Structured Review

Eurofins oligos
Oligos, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/oligos/product/Eurofins
Average 93 stars, based on 3 article reviews
Price from $9.99 to $1999.99
oligos - by Bioz Stars, 2020-02
93/100 stars

Images

Related Articles

Clone Assay:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: .. The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington). .. The presence of the correct insert within the recombinant pSUPER vector was confirmed by sequencing using the M13 primer GTAAAACGACGGCCAGT.

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: .. The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Centrifugation:

Article Title: Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat
Article Snippet: Somatic Cells were sonicated a total of 4 rounds, while hESCs were sonicated for 6 rounds, with brief vortex and centrifugation at 4°C between each round to obtain an average shear size of 250–300bp. .. All oligos used, described in , were obtained from Eurofins MWG Operon.

Amplification:

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: Amplicon lengths were 93 base pairs (bp) for RHD exon 7, 74 bp for RHD exon 10, and 94 bp for GAPDH . .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification.

Synthesized:

Article Title: Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification
Article Snippet: .. Each of these oligos, including the fluorophores and biotin, was synthesized by Eurofins MWG Operon (Huntsville, AL, USA). .. Relaxation assays Wheat germ topoisomerase I (Topo IB) (Promega, Madison, WI, USA), Topo IV, yTopo II and hTopo IIα were incubated with plasmid pBR322 (New England Biolabs) at protein: DNA concentrations of 25 nM:50 nM in a 60 µl reaction containing 40 mM Tris–HCl (pH 7.5), 6 mM MgCl2 , 100 mM KOAc, 1 mM DTT, 1 mM ATP, 0.1 mM EDTA and 50 µg/ml bovine serum albumin (BSA) (New England Biolabs).

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification. ..

Article Title: The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host
Article Snippet: .. The oligos for the engineered sequences were synthesized by and obtained from Eurofins MWG Operon. ..

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University). .. For histone and DNA binding, proteins were characterized as either MBP- or GST-fusions.

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: .. The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Construct:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: Paragraph title: Expression construct, site-directed mutagenesis and shRNA production ... The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington).

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: Diploid msh6 pol3–5DV strains were constructed by mating of the two haploids, one being MSH6 , and the other containing the POL3 plasmid pBL304 rescuing the msh6 pol3–5DV genotype, followed by deletion of the second MSH6 allele with a hphNT1 marker [ ] followed by selection for loss of the POL3 plasmid. .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in .

Article Title: Carcinogenic adducts induce distinct DNA polymerase binding orientations
Article Snippet: Paragraph title: DNA constructs ... All oligos were purchased from Eurofins MWG Operon.

Real-time Polymerase Chain Reaction:

Article Title: Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat
Article Snippet: Immunoprecipitated DNA was assessed by quantitative PCR (qPCR) on a Bio-Rad CFX96 Real-Time System with a C100™ Thermal Cycler using EvaGreen qPCR Mastermix (Mastermix-S, Applied Biological Materials). .. All oligos used, described in , were obtained from Eurofins MWG Operon.

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: Paragraph title: Real-time PCR ... All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification.

Article Title: PDGFRα+ stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland
Article Snippet: Paragraph title: qPCR and ddPCR ... All oligos were from Eurofins Genomics and all probes were from Integrated DNA Technologies.

Incubation:

Article Title: Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells
Article Snippet: Following overnight incubation, cell medium was replaced with fresh DMEM containing 10% FCS without antibiotics. .. The oligos were purchased as single strands, one labelled with the infrared IR-800 dye and the other unlabelled (Eurofins, Ebersberg, Germany).

Article Title: Carcinogenic adducts induce distinct DNA polymerase binding orientations
Article Snippet: All oligos were purchased from Eurofins MWG Operon. .. Briefly, 20 nmol oligonucleotide containing a single guanine was incubated with 500 nmol 2-(N -acetoxy-N -acetyl)aminofluorene (AAAF) for 1 h at 37°C in a degassed solution containing 20% ethanol and 2 mM sodium citrate, pH 6.8.

Expressing:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: Paragraph title: Expression construct, site-directed mutagenesis and shRNA production ... The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington).

Article Title: Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells
Article Snippet: Cells were transfected using Lipofectamine LTX and PLUS Reagent with 2 μg pSG5 or pSG5-AR expression vectors. .. The oligos were purchased as single strands, one labelled with the infrared IR-800 dye and the other unlabelled (Eurofins, Ebersberg, Germany).

