Journal: Nature Communications

Article Title: Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

doi: 10.1038/ncomms12023

Figure Lengend Snippet: RNA structure. ( a ) Schematic depiction of resolving the proximal sites of an RNA. Orange arrow: RNase I cutting site. ( b ) The ‘cut and ligated' products mapped to Snora73 . Black regions: ligation junctions. Vertical colour bar: a cluster of read pairs supporting a pair of proximity sites. ( c ) Density of RNase I cuts. ( d ) Heatmap of the ligation frequencies between any two positions of the RNA. Each coloured circle corresponds to a vertical colour bar in a and represents a pair of proximal sites. ( e ) Footprint of single-stranded regions (red in colour scale) and inferred proximal sites (arrows of the same colour) on the accepted secondary structure. ( f ) A pair of inferred proximal sites, which were not supported by sequenced-based secondary structure, are physically close in vivo , supposedly due to protein-assisted RNA folding.

Article Snippet: Both RNase I and sonication-based fragmentation leave 5′-OH and 3′-P ends, incompatible with RNA ligation, which suppress undesirable RNA ligations.

Techniques: Ligation, In Vivo

Journal: Nucleic Acids Research

Article Title: Isolation and genome-wide characterization of cellular DNA:RNA triplex structures

doi: 10.1093/nar/gky1305

Figure Lengend Snippet: Enrichment of triplex-forming RNAs. ( A ) Schematic overview of the method to enrich DNA-associated RNA. ( B ) RT-qPCR monitoring the indicated RNAs recovered from HeLa S3 cells, nuclei and purified chromatin. Values are normalized to cellular RNA (±SEM, N = 3). ( C ) Polyacrylamide gel electrophoresis of 5′-labeled RNA enriched by SPRI-size selection. Control samples were treated with DNase I before size selection or with RNase A before gel loading. ( D ) RT-qPCR analysis of DNA-associated RNA from HeLa S3 cells isolated by SPRI-size selection. Values are normalized to cellular RNA. Control samples were treated with DNase I before size selection (±SEM, N = 3). ( E ) RNA-seq profiles for KHPS1 in DNA-associated RNAs (DNA-IP) and nuclear RNA from U2OS cells. The overlap with the TFR of KHPS1 is shaded. Minus (–) and plus (+) strands are shown.

Article Snippet: Finally, samples were incubated for 5 min at 37°C with RNase I (3.125 mU/μl, Thermo Fisher Scientific) to yield RNA with an average size of 100–150 nucleotides.

Techniques: Quantitative RT-PCR, Purification, Polyacrylamide Gel Electrophoresis, Labeling, Selection, Isolation, RNA Sequencing Assay

Journal: Nucleic Acids Research

Article Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

doi: 10.1093/nar/gkx362

Figure Lengend Snippet: Deamination assay of HEK293T cell lysate expressing the wild-type A3B and mutants. (A, B) Quantified deamination results under conditions with RNase A ( A ) and without RNase A ( B ). ( C ) The percentage of the product with cell lysate of 2 μg total protein is also shown in bar graphs for comparison. ( D ) The represented results of deamination assay for wild-type A3B, 4Y and W+4Y mutants under the condition with RNase A. ( E ) The amount of A3B and mutants in the 293T cells lysate are normalized to the similar levels, and confirmed by western blot. (F, G) EMSA assay of MBP-A3B-CD1m and MBP-A3B-CD1-4Y mutant with 30 nt ssDNA (F) and 50nt RNA ( G ).

Article Snippet: Deamination assays of mutants that neutralized the positively charged regions on CD1 under the conditions with and without RNase A, allowed us to distinguish different interactions with ssDNA and RNA.

