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  • 91
    Thermo Fisher dna sequence flanking rs28386840
    Dna Sequence Flanking Rs28386840, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore oligo nucleotide sequences
    Oligo Nucleotide Sequences, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    TaKaRa dna rna sequences
    Dna Rna Sequences, supplied by TaKaRa, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Oxford Nanopore sequence dna rna molecules
    Sequence Dna Rna Molecules, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 91/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Metabion International AG rna dna labelled sequences
    Rna Dna Labelled Sequences, supplied by Metabion International AG, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Gene Codes Inc sequencher dna sequence assembly software
    Sequencher Dna Sequence Assembly Software, supplied by Gene Codes Inc, used in various techniques. Bioz Stars score: 85/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Genewiz dna sequences
    Dna Sequences, supplied by Genewiz, used in various techniques. Bioz Stars score: 92/100, based on 385 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    MWG-Biotech dna sequences
    Dna Sequences, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 92/100, based on 148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    OriGene dna sequences
    Dna Sequences, supplied by OriGene, used in various techniques. Bioz Stars score: 93/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher rna sequence
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Rna Sequence, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 113 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Metabion International AG rna dna labeled sequences
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Rna Dna Labeled Sequences, supplied by Metabion International AG, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Becton Dickinson rna dna sequencing
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Rna Dna Sequencing, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 92/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Kaneka Corp dna sequences
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Dna Sequences, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 92/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Tech Dragon dna sequences
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Dna Sequences, supplied by Tech Dragon, used in various techniques. Bioz Stars score: 92/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GATC Biotech nucleotide sequences
    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular <t>RNA-protein</t> complexes composed of FR-α mRNA cis- element bound to <t>hnRNP-E1</t> following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations
    Nucleotide Sequences, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 92/100, based on 144 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna sequences
    Contents of biopolymers of the extracellular polymeric substances from <t>biofilm</t> samples harvested at T5. The <t>DNA</t> content was
    Dna Sequences, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 483 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Sangon Biotech dna sequences
    The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. <t>[FIP]</t> = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst <t>DNA</t> polymerase] = 8 U/µL.
    Dna Sequences, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 93/100, based on 532 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rna sequencing whole genome dna sequencing
    The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. <t>[FIP]</t> = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst <t>DNA</t> polymerase] = 8 U/µL.
    Rna Sequencing Whole Genome Dna Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    ATDBio dna sequences
    The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. <t>[FIP]</t> = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst <t>DNA</t> polymerase] = 8 U/µL.
    Dna Sequences, supplied by ATDBio, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Midland Certified Reagent dna sequence
    The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. <t>[FIP]</t> = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst <t>DNA</t> polymerase] = 8 U/µL.
    Dna Sequence, supplied by Midland Certified Reagent, used in various techniques. Bioz Stars score: 92/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Horizon Discovery rna sequence
    IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with <t>shRNA</t> against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control <t>RNA</t> sequence
    Rna Sequence, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 90/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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 527 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Pacific Biosciences dna sequences
    Basic stages of the Single Molecule Real-Time (SMRT) <t>DNA</t> sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.
    Dna Sequences, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Volpi AG dna sequences
    A range of images displaying characteristics of <t>DNA</t> <t>halo</t> preparations. Nucleoskeleton-associated DNA is anchored to the residual nucleus, while extracted, non-associated DNA forms the faint halo surrounding the structure. DNA has been stained using DAPI and can be seen in blue. Panel a displays a representative DNA Halo preparation that has been subjected to immuno-FISH using a painting probe for chromosome 17 (red) and the proliferation nucleolar marker pKi67 (green). Panel b displays another DNA Halo preparation with again the nucleolar proliferation marker pKi67 in green and CCND1 gene loci in red. Panel c is a DNA Halo preparation displaying a proliferating cell that has incorporated bromo-deoxy-uridine during DNA replication (red), DNA in blue and telomere sequences revealed with a PNA-telo probe in green. Panel d shows a residual nucleus surrounded by a halo of DNA visualised by feSEM. The morphology of the residual nucleus (RN) and surrounding DNA halo (DH) Magnification = 6 k scale bar = 2.5 µm. Panel e displays extracted, supercoiled DNA (white arrowheads) within the DNA halo, scale bar 300 nm. Panels f and g are representative control and HGPS fibroblasts with lamin A revealed by indirect immunofluorescence in unextracted cells, respectively and lamin A distribution present in residual nuclei of DNA halo preparations in extracted cells ( h and i ). Panels j – m display representative images of DNA halo preparations with telomeres in green in proliferating control and HGPS fibroblasts ( j and k , respectively) revealed with anti-Ki67 staining (red) and senescent control and HGPS fibroblasts ( l and m , respectively). Note in the HGPS cells telomere signals are located out with the residual nuclei. Scale bars in panels b and f = 10 μm
    Dna Sequences, supplied by Volpi AG, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    ATG:biosynthetics dna sequence
    A range of images displaying characteristics of <t>DNA</t> <t>halo</t> preparations. Nucleoskeleton-associated DNA is anchored to the residual nucleus, while extracted, non-associated DNA forms the faint halo surrounding the structure. DNA has been stained using DAPI and can be seen in blue. Panel a displays a representative DNA Halo preparation that has been subjected to immuno-FISH using a painting probe for chromosome 17 (red) and the proliferation nucleolar marker pKi67 (green). Panel b displays another DNA Halo preparation with again the nucleolar proliferation marker pKi67 in green and CCND1 gene loci in red. Panel c is a DNA Halo preparation displaying a proliferating cell that has incorporated bromo-deoxy-uridine during DNA replication (red), DNA in blue and telomere sequences revealed with a PNA-telo probe in green. Panel d shows a residual nucleus surrounded by a halo of DNA visualised by feSEM. The morphology of the residual nucleus (RN) and surrounding DNA halo (DH) Magnification = 6 k scale bar = 2.5 µm. Panel e displays extracted, supercoiled DNA (white arrowheads) within the DNA halo, scale bar 300 nm. Panels f and g are representative control and HGPS fibroblasts with lamin A revealed by indirect immunofluorescence in unextracted cells, respectively and lamin A distribution present in residual nuclei of DNA halo preparations in extracted cells ( h and i ). Panels j – m display representative images of DNA halo preparations with telomeres in green in proliferating control and HGPS fibroblasts ( j and k , respectively) revealed with anti-Ki67 staining (red) and senescent control and HGPS fibroblasts ( l and m , respectively). Note in the HGPS cells telomere signals are located out with the residual nuclei. Scale bars in panels b and f = 10 μm
    Dna Sequence, supplied by ATG:biosynthetics, used in various techniques. Bioz Stars score: 93/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular RNA-protein complexes composed of FR-α mRNA cis- element bound to hnRNP-E1 following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations