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: All oligos were obtained from Eurofins Genomics LLC. .. Validation of successful deletion of the IL1RAPL1 enhancer and the impact on allele expression by SNP genotyping. ( a ) Ethidium bromide-stained agarose gel images showing PCR results from individual clones exposed transiently to the gRNA pair flanking the enhancer locus.

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Article Title: PDGFRα+ stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland
Article Snippet: Transcript levels were normalized to endogenous β-actin transcripts and compared to vehicle control stromal expression set at 1. .. All oligos were from Eurofins Genomics and all probes were from Integrated DNA Technologies.

shRNA:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: Paragraph title: Expression construct, site-directed mutagenesis and shRNA production ... The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington).

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: Rab20 knockdown with the pSIREN system Using the Clontech online shRNA design tool, four oligos were designed against Mus musculus Rab20 : 1, 5′-CTGACAGAAACAGCCAACA-3′; 2, 5′-CCAACAATGACTGCCTGTT-3′; 3, 5′-CACCCAAACAGACTAGATC-3′ and 4, 5′-CCGCTATCATCCTTACATA-3′. .. The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification.

Western Blot:

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. For western blotting, transfected macrophages from 25-cm2 flasks were sorted for DsRed by using a BD Aria II sorter (BD Biosciences, San Jose, CA).

Transformation Assay:

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in . ..

Hybridization:

Article Title: Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells
Article Snippet: The oligos were purchased as single strands, one labelled with the infrared IR-800 dye and the other unlabelled (Eurofins, Ebersberg, Germany). .. Hybridisation of the oligos was performed by mixing 1 μM labelled oligo with 1 μM unlabelled oligo.

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligo hybridization was checked by 20% PAGE followed by fluorescent imaging of the FAM-labeled duplex as well as by SYBR Gold (Thermo) staining of ssDNA. .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

High Performance Liquid Chromatography:

Article Title: Carcinogenic adducts induce distinct DNA polymerase binding orientations
Article Snippet: All oligos were purchased from Eurofins MWG Operon. .. Oligos were purified by HPLC using a C18 column.

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification. ..

Article Title: Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes - Human TnIc as a Model
Article Snippet: .. Oligos and primers used in plasmid construction were purchased from Eurofins MWG Operon (Ebersberg, Germany) and were subjected to HPLC purification. .. The sequences and labeling sites of these oligos are listed in .

Transfection:

Article Title: Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells
Article Snippet: Twenty-four hours after transfection, cells were treated with 10 nM R1881 for 1 h. Cells were then washed twice with ice-cold PBS and harvested by scraping in ice-cold PBS buffer containing PIs. .. The oligos were purchased as single strands, one labelled with the infrared IR-800 dye and the other unlabelled (Eurofins, Ebersberg, Germany).

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Immunoprecipitation:

Article Title: Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat
Article Snippet: Immunoprecipitated DNA was assessed by quantitative PCR (qPCR) on a Bio-Rad CFX96 Real-Time System with a C100™ Thermal Cycler using EvaGreen qPCR Mastermix (Mastermix-S, Applied Biological Materials). .. All oligos used, described in , were obtained from Eurofins MWG Operon.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Digital PCR:

Article Title: PDGFRα+ stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland
Article Snippet: First strand cDNA for droplet digital PCR (ddPCR) was prepared using qScript cDNA supermix (QuantaBio). .. All oligos were from Eurofins Genomics and all probes were from Integrated DNA Technologies.

Imaging:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligo hybridization was checked by 20% PAGE followed by fluorescent imaging of the FAM-labeled duplex as well as by SYBR Gold (Thermo) staining of ssDNA. .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Polymerase Chain Reaction:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: All oligos were obtained from Eurofins Genomics LLC. .. Validation of successful deletion of the IL1RAPL1 enhancer and the impact on allele expression by SNP genotyping. ( a ) Ethidium bromide-stained agarose gel images showing PCR results from individual clones exposed transiently to the gRNA pair flanking the enhancer locus.

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: The PCR assay targeted the RhD gene, RHD (accession number NT_004610.19). .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification.

Sonication:

Article Title: Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat
Article Snippet: Somatic Cells were sonicated a total of 4 rounds, while hESCs were sonicated for 6 rounds, with brief vortex and centrifugation at 4°C between each round to obtain an average shear size of 250–300bp. .. All oligos used, described in , were obtained from Eurofins MWG Operon.