Techniques: Expressing, Western Blot, Mutagenesis

Journal: Nucleic Acids Research

Article Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

doi: 10.1093/nar/gkx362

Figure Lengend Snippet: Analysis of the oligomeric status of the wild-type A3B. ( A ) Western blot of FPLC fractions of HEK293T cell lysate expressing A3B and A3G under no RNase A and with RNase A conditions. α-tubulin is an endogenous control. The fraction shift of A3B under with RNase A condition is due to the slightly variation of FPLC, as shown in Supplementary Figure S5A . ( B ) Western blot of FPLC fractions from MDA-MB231 cells lysate, showing the endogenous A3B. ( C ) The deamination activity of A3B FPLC fractions from A.

Article Snippet: Deamination assays of mutants that neutralized the positively charged regions on CD1 under the conditions with and without RNase A, allowed us to distinguish different interactions with ssDNA and RNA.

Techniques: Western Blot, Fast Protein Liquid Chromatography, Expressing, Multiple Displacement Amplification, Activity Assay

Journal: Nucleic Acids Research

Article Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

doi: 10.1093/nar/gkx362

Figure Lengend Snippet: Deamination assay of HEK293T cell lysate expressing patch 1 and 2 mutants. (A, B) Quantified deamination results under conditions with RNase A ( A ) and without RNase A ( B ). ( C ) The percentage of the product with cell lysate of 2 μg total protein is also shown in bar graphs for comparison. ( D ) The represented results of deamination assay for wild-type A3B, 4Y and W+4Y mutants under the condition with RNase A and without RNase A. ( E ) The expression of A3B and mutants in the 293T cells lysate are at similar levels, confirmed by western blot.

Article Snippet: Deamination assays of mutants that neutralized the positively charged regions on CD1 under the conditions with and without RNase A, allowed us to distinguish different interactions with ssDNA and RNA.

Techniques: Expressing, Western Blot

Journal: Frontiers in Molecular Neuroscience

Article Title: RNase A Promotes Proliferation of Neuronal Progenitor Cells via an ERK-Dependent Pathway

doi: 10.3389/fnmol.2018.00428

Figure Lengend Snippet: Proliferation inhibitor Ara-C blocks the effect of RNase A on NPC proliferation. Mixed mouse cortex and hippocampus cultures were treated with 100 μg/ml Qiagen RNase A (R) at 1 DIV. Mock control (M) represents samples to which no extra material had been added. At 2 DIV, Ara-C (final 1 μM) was added into the culture. After two more days, cultures were harvested and immunostained using MAP2 and Nestin antibodies. DAPI staining was also performed to label cell nuclei. ( A ) Representative images. ( B ) Quantification of the percentage of Nestin + NPCs in total cells (indicated by DAPI stain, upper panel) and in the sum of MAP2 + neurons and Nestin + NPCs (lower panel). Five non-overlapping images under the microscope were randomly selected to determine the averages of cell numbers. Means and SD of three experiments are shown. Scale bars, 100 μm. Statistical analyses were performed using two-way ANOVA with Bonferroni's test. *** P

Article Snippet: Similar to RNase A from Invitrogen (Figure ), Qiagen RNase A also increased NPC population in neuronal cultures, as the percentage of Nestin+ NPCs in total cells was increased by RNase A compared to BSA control (Figures upper).

Techniques: Acetylene Reduction Assay, Staining, Microscopy

Journal: Frontiers in Molecular Neuroscience

Article Title: RNase A Promotes Proliferation of Neuronal Progenitor Cells via an ERK-Dependent Pathway

doi: 10.3389/fnmol.2018.00428

Figure Lengend Snippet: Qiagen RNase A also increases the NPC population in neuronal cultures. Qiagen RNase A (100 μg/ml) and BSA (100 μg/ml) were added into neuronal cultures at 1 DIV for 3 days. Mock control without adding any protein was also included. At 4 DIV, cells were fixed and immunostained with Nestin and MAP2 antibodies. Counter-staining with DAPI was performed to determine the total cell number. (A) Representative images. Scale bars, 50 μm. (B) Quantifications of the percentage of Nestin + cells in the total DAPI + cells (upper) and the sum of MAP2 + and Nestin + cells (bottom). Mean and SD of four experiments are shown. Statistical analyses were performed using one-way ANOVA. * P

Article Snippet: Similar to RNase A from Invitrogen (Figure ), Qiagen RNase A also increased NPC population in neuronal cultures, as the percentage of Nestin+ NPCs in total cells was increased by RNase A compared to BSA control (Figures upper).

