells ( arrows ), in the crypt, and the lamina propria ( asterisks ) of the colon from gmNZ9000-treated mice. Bars 50 μm. Normal colon and Inflamed colon mean colons from healthy (mice that drank sterile water) or colitis (mice that drank DSS in the water) mice, respectively. Similar results were seen in two different mice. Representative images are shown

Techniques Used: Mouse Assay, Polymerase Chain Reaction, DNA Sequencing, Immunohistochemistry, Staining

Related Articles

Amplification:

Article Title: AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells
Article Snippet: .. DNA sequences from amplified VDJ regions were determined by Sanger sequencing (MWG Eurofins; Germany) and the respective VDJ regions were identified using IMGT/V-quest search page at www.IMGT.org , . .. After determining the VDJ usage of the samples, the genomic region spanning VDJ to Sμ was PCR amplified (Phusion proof-reading Polymerase, Biozym), using an Sμ-specific reverse primer in combination with V-specific forward primers (primer list in Supporting Information ).

Binding Assay:

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain
Article Snippet: .. DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon. .. For fluorescence studies, 5′-FLUO-(Tel22)-TAMRA-3′ (F-Tel22-T) [where fluorescein (FLUO) and tetramethylrhodamine (TAMRA) are fluorescent dyes] were synthesized by Sigma Aldrich.

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain
Article Snippet: .. The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon. .. For fluorescence studies, 5′-FLUO-(Tel22)-TAMRA-3′ (F-Tel22-T) [where fluorescein (FLUO) and tetramethylrhodamine (TAMRA) are fluorescent dyes] were synthesized by Sigma Aldrich.

Fluorescence:

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain
Article Snippet: .. DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon. .. For fluorescence studies, 5′-FLUO-(Tel22)-TAMRA-3′ (F-Tel22-T) [where fluorescein (FLUO) and tetramethylrhodamine (TAMRA) are fluorescent dyes] were synthesized by Sigma Aldrich.

Synthesized:

Article Title: Assembly of Designer TAL Effectors by Golden Gate Cloning
Article Snippet: .. DNA sequences for the AvrBs3 N- and C-termini were codon-optimized using the Nicotiana tabacum codon usage (GENEius software from MWG Eurofins, Ebersberg, Germany) and were synthesized by this company. .. Both synthesized fragments do not contain any BpiI or BsaI restriction sites.

Adsorption:

Article Title: Efficient Antifouling Surface for Quantitative Surface Plasmon Resonance Based Biosensor Analysis
Article Snippet: .. DNA Sequence and Adsorption Protocol 43 base thiolated ssDNA oligonucleotides (MWG Eurofins) were kept in their oxidized form DNA-(CH2 )6 -S-S-(CH2 )6 -DNA in order to protect the thiol group from forming undesired oxidation products. ..

Sequencing:

Article Title: Recombinant AfusinC, an anionic fungal CSαβ defensin from Aspergillus fumigatus, exhibits antimicrobial activity against gram-positive bacteria
Article Snippet: .. The DNA sequence coding for AfusinC (afuC gene) was synthesised by Eurofins Genomics (Germany). .. This DNA sequence was optimised for codon usage in E . coli .

Article Title: Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction
Article Snippet: .. The purified PCR product was ligated into the pGEM-T plasmid (Promega) and the DNA sequence determined by automated sequencing (Eurofins-MWG Europe, Ebersberg, Germany) using T7 sense, SP6 anti-sense, and HmTSP-specific primers. ..

Article Title: Efficient Antifouling Surface for Quantitative Surface Plasmon Resonance Based Biosensor Analysis
Article Snippet: .. DNA Sequence and Adsorption Protocol 43 base thiolated ssDNA oligonucleotides (MWG Eurofins) were kept in their oxidized form DNA-(CH2 )6 -S-S-(CH2 )6 -DNA in order to protect the thiol group from forming undesired oxidation products. ..