Binding Assay:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: For DNA binding analysis, complementary 12-bp DNA oligonucleotides with the following sequences [FAM-5′-CCATGXGCTGAC-3′ and 5′-GTCAGYGCATGG-3′ (UnDNA: X and Y are cytosine, He5mC: X is 5mC and Y is cytosine, Sy5mC: X and Y are 5mC, He5hmC: X is 5hmC and Y is cytosine, Sy5hmC: X and Y are 5hmC)] were resuspending in STE buffer (10 mM Tris–HCl pH 8.0, 100 mM NaCl, 1 mM EDTA). .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Marker:

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: Diploid msh6 pol3–5DV strains were constructed by mating of the two haploids, one being MSH6 , and the other containing the POL3 plasmid pBL304 rescuing the msh6 pol3–5DV genotype, followed by deletion of the second MSH6 allele with a hphNT1 marker [ ] followed by selection for loss of the POL3 plasmid. .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in .

Fluorescence:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Paragraph title: Fluorescence polarization ... Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Mutagenesis:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: Paragraph title: Expression construct, site-directed mutagenesis and shRNA production ... The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington).

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: Cells were subsequently selected for URA3 loss and screening for strains containing the pol3–5DV mutation. .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in .

Article Title: Mismatch repair-dependent mutagenesis in nondividing cells
Article Snippet: .. Oligos were 40 nt in length and differed by one centrally located nucleotide from the mutant chromosomal sequence and were gel purified (Eurofins MWG Operon); sequences of oligos are listed in . ..

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Article Title: The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host
Article Snippet: The nonsynonymous mutation of CGC (Arginine) for the least favored codon of Leucine was chosen as it is one of the least conserved residues within the region, as denoted by PDBsum’s residue conservation calculations , . .. The oligos for the engineered sequences were synthesized by and obtained from Eurofins MWG Operon.

Isolation:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Electrophoretic Mobility Shift Assay:

Article Title: Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells
Article Snippet: Paragraph title: Electrophoretic mobility shift assay ... The oligos were purchased as single strands, one labelled with the infrared IR-800 dye and the other unlabelled (Eurofins, Ebersberg, Germany).

Purification:

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in . ..

Article Title: Mismatch repair-dependent mutagenesis in nondividing cells
Article Snippet: .. Oligos were 40 nt in length and differed by one centrally located nucleotide from the mutant chromosomal sequence and were gel purified (Eurofins MWG Operon); sequences of oligos are listed in . ..

Article Title: Carcinogenic adducts induce distinct DNA polymerase binding orientations
Article Snippet: All oligos were purchased from Eurofins MWG Operon. .. Oligos were purified by HPLC using a C18 column.

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification. ..

Article Title: Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes - Human TnIc as a Model
Article Snippet: .. Oligos and primers used in plasmid construction were purchased from Eurofins MWG Operon (Ebersberg, Germany) and were subjected to HPLC purification. .. The sequences and labeling sites of these oligos are listed in .

Sequencing:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: The sequence of the forward oligo included the siRNA sequence in sense (5′) and antisense (3′) orientation separated by the CTCGAG nucleotide-specific loop sequence (hairpin). .. The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington).

Article Title: Mismatch repair-dependent mutagenesis in nondividing cells
Article Snippet: .. Oligos were 40 nt in length and differed by one centrally located nucleotide from the mutant chromosomal sequence and were gel purified (Eurofins MWG Operon); sequences of oligos are listed in . ..

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Article Title: Scalable Low-Cost Fabrication of Disposable Paper Sensors for DNA Detection
Article Snippet: The oligos were purchased from Eurofins. .. The sequence for the probe ssDNA is 5′-Cy3[SP-3] AGAGAACCTGGG[TTT]4 [SP-3][AmC7-Q]-3′, and the sequence for the target DNA is 5′-[Cy5]AAAAAAA···ACCCAGGTTCTCT-3′.

Article Title: Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification
Article Snippet: The sequence of the complementary bottom strand is 3′–GTAGCAGTAGGAGCCGCG-[Alexa546]-GCACGCATTGACAGGCGGGACGACGCTCACC–5′ ( A). .. Each of these oligos, including the fluorophores and biotin, was synthesized by Eurofins MWG Operon (Huntsville, AL, USA).

Article Title: The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host
Article Snippet: Paragraph title: Sequence design ... The oligos for the engineered sequences were synthesized by and obtained from Eurofins MWG Operon.