Techniques: Staining

Journal: Nucleic Acids Research

Article Title: A novel role for CARM1 in promoting nonsense-mediated mRNA decay: potential implications for spinal muscular atrophy

doi: 10.1093/nar/gkv1334

Figure Lengend Snippet: CARM1 can be co-immunoprecipitated with UPF1 and the interaction between UPF1 and the β-Globin T39 mutant (MT) decreases with CARM1 knockdown. ( A ) Total cell lysates were prepared from MN-1 cells and subjected to immunoprecipitation with an IgG CTRL or UPF1 antibodies. Immunoprecipitated proteins were then analysed by western blot using antibodies against UPF1 and CARM1. ( B ) UPF1 immunoprecipitation experiments were performed with or without (w/o) pretreatment of the cell lysate with RNase A (1 μg/ml) for 30 min at 37°C. ( C ) Then, the CARM1/UPF1 ratios in response to the RNase A treatments were assessed. Values shown in the bar graph are means +/− SEM ( n = 3). ( D ) The MT reporter was transiently transfected either into the MN-1 pGIPZ CTRL or the MN-1 shCARM1 cell line. RT-PCR analysis was performed using primers specific for the MT mRNA or pre-mRNA, on total RNA extracted from the CTRL (left panel) or shCARM1 (right panel). ( E ) β-Globin mRNA levels, shown here as percent bound to UPF1, were normalized to overall immunoprecipated UPF1 levels and Gapdh mRNA was used as a loading control. Data are means +/− SEM ( n = 3).

Article Snippet: For RNase A treatment (Qiagen, 19101), the cell pellets were first incubated with lysis buffer.

Techniques: Immunoprecipitation, Mutagenesis, Western Blot, Transfection, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: Isolation and Characterization of a Single-Stranded DNA Virus Infecting the Marine Diatom Chaetoceros sp. Strain SS628-11 Isolated from Western JAPAN

doi: 10.1371/journal.pone.0082013

Figure Lengend Snippet: Nucleic acids analysis of Csp07DNAVgenome. (A) Csp07DNAV genome. Extracts of DNA (lane 1) and RNA (lane 2). (B) Nucleic acids of Csp07DNAV without treatment (lane 1), 100°C for 5 min (lane 2), treated with DNase I (lane 3), RNase A (lane 4), and S1 nuclease (lane 5). The samples were electrophoresed on a formaldehyde-agarose gel.

Article Snippet: Aliquots (4 µl) of the nucleic acid solution were digested with DNase I (0.5 U•µl−1 ; Takara Bio) at 37°C for 1 h, incubated with RNase A (0.025 µg•µl−1 ; Nippon Gene) at 37°C for 1 h, and digested with S1 nuclease (0.7 U•µl−1 ; Takara Bio) at 23°C for 15 min or boiled at 100°C for 5 min. Nucleic acid extracts that were kept on ice without treatment served as controls.

Techniques: Agarose Gel Electrophoresis

Journal: Scientific Reports

Article Title: Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

doi: 10.1038/srep36628

Figure Lengend Snippet: Profile fitting to the hkl = −8 1 0 peak from ribonuclease A crystal using four asymmetric functions. ( a ) Gaussian convolved with two back-to-back exponentials fit. ( b ) Pseudo-Voigt function convolved with two back-to-back exponentials fit. ( c ) Gaussian convolved with Ikeda–Carpenter function fit. ( d ) Gaussian convolved with Landau function fit. In panels ( a–c ), SciPy was used to fit the functions and results were plotted by Gnuplot. In panel ( d ), because Gaussian convolved with Landau function contains convolution part in the equation, ROOT was used to fit the function and plot the results. Both four points of the outside regions of the integration region were used as the background region.