Article Title: AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells
Article Snippet: .. DNA sequences from amplified VDJ regions were determined by Sanger sequencing (MWG Eurofins; Germany) and the respective VDJ regions were identified using IMGT/V-quest search page at www.IMGT.org , . .. After determining the VDJ usage of the samples, the genomic region spanning VDJ to Sμ was PCR amplified (Phusion proof-reading Polymerase, Biozym), using an Sμ-specific reverse primer in combination with V-specific forward primers (primer list in Supporting Information ).

Nuclear Magnetic Resonance:

Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain
Article Snippet: .. DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon. .. For fluorescence studies, 5′-FLUO-(Tel22)-TAMRA-3′ (F-Tel22-T) [where fluorescein (FLUO) and tetramethylrhodamine (TAMRA) are fluorescent dyes] were synthesized by Sigma Aldrich.

Polyacrylamide Gel Electrophoresis:

Article Title: AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells
Article Snippet: .. DNA sequences from amplified VDJ regions were determined by Sanger sequencing (MWG Eurofins; Germany) and the respective VDJ regions were identified using IMGT/V-quest search page at www.IMGT.org , . .. After determining the VDJ usage of the samples, the genomic region spanning VDJ to Sμ was PCR amplified (Phusion proof-reading Polymerase, Biozym), using an Sμ-specific reverse primer in combination with V-specific forward primers (primer list in Supporting Information ).

Polymerase Chain Reaction:

Article Title: Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction
Article Snippet: .. The purified PCR product was ligated into the pGEM-T plasmid (Promega) and the DNA sequence determined by automated sequencing (Eurofins-MWG Europe, Ebersberg, Germany) using T7 sense, SP6 anti-sense, and HmTSP-specific primers. ..

Purification:

Article Title: Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction
Article Snippet: .. The purified PCR product was ligated into the pGEM-T plasmid (Promega) and the DNA sequence determined by automated sequencing (Eurofins-MWG Europe, Ebersberg, Germany) using T7 sense, SP6 anti-sense, and HmTSP-specific primers. ..

Plasmid Preparation:

Article Title: Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction
Article Snippet: .. The purified PCR product was ligated into the pGEM-T plasmid (Promega) and the DNA sequence determined by automated sequencing (Eurofins-MWG Europe, Ebersberg, Germany) using T7 sense, SP6 anti-sense, and HmTSP-specific primers. ..

Software:

Article Title: Assembly of Designer TAL Effectors by Golden Gate Cloning
Article Snippet: .. DNA sequences for the AvrBs3 N- and C-termini were codon-optimized using the Nicotiana tabacum codon usage (GENEius software from MWG Eurofins, Ebersberg, Germany) and were synthesized by this company. .. Both synthesized fragments do not contain any BpiI or BsaI restriction sites.

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    Eurofins random dna sequence generator
    BRCA1 preferably binds to <t>DNA</t> after CPT11 treatment and Splayed-arm shaped DNA. ( A ) The comparison in DNA binding affinity of BRCA1 with or without CPT11 treatment in <t>EMSA.</t> Various amounts of unlabeled dsDNA (40bp) were added to see the difference of binding affinity with or without CPT11 treatment. C, control; T, CPT11 treatment. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( B ) Graphical representation and statistical analysis of data from Figure 2 A (* P
    Random Dna Sequence Generator, supplied by Eurofins, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins dna sequences
    Telomere <t>DNA</t> G-quadruplex unfolding by arginine to alanine mutants of <t>UP1+RGG</t> monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.
    Dna Sequences, supplied by Eurofins, used in various techniques. Bioz Stars score: 92/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BRCA1 preferably binds to DNA after CPT11 treatment and Splayed-arm shaped DNA. ( A ) The comparison in DNA binding affinity of BRCA1 with or without CPT11 treatment in EMSA. Various amounts of unlabeled dsDNA (40bp) were added to see the difference of binding affinity with or without CPT11 treatment. C, control; T, CPT11 treatment. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( B ) Graphical representation and statistical analysis of data from Figure 2 A (* P