Article Title: Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes - Human TnIc as a Model
Article Snippet: Tr-80 -I is a G4-forming sequence from the noncoding strand fragment of human TnIc promoter localized between −97 and −73 bp to the TSS, while oligo Tr-80 -II is its C-rich complimentary strand. .. Oligos and primers used in plasmid construction were purchased from Eurofins MWG Operon (Ebersberg, Germany) and were subjected to HPLC purification.

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: .. The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Selection:

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: Diploid msh6 pol3–5DV strains were constructed by mating of the two haploids, one being MSH6 , and the other containing the POL3 plasmid pBL304 rescuing the msh6 pol3–5DV genotype, followed by deletion of the second MSH6 allele with a hphNT1 marker [ ] followed by selection for loss of the POL3 plasmid. .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in .

Labeling:

Article Title: Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD
Article Snippet: Primers and probes targeting RHD exons 7 and 10 were set up in a duplex with both probes labeled with FAM, which provided increased sensitivity . .. All oligos were synthesized by Eurofins MWG (Eurofins MWG Operon, Edersberg, Germany) with HPLC purification.

Article Title: Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes - Human TnIc as a Model
Article Snippet: Oligos and primers used in plasmid construction were purchased from Eurofins MWG Operon (Ebersberg, Germany) and were subjected to HPLC purification. .. The sequences and labeling sites of these oligos are listed in .

Polyacrylamide Gel Electrophoresis:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligo hybridization was checked by 20% PAGE followed by fluorescent imaging of the FAM-labeled duplex as well as by SYBR Gold (Thermo) staining of ssDNA. .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Staining:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligo hybridization was checked by 20% PAGE followed by fluorescent imaging of the FAM-labeled duplex as well as by SYBR Gold (Thermo) staining of ssDNA. .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Chromatin Immunoprecipitation:

Article Title: Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat
Article Snippet: Paragraph title: Quantitative Chromatin Immunoprecipitation (qChIP) ... All oligos used, described in , were obtained from Eurofins MWG Operon.

Plasmid Preparation:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: .. The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington). .. The presence of the correct insert within the recombinant pSUPER vector was confirmed by sequencing using the M13 primer GTAAAACGACGGCCAGT.

Article Title: Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans
Article Snippet: Diploid msh6 pol3–5DV strains were constructed by mating of the two haploids, one being MSH6 , and the other containing the POL3 plasmid pBL304 rescuing the msh6 pol3–5DV genotype, followed by deletion of the second MSH6 allele with a hphNT1 marker [ ] followed by selection for loss of the POL3 plasmid. .. Oligos used for transformation were gel purified (Eurofins MWG Operon); the sequences are listed in .

Article Title: Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes - Human TnIc as a Model
Article Snippet: .. Oligos and primers used in plasmid construction were purchased from Eurofins MWG Operon (Ebersberg, Germany) and were subjected to HPLC purification. .. The sequences and labeling sites of these oligos are listed in .

Article Title: Identification of an immune-regulated phagosomal Rab cascade in macrophages
Article Snippet: .. The oligos were synthesized by Eurofins MWG Operon (Munich, Germany) and cloned into the RNAi-Ready pSIREN-DsRed-Express vector according to the recommended protocol, followed by sequence verification. .. Macrophages were transfected with plasmids expressing the shRNAs mentioned above, or scrambled shRNA as control, by using JetPEI-Macrophage.

Software:

Article Title: PDGFRα+ stromal adipocyte progenitors transition into epithelial cells during lobulo-alveologenesis in the murine mammary gland
Article Snippet: Droplets were cycled in a Bio-Rad C1000 at 95 °C for 10 min; 50× (94 °C −30 s, 61 °C − 60 s); 98 °C for 10 min, then 4 °C until analysis on the QX200 droplet reader using the QuantaSoft v1.4.0 software provided by Bio-Rad. .. All oligos were from Eurofins Genomics and all probes were from Integrated DNA Technologies.

DNA Hybridization:

Article Title: Scalable Low-Cost Fabrication of Disposable Paper Sensors for DNA Detection
Article Snippet: For the DNA hybridization, the ssDNA containing amine functionalities in one end and Cy3 fluorophore on another end was used as the primary ligand, and the complementary DNA containing Cy5 fluorophore was used to detect the DNA hybridization. .. The oligos were purchased from Eurofins.