    Journal: The Journal of Biological Chemistry

    Article Title: Incrimination of Heterogeneous Nuclear Ribonucleoprotein E1 (hnRNP-E1) as a Candidate Sensor of Physiological Folate Deficiency *

    doi: 10.1074/jbc.M111.230938

    Figure Lengend Snippet: Slot blot hybridization analysis ( A and B ) to detect enrichment of intracellular RNA-protein complexes composed of FR-α mRNA cis- element bound to hnRNP-E1 following exposure of HeLa-IU 1 - HF cells to increasing physiologically relevant concentrations

    Article Snippet: Because HeLa-IU1 - HF cells have a basal expression rate of FR that is further increased by l -homocysteine at the translational level , we transfected these cells with siRNA directed against hnRNP-E1/PCBP1 mRNA ( ) and a non-targeted scrambled RNA sequence (from Invitrogen).

    Techniques: Dot Blot, Hybridization

    Effect of RNA interference using siRNA against hnRNP-E1 mRNA on the rates of biosynthesis of newly synthesized hnRNP-E1 in HeLa-IU 1 - HF cells with simultaneous evaluation of the biosynthetic rate of newly synthesized FR under basal conditions and after

    Journal: The Journal of Biological Chemistry

    Article Title: Incrimination of Heterogeneous Nuclear Ribonucleoprotein E1 (hnRNP-E1) as a Candidate Sensor of Physiological Folate Deficiency *

    doi: 10.1074/jbc.M111.230938

    Figure Lengend Snippet: Effect of RNA interference using siRNA against hnRNP-E1 mRNA on the rates of biosynthesis of newly synthesized hnRNP-E1 in HeLa-IU 1 - HF cells with simultaneous evaluation of the biosynthetic rate of newly synthesized FR under basal conditions and after

    Article Snippet: Because HeLa-IU1 - HF cells have a basal expression rate of FR that is further increased by l -homocysteine at the translational level , we transfected these cells with siRNA directed against hnRNP-E1/PCBP1 mRNA ( ) and a non-targeted scrambled RNA sequence (from Invitrogen).