Article Snippet: Preparation of ribonuclease A crystal and neutron and X-ray diffraction experiments Bovine pancreatic ribonuclease A was purchased from Sigma-Aldrich and crystalized as previously described .

Techniques:

Journal: Scientific Reports

Article Title: Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

doi: 10.1038/srep36628

Figure Lengend Snippet: Plots of parameters related to peak profile against TOF in ribonuclease A neutron diffraction data. The peaks whose I/σ(I ) is over 5 and obtained by one detector located at 51° in 2 θ center and one crystal orientation were used. ( a ) Plot of parameter β against TOF. The peaks whose β errors are less than 1 were used. ( b ) Plot of parameter σ . The peaks whose σ errors are less than 10000 were used.

Article Snippet: Preparation of ribonuclease A crystal and neutron and X-ray diffraction experiments Bovine pancreatic ribonuclease A was purchased from Sigma-Aldrich and crystalized as previously described .

Techniques:

Journal: Scientific Reports

Article Title: Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

doi: 10.1038/srep36628

Figure Lengend Snippet: Two examples of profile fitting to the weak peaks from ribonuclease A crystal using Gaussian convolved with two back-to-back exponentials. Red solid line: fitting function. Black points and line: weak peak profile. These peaks were obtained by detector located at 118° in 2 θ center and one crystal orientation. Both four points of outside regions of the integration region were used as the background region. ( a ) Peak hkl is 11 3 16. ( b ) Peak hkl is 11 3 20.

Article Snippet: Preparation of ribonuclease A crystal and neutron and X-ray diffraction experiments Bovine pancreatic ribonuclease A was purchased from Sigma-Aldrich and crystalized as previously described .

Techniques:

Journal: Journal of the American Chemical Society

Article Title: Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents

doi: 10.1021/ja0354566

Figure Lengend Snippet: Measuring single-turnover kinetics of RNase A. (a) Left: a schematic of the microfluidic network. Right: a false-color fluorescence microphotograph (2 s exposure showing time-averaged fluorescence intensity of moving plugs and oil; sample consumption was 33 nL/s). The dashed white lines trace the walls of the microchannel. (b) Graph of reaction progress at a pH of 7.5. Shown are experimental kinetic data (left axis) for three substrate concentrations (• 5.8 μM, ▪ 3.3 μM, ▴ 0.8 μM) obtained from images such as that shown in part a with fits of the reaction progress (solid lines). Also shown is a mixing curve using the Fluo-4/Ca 2+ system (right axis, ▽ in the same microfluidic device with fit (dashed line) of an explicit mixing function). (c) Graph of reaction progress at pH of 6.0. Shown are experimental kinetic data (left axis) for three substrate concentrations (• 5.8 μM, ▪ 3.3 μM, ♦ 1.6 μM) with fits of the reaction progress (solid lines). Also shown is the same mixing curve as in part b.

Article Snippet: Ribonuclease A solution (EC 3.1.27.5) was obtained from USB Corp. and generously provided by A. V. Korennykh and Prof. J.

Techniques: Fluorescence

Journal: Protein Science : A Publication of the Protein Society

Article Title: Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies

doi: 10.1110/ps.036939.108

Figure Lengend Snippet: The binding isotherm of RNase A and 3′-CMP. RNase A (55 μM) in 0.2 M sodium acetate buffer, pH 6.0 containing 0.2 M NaCl, was titrated with small injections of 3′-CMP solution in the same buffer. The enthalpy data were fitted to a single site binding model. ( A ) Binding isotherm for refolded RNase A; ( B ) binding isotherm for Sigma RNase A.

Article Snippet: The second interfacial precipitate (lane 4) shows a single band of RNase A having a purity comparable to that of commercially available RNase A (type XIIA) from Sigma Chemical Co. (lane 3).