DNA Binding Assay:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University). .. For histone and DNA binding, proteins were characterized as either MBP- or GST-fusions.

Negative Control:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

FP Assay:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University). .. Proteins were titrated with 10 nM FAM-ligand in FP assay buffer (25 mM HEPES pH 7.5, 100 mM NaCl, 0.05% NP-40).

Agarose Gel Electrophoresis:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

Oligonucleotide Synthesis:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University). .. For histone and DNA binding, proteins were characterized as either MBP- or GST-fusions.

BAC Assay:

Article Title: Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene
Article Snippet: Below the genomic map is a representation of the IL1RAPL1 primary transcript followed by the relative position of BAC clones. ( b ) Inverted ethidium bromide-stained agarose gel image showing RT-PCR results with primers spanning SNPs A, B, C and D. Each gel shows RT-PCR results for a negative control water sample, cDNA prepared with reverse transcriptase (+RT) and without reverse transcriptase (− RT) for parental RPE1 and SETDB1 mutant S40. ( c ) DNA sequence traces for SNPs A, B, C and D in RPE1 genomic DNA, genomic DNA isolated from a somatic cell hybrid in which the RPE1 Xa is the only human chromosome present, and cDNA samples from RPE1 and SETDB1 mutant S40. .. All oligos were obtained from Eurofins Genomics LLC.

High Throughput Screening Assay:

Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance
Article Snippet: For histone binding analysis, H3(1–20) peptides functionalized with N- or C-terminal 5-carboxyfluorescein (FAM) were synthesized by the High Throughput Peptide Synthesis and Array (HTPSA) Core Facility at UNC Chapel Hill. .. Oligos containing 5mC were synthesized by Eurofins Genomics, and those containing 5hmC were synthesized by the Keck Oligonucleotide Synthesis Facility (Yale University).

Recombinant:

Article Title: The co-chaperone and reductase ERdj5 facilitates rod opsin biogenesis and quality control
Article Snippet: The oligos were ordered from MWG Eurofins (Abingdon, UK) and were cloned to pSUPER vector (OligoEngine, Washington). .. The presence of the correct insert within the recombinant pSUPER vector was confirmed by sequencing using the M13 primer GTAAAACGACGGCCAGT.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 79
    Eurofins bp oligo
    Ligation of solution phase DNA to a bead-immobilized vector. ( A ) A fluorescence-based assay for determining extent of ligation. Beads with immobilized vector are incubated with a Alexa 488 fluorescent <t>oligo.</t> The extent of ligation is measured via flow cytometry. Bead loading was at 1 ng vector DNA <t>(pHISZ)/ug</t> bead vector. Positive: Beads in which pHISZ vector is fully fluorescently labeled. Ligation: Beads after ligation. Negative: Beads in which pHISZ vector is not fluorescently labeled. The extent of ligation f is measured as a percentage of the Positive signal. ( B ) Extent of ligation is reduced at high bead loadings.
    Bp Oligo, supplied by Eurofins, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bp oligo/product/Eurofins
    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bp oligo - by Bioz Stars, 2020-02
    79/100 stars
      Buy from Supplier

    77
    Eurofins single stranded dna oligomers
    FRET Measurements for <t>LSP,</t> HSP and NS <t>DNA.</t> Representative fluorescence emission spectra of 3.4 nM FAM/TAMRA labeled DNA with TFAM or TFAM 1-179 titrated as indicated, ( A ) LSP DNA with TFAM (0–23.8 nM), ( B ) HSP1 DNA with TFAM (0–40.8 nM), ( C ) NS DNA with TFAM (0–40.8 nM), ( D ) LSP DNA with TFAM 1-179 (0–40.8 nM), ( E ) HSP1 DNA with TFAM 1-179 (0–40.8 nM), ( F ) NS DNA with TFAM 1-179 (0–40.8 nM).
    Single Stranded Dna Oligomers, supplied by Eurofins, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/single stranded dna oligomers/product/Eurofins
    Average 77 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    single stranded dna oligomers - by Bioz Stars, 2020-02
    77/100 stars
      Buy from Supplier