    Techniques: Synthesized

    Comparison of the Influence of dl - and l -Homocysteine on RNA-Protein Interactions Involving 18-Base FR-α mRNA cis-Element (and Various Other mRNAs) and Purified hnRNP-E1

    Journal: The Journal of Biological Chemistry

    Article Title: Incrimination of Heterogeneous Nuclear Ribonucleoprotein E1 (hnRNP-E1) as a Candidate Sensor of Physiological Folate Deficiency *

    doi: 10.1074/jbc.M111.230938

    Figure Lengend Snippet: Comparison of the Influence of dl - and l -Homocysteine on RNA-Protein Interactions Involving 18-Base FR-α mRNA cis-Element (and Various Other mRNAs) and Purified hnRNP-E1

    Article Snippet: Because HeLa-IU1 - HF cells have a basal expression rate of FR that is further increased by l -homocysteine at the translational level , we transfected these cells with siRNA directed against hnRNP-E1/PCBP1 mRNA ( ) and a non-targeted scrambled RNA sequence (from Invitrogen).

    Techniques: Purification

    Contents of biopolymers of the extracellular polymeric substances from biofilm samples harvested at T5. The DNA content was

    Journal: Applied and Environmental Microbiology

    Article Title: Metagenome Survey of a Multispecies and Alga-Associated Biofilm Revealed Key Elements of Bacterial-Algal Interactions in Photobioreactors

    doi: 10.1128/AEM.01641-13

    Figure Lengend Snippet: Contents of biopolymers of the extracellular polymeric substances from biofilm samples harvested at T5. The DNA content was

    Article Snippet: To further verify these data, we analyzed the DNA sequences of the mature PBR biofilm obtained by pyrosequencing and Illumina-based sequencing for the presence of hypervariable regions of rRNA gene fragments.

    Techniques:

    The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. [FIP] = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst DNA polymerase] = 8 U/µL.

    Journal: Scientific Reports

    Article Title: Magnetic-Immuno-Loop-Mediated Isothermal Amplification Based on DNA Encapsulating Liposome for the Ultrasensitive Detection of P-glycoprotein

    doi: 10.1038/s41598-017-10133-3

    Figure Lengend Snippet: The real-time fluorescence curves of magnetic liposome-Im-LAMP assay reactions with different concentrations of P-gp:0 pg/ml (curve a), 160 pg/ml (curve b), 16 pg/ml (curve c), 1.6 pg/ml (curve d), 0.16 pg/ml (curve e), 1.6*10 −2 pg/ml (curve f). ( B ) The relationship between cycle time and log concentrations of P-gp. The results are average values of three repetitive measurements. ( C ) Specificity of magnetic liposome-Im-LAMP assay detection of P-gp: the real-time fluorescence curves of Im-LAMP reactions with different reference proteins, bovine serum albumin (BSA), carcinoembryonic antigen (CEA), hemoglobin (HGB), immunoglobulin G (IgG) and the blank. The Im-LAMP reactions were performed in a volume of 10 µL. [FIP] = [BIP] = 1.6 µM, [B3] = [F3] = 0.2 µM, [Bst DNA polymerase] = 8 U/µL.

    Article Snippet: The DNA sequences: FIP, BIP, B3, F3, and the template DNA (Table in supporting information) used in this study were synthesized and purified with high-performance liquid chromatography (HPLC) by Sangon Biotechnology Co. Ltd. (Shanghai, People’s Republic of China).

    Techniques: Fluorescence, Lamp Assay

    IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with shRNA against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control RNA sequence

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses

    doi: 10.1073/pnas.1616942114

    Figure Lengend Snippet: IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with shRNA against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control RNA sequence

    Article Snippet: Naive CD4+ T cells (2 × 104 cells) were activated with allergen-loaded APCs (2 × 104 cells) or anti-CD3/CD28 antibodies with or without activin-A for 2.5 d. Cells were spun with lentivirus containing GFP-expressing shRNA against human AHR , IRF4 , or a scrambled RNA sequence (Dharmacon) and 8 μg/mL polybrene (Sigma–Aldrich).

    Techniques: Cell Differentiation, Activated Clotting Time Assay, Transduction, shRNA, Sequencing

    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:

    Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.

    Journal: PLoS ONE

    Article Title: HLA Typing for the Next Generation

    doi: 10.1371/journal.pone.0127153

    Figure Lengend Snippet: Basic stages of the Single Molecule Real-Time (SMRT) DNA sequencing method. SMRTbell adaptors are ligated onto the ends of a blunt-ended PCR amplicon to facilitate continuous sequencing of both strands of the amplicon. The entire sequence generated may include multiple copies of the sense and anti-sense strands of the PCR amplicon in a single read known as the Continuous Long Read (CLR). The post-sequencing bioinformatic post-processes are able to break down the CLR into shorter sub-reads, which encompass the sequence of one strand of the amplicon. These sub-reads can then be compared and used to create a consensus sequence.