    Journal: International Journal of Biological Sciences

    Article Title: “DNA Binding Region” of BRCA1 Affects Genetic Stability through modulating the Intra-S-Phase Checkpoint

    doi: 10.7150/ijbs.14242

    Figure Lengend Snippet: BRCA1 preferably binds to DNA after CPT11 treatment and Splayed-arm shaped DNA. ( A ) The comparison in DNA binding affinity of BRCA1 with or without CPT11 treatment in EMSA. Various amounts of unlabeled dsDNA (40bp) were added to see the difference of binding affinity with or without CPT11 treatment. C, control; T, CPT11 treatment. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( B ) Graphical representation and statistical analysis of data from Figure 2 A (* P

    Article Snippet: Electrophoretic mobility shift assay HPLC purified oligodeoxynucleotides used in EMSA were designed with Random DNA sequence generator ( http://users-birc.au.du ), and were purchased from eurofins MWG operon.

    Techniques: Binding Assay, Concentration Assay, Labeling

    BRCA1 directly binds to DNA in vitro . ( A ) Binding of full-length MBP-BRCA1 to dsDNA by EMSA. The identity of the samples is shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( B ) Identification of the DBR of BRCA1 using GST-BRCA1 fragments. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( C ) Identification of the DBR of BRCA1 using MBP-BRCA1 fragments. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( D ) Validation of the DBR of BRCA1 using full-length BRCA1 deficient in the DBR (421-701aa) by EMSA. The identities of the samples are shown on the figure. The concentration of labeled dsDNA is 40nM. ( E ) In vitro stability of complex of the DBR of BRCA1 421-701aa and splayed-arm DNA or the DBR alone, and N-terminus sequencing of 3 BRCA1 fragments cleaved from the DBR alone (A, B, C). The DNA-BRCA1 complex and BRCA1 alone were incubated at room temperature for 12 days. The proteins were separated by SDS-PAGE, electroblotted to PDVF membranes, and the bands on the membrane were excised for N-terminus sequencing to identify the N-terminal sequence of the cleaved fragments. ( F ) N-and C-terminus of DBR (421-701aa) binds to dsDNA in EMSA. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( G ) BRCA1 binds dsDNA in a sequence-independent manner in EMSA. The sequences of 3 dsDNA with random sequences are listed in Table S1 . The concentration of labeled dsDNA and proteins are 40nM and 0, 100 or 200nM, respectively. ( H ) The binding affinity of BRCA1 421-701aa to various lengths of dsDNA in EMSA. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( I ) The image of binding of BRCA1 421-988aa or 281-701aa to plasmid DNA by atomic force microscopy. The white dots are the protein and the red structures are plasmid DNA. ( J ) A model of BRCA1 binding to dsDNA.

    Journal: International Journal of Biological Sciences

    Article Title: “DNA Binding Region” of BRCA1 Affects Genetic Stability through modulating the Intra-S-Phase Checkpoint

    doi: 10.7150/ijbs.14242

    Figure Lengend Snippet: BRCA1 directly binds to DNA in vitro . ( A ) Binding of full-length MBP-BRCA1 to dsDNA by EMSA. The identity of the samples is shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( B ) Identification of the DBR of BRCA1 using GST-BRCA1 fragments. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( C ) Identification of the DBR of BRCA1 using MBP-BRCA1 fragments. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and protein are 40nM and 100nM, respectively. ( D ) Validation of the DBR of BRCA1 using full-length BRCA1 deficient in the DBR (421-701aa) by EMSA. The identities of the samples are shown on the figure. The concentration of labeled dsDNA is 40nM. ( E ) In vitro stability of complex of the DBR of BRCA1 421-701aa and splayed-arm DNA or the DBR alone, and N-terminus sequencing of 3 BRCA1 fragments cleaved from the DBR alone (A, B, C). The DNA-BRCA1 complex and BRCA1 alone were incubated at room temperature for 12 days. The proteins were separated by SDS-PAGE, electroblotted to PDVF membranes, and the bands on the membrane were excised for N-terminus sequencing to identify the N-terminal sequence of the cleaved fragments. ( F ) N-and C-terminus of DBR (421-701aa) binds to dsDNA in EMSA. The identities of the samples are shown on the figure. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( G ) BRCA1 binds dsDNA in a sequence-independent manner in EMSA. The sequences of 3 dsDNA with random sequences are listed in Table S1 . The concentration of labeled dsDNA and proteins are 40nM and 0, 100 or 200nM, respectively. ( H ) The binding affinity of BRCA1 421-701aa to various lengths of dsDNA in EMSA. The concentration of labeled dsDNA and proteins are 40nM and 100nM, respectively. ( I ) The image of binding of BRCA1 421-988aa or 281-701aa to plasmid DNA by atomic force microscopy. The white dots are the protein and the red structures are plasmid DNA. ( J ) A model of BRCA1 binding to dsDNA.