    93
    Eurofins dna oligonucleotides
    Detection of AAV2-specific small RNAs by Northern blot analysis. (A) Northern blot analysis of DNase treated total RNA extracts from HeLa cells, either none infected (Mock), or infected with AAV2, AAV2 and Ad2, AAV2 and HSV1, Ad2, or HSV1, harvested at the indicated time points. Total RNA extracts separated on 15% PAA-Urea gels, transferred to a positively charged membrane were hybridized with radiolabeled <t>DNA</t> probes directed against the depicted AAV2 small RNA sR-108, the human miRNA hsa-let-7a, or the cellular U6-snRNA, respectively. To the right detected small RNAs are indicated. (B) Experimental procedure as in (A) but RNAs were detected by a radiolabeled <t>DNA/LNA</t> probe directed against the AAV2 small RNA sR-108. (C) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA probe directed against the AAV2 small RNA sR-271. (D) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA/LNA probe targeting the AAV2 small RNA sR-1862. To the left, the molecular sizes of the bands of the miRNA ladder and the ssRNA ladder, respectively, are depicted.
    Dna Oligonucleotides, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna oligonucleotides/product/Eurofins
    Average 93 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    dna oligonucleotides - by Bioz Stars, 2020-02
    93/100 stars
      Buy from Supplier

    82
    Eurofins cy3 labeled oligonucleotides
    Visualization of Horse DNA nanostructure entry and lysosomal compartment localization in HL-60/ADR cells to induce cell death. (A) <t>Cy3-labeled</t> Horse DNA nanostructures (561 nm excitation) and Lysotracker Green fluorescent molecules (488 nm excitation)
    Cy3 Labeled Oligonucleotides, supplied by Eurofins, used in various techniques. Bioz Stars score: 82/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cy3 labeled oligonucleotides/product/Eurofins
    Average 82 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    cy3 labeled oligonucleotides - by Bioz Stars, 2020-02
    82/100 stars
      Buy from Supplier

    Image Search Results


    Ligation of solution phase DNA to a bead-immobilized vector. ( A ) A fluorescence-based assay for determining extent of ligation. Beads with immobilized vector are incubated with a Alexa 488 fluorescent oligo. The extent of ligation is measured via flow cytometry. Bead loading was at 1 ng vector DNA (pHISZ)/ug bead vector. Positive: Beads in which pHISZ vector is fully fluorescently labeled. Ligation: Beads after ligation. Negative: Beads in which pHISZ vector is not fluorescently labeled. The extent of ligation f is measured as a percentage of the Positive signal. ( B ) Extent of ligation is reduced at high bead loadings.

    Journal: PLoS ONE

    Article Title: Automated Solid-Phase Subcloning Based on Beads Brought into Proximity by Magnetic Force

    doi: 10.1371/journal.pone.0037429

    Figure Lengend Snippet: Ligation of solution phase DNA to a bead-immobilized vector. ( A ) A fluorescence-based assay for determining extent of ligation. Beads with immobilized vector are incubated with a Alexa 488 fluorescent oligo. The extent of ligation is measured via flow cytometry. Bead loading was at 1 ng vector DNA (pHISZ)/ug bead vector. Positive: Beads in which pHISZ vector is fully fluorescently labeled. Ligation: Beads after ligation. Negative: Beads in which pHISZ vector is not fluorescently labeled. The extent of ligation f is measured as a percentage of the Positive signal. ( B ) Extent of ligation is reduced at high bead loadings.

    Article Snippet: Solution-to-bead ligation of the fluorescent capping oligo to M270-pHISZ was performed similarly but used 10 pmol of an 18 bp oligo containing a BamHI site and a 5′-AlexaFluor 488 (Eurofins MWG Operon, Ebersberg, Germany).

    Techniques: Ligation, Plasmid Preparation, Fluorescence, Incubation, Flow Cytometry, Cytometry, Labeling

    FRET Measurements for LSP, HSP and NS DNA. Representative fluorescence emission spectra of 3.4 nM FAM/TAMRA labeled DNA with TFAM or TFAM 1-179 titrated as indicated, ( A ) LSP DNA with TFAM (0–23.8 nM), ( B ) HSP1 DNA with TFAM (0–40.8 nM), ( C ) NS DNA with TFAM (0–40.8 nM), ( D ) LSP DNA with TFAM 1-179 (0–40.8 nM), ( E ) HSP1 DNA with TFAM 1-179 (0–40.8 nM), ( F ) NS DNA with TFAM 1-179 (0–40.8 nM).