    Article Snippet: The DNA sequences derived from Pacific Biosciences’ SMRT sequencing technologies underwent post-processing using the SMRT analysis tool v2.1, and were assigned HLA types using Anthony Nolan in-house Bioinformatics methods.

    Techniques: DNA Sequencing, Polymerase Chain Reaction, Amplification, Sequencing, Generated

    A range of images displaying characteristics of DNA halo preparations. Nucleoskeleton-associated DNA is anchored to the residual nucleus, while extracted, non-associated DNA forms the faint halo surrounding the structure. DNA has been stained using DAPI and can be seen in blue. Panel a displays a representative DNA Halo preparation that has been subjected to immuno-FISH using a painting probe for chromosome 17 (red) and the proliferation nucleolar marker pKi67 (green). Panel b displays another DNA Halo preparation with again the nucleolar proliferation marker pKi67 in green and CCND1 gene loci in red. Panel c is a DNA Halo preparation displaying a proliferating cell that has incorporated bromo-deoxy-uridine during DNA replication (red), DNA in blue and telomere sequences revealed with a PNA-telo probe in green. Panel d shows a residual nucleus surrounded by a halo of DNA visualised by feSEM. The morphology of the residual nucleus (RN) and surrounding DNA halo (DH) Magnification = 6 k scale bar = 2.5 µm. Panel e displays extracted, supercoiled DNA (white arrowheads) within the DNA halo, scale bar 300 nm. Panels f and g are representative control and HGPS fibroblasts with lamin A revealed by indirect immunofluorescence in unextracted cells, respectively and lamin A distribution present in residual nuclei of DNA halo preparations in extracted cells ( h and i ). Panels j – m display representative images of DNA halo preparations with telomeres in green in proliferating control and HGPS fibroblasts ( j and k , respectively) revealed with anti-Ki67 staining (red) and senescent control and HGPS fibroblasts ( l and m , respectively). Note in the HGPS cells telomere signals are located out with the residual nuclei. Scale bars in panels b and f = 10 μm

    Journal: Biogerontology

    Article Title: Farnesyltransferase inhibitor and rapamycin correct aberrant genome organisation and decrease DNA damage respectively, in Hutchinson–Gilford progeria syndrome fibroblasts

    doi: 10.1007/s10522-018-9758-4

    Figure Lengend Snippet: A range of images displaying characteristics of DNA halo preparations. Nucleoskeleton-associated DNA is anchored to the residual nucleus, while extracted, non-associated DNA forms the faint halo surrounding the structure. DNA has been stained using DAPI and can be seen in blue. Panel a displays a representative DNA Halo preparation that has been subjected to immuno-FISH using a painting probe for chromosome 17 (red) and the proliferation nucleolar marker pKi67 (green). Panel b displays another DNA Halo preparation with again the nucleolar proliferation marker pKi67 in green and CCND1 gene loci in red. Panel c is a DNA Halo preparation displaying a proliferating cell that has incorporated bromo-deoxy-uridine during DNA replication (red), DNA in blue and telomere sequences revealed with a PNA-telo probe in green. Panel d shows a residual nucleus surrounded by a halo of DNA visualised by feSEM. The morphology of the residual nucleus (RN) and surrounding DNA halo (DH) Magnification = 6 k scale bar = 2.5 µm. Panel e displays extracted, supercoiled DNA (white arrowheads) within the DNA halo, scale bar 300 nm. Panels f and g are representative control and HGPS fibroblasts with lamin A revealed by indirect immunofluorescence in unextracted cells, respectively and lamin A distribution present in residual nuclei of DNA halo preparations in extracted cells ( h and i ). Panels j – m display representative images of DNA halo preparations with telomeres in green in proliferating control and HGPS fibroblasts ( j and k , respectively) revealed with anti-Ki67 staining (red) and senescent control and HGPS fibroblasts ( l and m , respectively). Note in the HGPS cells telomere signals are located out with the residual nuclei. Scale bars in panels b and f = 10 μm

    Article Snippet: Performing FISH on these preparations, named HALO-FISH using telomere specific probes can delineate specific DNA sequences (Volpi and Bridger ; de Lange ).

    Techniques: Staining, Fluorescence In Situ Hybridization, Marker, Immunofluorescence