    Article Snippet: Electrophoretic mobility shift assay HPLC purified oligodeoxynucleotides used in EMSA were designed with Random DNA sequence generator ( http://users-birc.au.du ), and were purchased from eurofins MWG operon.

    Techniques: In Vitro, Binding Assay, Concentration Assay, Labeling, Sequencing, Incubation, SDS Page, Plasmid Preparation, Microscopy

    Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

    Article Snippet: DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Spectroscopy, Protein Concentration, Titration

    Interaction of RGG-box with the single stranded and G-quadruplex DNA monitored through NMR spectroscopy. ( A ) 2D 15 N– 1 H HSQC spectrum of the free RGG-box (black) and in complex with Tel22ss at 1:6 protein to DNA molar ratio (red). No significant chemical shift perturbations were observed for this interaction. Single stranded Tel22ss is shown as a cartoon. ( B ) 2D 15 N– 1 H HSQC spectrum of the RGG-box (black) and in complex with Tel22 at 1:6 protein to DNA molar ratio (red). Specific chemical shift perturbations were observed for several residues (marked with green arrows). A representative cartoon of monomeric G-quadruplex form of Tel22 is shown (only one conformation in K + ion is shown). ( C ) A subset of residues of RGG-box that show specific chemical shift perturbation upon addition of Tel22 is shown. The RGG-box and Tel22 complex was in fast exchange (weak binding) as we observed continuous movement of resonance peaks upon addition of increasing amount of the Tel22 DNA. Three steps of titration at different protein to DNA ratios are shown: black at 1:0, green at 1: 1, and red at 1:6. ( D ) The titration curves showing chemical shift change plotted as a function of increasing DNA:protein ratio for 14 interacting residues of the RGG-box is shown.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Interaction of RGG-box with the single stranded and G-quadruplex DNA monitored through NMR spectroscopy. ( A ) 2D 15 N– 1 H HSQC spectrum of the free RGG-box (black) and in complex with Tel22ss at 1:6 protein to DNA molar ratio (red). No significant chemical shift perturbations were observed for this interaction. Single stranded Tel22ss is shown as a cartoon. ( B ) 2D 15 N– 1 H HSQC spectrum of the RGG-box (black) and in complex with Tel22 at 1:6 protein to DNA molar ratio (red). Specific chemical shift perturbations were observed for several residues (marked with green arrows). A representative cartoon of monomeric G-quadruplex form of Tel22 is shown (only one conformation in K + ion is shown). ( C ) A subset of residues of RGG-box that show specific chemical shift perturbation upon addition of Tel22 is shown. The RGG-box and Tel22 complex was in fast exchange (weak binding) as we observed continuous movement of resonance peaks upon addition of increasing amount of the Tel22 DNA. Three steps of titration at different protein to DNA ratios are shown: black at 1:0, green at 1: 1, and red at 1:6. ( D ) The titration curves showing chemical shift change plotted as a function of increasing DNA:protein ratio for 14 interacting residues of the RGG-box is shown.