Techniques: Binding Assay

Journal: Protein Science : A Publication of the Protein Society

Article Title: Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies

doi: 10.1110/ps.036939.108

Figure Lengend Snippet: Spectroscopic characterization of refolded RNase A. ( A ) Fluorescence emission spectra of RNase A. The samples at a concentration of 100 μg/mL −1 (∼7 μM) were excited at 278 nm and the emission spectra from 290 to 400 nm were recorded, using excitation and emission slit widths of 2 nm and 5 nm, respectively. Fluorescence spectra of unfolded RNase A (3), refolded RNase A (2), Sigma RNase A (1) are shown after correction for buffer contribution. ( B ) The far-UV CD spectra of refolded RNase A (○) and Sigma RNase A (△) for 0.5 mg/mL −1 protein recorded in a 1-mm path length cuvette from 200 to 250 nm. ( C ) The near-UV CD spectra of the two samples recorded for 0.5 mg/mL −1 protein in a 1-cm path length cuvette from 250 to 350 nm. The symbols are the same as in B .

Article Snippet: The second interfacial precipitate (lane 4) shows a single band of RNase A having a purity comparable to that of commercially available RNase A (type XIIA) from Sigma Chemical Co. (lane 3).

Techniques: Fluorescence, Concentration Assay

Journal: Protein Science : A Publication of the Protein Society

Article Title: Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies

doi: 10.1110/ps.036939.108

Figure Lengend Snippet: TPP purification monitored by SDS-PAGE. ( A ) Fifteen percent SDS-PAGE analysis of RNase A inclusion bodies at different steps of TPP; (lane 1 ) unwashed inclusion bodies; (lane 2 ) washed inclusion bodies with 50 mM PBS/pH 7.4/1 mM EDTA containing 2 M urea; (lane 3 ) commercial RNase A (Sigma Chemical Co.); (lane 4 ) refolded RNase A obtained from interfacial precipitate of second TPP; (lane 5 ) interfacial precipitate of first TPP; (lane 6 ) aqueous phase of second TPP. ( B ) Fifteen percent SDS-PAGE analysis of inclusion bodies of CcdB mutants subjected to TPP; (lane 1 ) unwashed inclusion bodies of CcdB-F17P; (lane 2 ) washed inclusion bodies of CcdB-F17P with 50 mM PBS/pH 7.4/0.5% Triton X-100; (lane 3 ) interfacial precipitate of first TPP; (lane 4 ) aqueous phase of second TPP; (lane 5 ) refolded and purified CcdB-F17P by TPP; (lane 6 ) molecular weight marker; (lane 7 ) unwashed inclusion bodies of CcdB-M97K; (lane 8 ) washed inclusion bodies of CcdB-M97K; (lane 9 ) interfacial precipitate of first TPP; (lane 10 ) aqueous phase of second TPP; (lane 11 ) refolded and purified CcdB-M97K by TPP. ( C ) Fifteen percent SDS-PAGE analysis of inclusion bodies of CD4D12 subjected to TPP CD4D12; (lane 1 ) molecular weight marker; (lane 2 ) unwashed inclusion bodies of CD4D12; (lane 3 ) washed inclusion bodies of CD4D12 with 50 mM PBS/pH 7.4/0.5% Triton X-100; (lane 4 ) interfacial precipitate of first TPP; (lane 5 ) aqueous phase of second TPP; (lane 6 ) refolded and purified CD4D12 by TPP; (lane 7 ) refolded and purified CD4D12 after subjected to the 50-kDa polyethersulfone membrane (PALL Lifesciences) once; (lane 8 ) refolded and purified CD4D12 after subjected to the 50-kDa polyethersulfone membrane (PALL Lifesciences) twice; (lane 9 ) refolded and purified CD4D12 in the absence of DTT.

Article Snippet: The second interfacial precipitate (lane 4) shows a single band of RNase A having a purity comparable to that of commercially available RNase A (type XIIA) from Sigma Chemical Co. (lane 3).