    Article Snippet: DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Nuclear Magnetic Resonance, Spectroscopy, Binding Assay, Titration

    Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

    Article Snippet: DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Spectroscopy, Protein Concentration, Titration

    Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

    Article Snippet: DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Nuclear Magnetic Resonance, Fluorescence, Spectroscopy, Titration, Labeling

    Interaction of UP1+RGG and UP1 with the single stranded and G-quadruplex DNA monitored through ITC. Raw and fitted isotherms are shown and the equilibrium K d s obtained upon fitting of the raw data is mentioned in each panel. ( A, B ) Interaction of UP1 with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( C, D ) Interaction of UP1+RGG with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( E, F ) Interaction of UP1 with the Na + and K + forms of Tel22 G-quadruplex DNA respectively. ( G, H ) Interaction of UP1+RGG with the Na + and K + forms of Tel22 G-quadruplex DNA respectively.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Interaction of UP1+RGG and UP1 with the single stranded and G-quadruplex DNA monitored through ITC. Raw and fitted isotherms are shown and the equilibrium K d s obtained upon fitting of the raw data is mentioned in each panel. ( A, B ) Interaction of UP1 with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( C, D ) Interaction of UP1+RGG with the single stranded Tel22ss DNA in the presence of 100 mM NaCl and 100 mM KCl respectively. ( E, F ) Interaction of UP1 with the Na + and K + forms of Tel22 G-quadruplex DNA respectively. ( G, H ) Interaction of UP1+RGG with the Na + and K + forms of Tel22 G-quadruplex DNA respectively.

    Article Snippet: DNA preparation for CD, NMR and fluorescence kinetics experiments The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques:

    Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set one. For each panel, top left is agarose gel image with lanes and quantitized boxes shown, top center is intensity line graph, top right is NS1 synthesized fluorescence intensity plot of DNA:SWCNT samples (y-axis is excitation wavelength, x-axis is emission wavelength), bottom left is fluorescence efficiency at each excitation wavelength in NS1 analysis (higher numbers correlate with greater dispersion). Lanes in agarose gel images and intensity line graph: 1. 25 bp ladder (black) 2. unloaded empty well (dark blue) 3. negative control with no SWCNT or PCR template (red) 4. positive control with only PCR template and no SWCNT (green) 5. 0.01 mg/mL DNA:SWCNT (purple) 6. 0.1 mg/mL (neon blue) 7. 1 mg/mL (orange) 8. 5 mg/mL (light blue) 9. 10 mg/mL (pink)10. 100 bp ladder (black). a) TG15:Mix; b) TG15:(6,5); c) Salmon:Mix; d)Salmon:(6,5). (By convention, naming of DNA:SWCNT complexes is as follows: “DNA sequence: type of SWCNT”.)

    Journal: PLoS ONE

    Article Title: The Effect of DNA-Dispersed Single-Walled Carbon Nanotubes on the Polymerase Chain Reaction

    doi: 10.1371/journal.pone.0094117

    Figure Lengend Snippet: Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set one. For each panel, top left is agarose gel image with lanes and quantitized boxes shown, top center is intensity line graph, top right is NS1 synthesized fluorescence intensity plot of DNA:SWCNT samples (y-axis is excitation wavelength, x-axis is emission wavelength), bottom left is fluorescence efficiency at each excitation wavelength in NS1 analysis (higher numbers correlate with greater dispersion). Lanes in agarose gel images and intensity line graph: 1. 25 bp ladder (black) 2. unloaded empty well (dark blue) 3. negative control with no SWCNT or PCR template (red) 4. positive control with only PCR template and no SWCNT (green) 5. 0.01 mg/mL DNA:SWCNT (purple) 6. 0.1 mg/mL (neon blue) 7. 1 mg/mL (orange) 8. 5 mg/mL (light blue) 9. 10 mg/mL (pink)10. 100 bp ladder (black). a) TG15:Mix; b) TG15:(6,5); c) Salmon:Mix; d)Salmon:(6,5). (By convention, naming of DNA:SWCNT complexes is as follows: “DNA sequence: type of SWCNT”.)

    Article Snippet: DNA sequences used were: E2 MRE , TG15 ( ) (Eurofins MWG Operon; Huntsville, AL), or salmon testes genomic DNA (Sigma-Aldrich; St. Louis, MO).