Techniques: Purification, SDS Page, Molecular Weight, Marker

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Calculated Kratky plots for native RNAse A and the simulated unfolded ensembles under different solvation conditions. The simulated scattering curves were calculated as described in the legend to . Filled circles identify the curve calculated

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Log-log plots of simulated small-angle x-ray scattering curves for unfolded RNAse A under different solvation conditions. (a) The simulated curves were calculated as described in the legend for , using Boltzmann weighting factors calculated for

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Experimental and fit SAXS curves for reduced and carboxyamidomethylated (RCAM) RNAse A at pH 7. Samples contained the indicated urea concentrations and approximately 5 mg/mL RCAM-RNAse A. The experimental data are shown as small points with error bars

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: The predicted change in conformational entropy, Δ S conf , for the transfer of reduced and unfolded RNAse A from an athermal solvent to conditions of favorable or unfavorable solvation. Δ S conf and the smoothed

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Log-log plots of experimental scattering curves for RCAM-RNAse A in solutions containing urea at the indicated concentrations, at pH 7 (a) and pH 3 (b). The graphs have been displaced by arbitrary amounts along the vertical axis for clarity, and Q has

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Simulated effects of solvation on the average radius of gyration and average intramolecular distances in unfolded RNAse A. (a) RMS radius of gyration as a function of Δ G solv . Cells in the smoothed histogram shown in were weighted according

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Distributions of accessible surface areas (ASA) of conformations in simulated ensembles of reduced and unfolded RNAse A. (a) The unweighted histogram for an ensemble of approximately 450,000 conformations calculated under the assumption of an athermal

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques:

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Histograms correlating accessible surface area and radius of gyration in unweighted and weighted ensembles of unfolded RNAse A. (a) The histogram derived directly from the ensemble of approximately 450,000 calculated conformations. (b) A smoothed histogram

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques: Derivative Assay

Journal:

Article Title: Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins

doi: 10.1016/j.jmb.2008.02.009

Figure Lengend Snippet: Fractal dimension of reduced and unfolded RNAse A as a function of urea concentration. The fractal dimension of the RCAM (a) and RCM (b) forms of RNAse A were determined as the negative slopes of log( I ) versus log( Q ) over the range of log( Q ) values from

Article Snippet: Bovine ribonuclease A (type XII-A) was purchased from Sigma Chemical Co. and used without further purification.

Techniques: Concentration Assay

Journal: Epigenetics

Article Title: MeCP2 interacts with chromosomal microRNAs in brain

doi: 10.1080/15592294.2017.1391429

Figure Lengend Snippet: Validation of RIP-seq data using qRT-PCR. MeCP2-RNA candidate interactions were validated in mouse primary cortical neurons using qRT PCR. (A) Data presented as percent of input (total chromatin RNA) bound by MeCP2 and normalized to the percent input bound in no antibody control samples. (B) MicroRNA miR-375 qRT PCR with and without RNase treatment. (C) MicroRNA miR-126 qRT PCR after RNase A treatment of MeCP2 bound RNAs in mouse primary cortical neurons. RNase A treatment of RNA isolated after MeCP2-RIP decreased amplification of miR-126 from both S1 and S2 chromatin fractions. (D) Let-7i qRT PCR after RNase A treatment of MeCP2 bound RNAs in mouse primary cortical neurons. RNase A treatment of RNA isolated after MeCP2-RIP decreased amplification of let-7i from both S1 and S2 chromatin fractions; S1, MNase sensitive chromatin fraction; S2, MNase resistant chromatin fraction; n = 3; t test * P

Article Snippet: For RNase digestion, immunopurified RNA was digested with RNase A solution (Sigma, R4642) at a final concentration of 10 µg/ml and incubated at RT for 10 min prior to RNA purification.

Techniques: Quantitative RT-PCR, Isolation, Amplification