    Techniques: Agarose Gel Electrophoresis, Synthesized, Fluorescence, Negative Control, Polymerase Chain Reaction, Positive Control, Sequencing

    Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set two. All parts of each figure panel are the same as in Figure 1 . a) E2 MRE:Mix; b) E2 MRE:(6,5); c) E2 MRE:Mix, No free template MRE; d) E2 MRE:(6,5), No free template MRE.

    Journal: PLoS ONE

    Article Title: The Effect of DNA-Dispersed Single-Walled Carbon Nanotubes on the Polymerase Chain Reaction

    doi: 10.1371/journal.pone.0094117

    Figure Lengend Snippet: Agarose gel electrophoresis images and analysis of gel images and old (4–10 months) DNA:SWCNT samples, set two. All parts of each figure panel are the same as in Figure 1 . a) E2 MRE:Mix; b) E2 MRE:(6,5); c) E2 MRE:Mix, No free template MRE; d) E2 MRE:(6,5), No free template MRE.

    Article Snippet: DNA sequences used were: E2 MRE , TG15 ( ) (Eurofins MWG Operon; Huntsville, AL), or salmon testes genomic DNA (Sigma-Aldrich; St. Louis, MO).

    Techniques: Agarose Gel Electrophoresis

    Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by arginine to alanine mutants of UP1+RGG monitored using CD spectroscopy. ( A, B ) Unfolding of K + form of Tel22 G-quadruplex DNA by TriRGG (A) and AllRGG (B) mutants. The G-quadruplex DNA was titrated with increasing molar excess of proteins. The black arrows in the spectra indicate the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C ) The normalized ellipticity at 295 nm of Tel22 at the final titration step (at 1:6 molar ratio of DNA to protein) for UP1, AllRGG, TriRGG and UP1+RGG showing the relative foldedness of the G-quadruplex structure.

    Article Snippet: The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Spectroscopy, Protein Concentration, Titration

    Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using CD spectroscopy. ( A, B ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( C, D ) Unfolding of K + and Na + forms of Tel22 G-quadruplex DNA by UP1+RGG. The G-quadruplex DNAs were titrated with increasing molar excess of proteins. The black arrow in the spectra indicates the gradual decrease in ellipticity at 295 nm with increasing protein concentration. ( E, F ) The ellipticity at 295 nm was normalized and plotted to show the relative foldedness of both K + and Na + forms of quadruplexes upon UP1 or UP1+RGG addition at each step of titration.

    Article Snippet: The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Spectroscopy, Protein Concentration, Titration

    Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

    Journal: Nucleic Acids Research

    Article Title: RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain

    doi: 10.1093/nar/gky854

    Figure Lengend Snippet: Telomere DNA G-quadruplex unfolding by UP1+RGG and UP1 monitored using NMR and fluorescence spectroscopy. ( A ) 1D 1 H NMR spectra of Na + form of Tel22 showing gradual loss of imino proton peaks upon titration with increasing concentrations of UP1 (blue) and UP1+RGG (red). ( B ) Unfolding of the 5′-FAM and 3′-TAMRA labeled K + form of Tel22 DNA G-quadruplex (5′FAM-Tel22-TAMRA3′) by UP1 (blue) and UP1+RGG (red) monitored by observing the emission of FAM at 516 nM. 5′FAM-Tel22-TAMRA3′ DNA was mixed with 4 molar equivalents of UP1 or UP1+RGG and the emission spectrum was recorded over a time period. ( C ) Proposed model for RGG-box assisted recognition and unfolding of telomere DNA G-quadruplex unfolding by UP1+RGG.

    Article Snippet: The DNA sequences (Table ) for binding studies with UP1, UP1+RGG and the RGG-box were ordered from Eurofins except the abasicloops-Tel22 DNA that was ordered from Dharmacon.

    Techniques: Nuclear Magnetic Resonance, Fluorescence, Spectroscopy, Titration, Labeling