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: FRET Measurements for LSP, HSP and NS DNA. Representative fluorescence emission spectra of 3.4 nM FAM/TAMRA labeled DNA with TFAM or TFAM 1-179 titrated as indicated, ( A ) LSP DNA with TFAM (0–23.8 nM), ( B ) HSP1 DNA with TFAM (0–40.8 nM), ( C ) NS DNA with TFAM (0–40.8 nM), ( D ) LSP DNA with TFAM 1-179 (0–40.8 nM), ( E ) HSP1 DNA with TFAM 1-179 (0–40.8 nM), ( F ) NS DNA with TFAM 1-179 (0–40.8 nM).

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques: Fluorescence, Labeling

    CD analysis. ( A ) CD scans in units of molar protein ellipticity of 10 µM TFAM and ( B ) TFAM 1-179 in the absence (red) and presence of equimolar concentrations of 25 bp LSP (black), HSP1 (cyan), and NS (magenta) DNA sequences. Spectra represent an average of three independent experiments. The experiental variation at 222 nm was

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: CD analysis. ( A ) CD scans in units of molar protein ellipticity of 10 µM TFAM and ( B ) TFAM 1-179 in the absence (red) and presence of equimolar concentrations of 25 bp LSP (black), HSP1 (cyan), and NS (magenta) DNA sequences. Spectra represent an average of three independent experiments. The experiental variation at 222 nm was

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques:

    DNA binding and bending of TFAM and TFAM 1-179. Binding curves of FRET effect for 3.4 nM FAM/TAMRA labeled DNA titrated with ( A ) TFAM, and ( B ) TFAM 1-179. Binding isotherms were fitted to a cooperative binding model. The change in end-to-end distance for FAM/TAMRA labeled DNA titrated with ( C ) TFAM and ( D ) TFAM 1-179. End-to-end distances were calculated using Equation 4 in the Supplementary Data . The change in end-to-end distance is relative to the distance between the FAM and TAMRA in the absence of protein. The data are an average of three independent experiments, except for five for TFAM with NS and six for TFAM with LSP, with error bars showing the standard deviation.

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: DNA binding and bending of TFAM and TFAM 1-179. Binding curves of FRET effect for 3.4 nM FAM/TAMRA labeled DNA titrated with ( A ) TFAM, and ( B ) TFAM 1-179. Binding isotherms were fitted to a cooperative binding model. The change in end-to-end distance for FAM/TAMRA labeled DNA titrated with ( C ) TFAM and ( D ) TFAM 1-179. End-to-end distances were calculated using Equation 4 in the Supplementary Data . The change in end-to-end distance is relative to the distance between the FAM and TAMRA in the absence of protein. The data are an average of three independent experiments, except for five for TFAM with NS and six for TFAM with LSP, with error bars showing the standard deviation.

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques: Binding Assay, Labeling, Standard Deviation

    DNA bending models. The estimated impact of TFAM-induced DNA bending visualized for the end-to-end distances for TFAM and TFAM 1-179 binding to LSP, HSP1 and NS DNA. Limiting FRET effect values were used for the estimation of bend angles. The calculated end-to-end distance for the LSP 25 bp DNA fragment is 82 Å. Assuming that TFAM induces a DNA kink, the bend angles corresponding to the end-to-end distances of 70 and 60 Å are shown. TFAM induces a greater bend in the DNA than TFAM 1-179. HMG-box proteins more typically create smooth bends in the DNA, and as illustrated, the apparent overall bend can be greater than the bend angles calculated from the kink-only model.

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: DNA bending models. The estimated impact of TFAM-induced DNA bending visualized for the end-to-end distances for TFAM and TFAM 1-179 binding to LSP, HSP1 and NS DNA. Limiting FRET effect values were used for the estimation of bend angles. The calculated end-to-end distance for the LSP 25 bp DNA fragment is 82 Å. Assuming that TFAM induces a DNA kink, the bend angles corresponding to the end-to-end distances of 70 and 60 Å are shown. TFAM induces a greater bend in the DNA than TFAM 1-179. HMG-box proteins more typically create smooth bends in the DNA, and as illustrated, the apparent overall bend can be greater than the bend angles calculated from the kink-only model.

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques: Binding Assay

    Thermodynamic analysis of TFAM binding to DNA. ITC analyses of TFAM binding to ( A ) LSP DNA, ( B ) HSP DNA and ( C ) NS DNA. The top panels show the raw heats absorbed from injecting a 10 µl aliquot of 40 µM DNA into a 10 µM solution of TFAM. The bottom panels show the integrated absorbed heats with respect to time with the heat of mixing subtracted. Molar ratio is DNA:TFAM.

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: Thermodynamic analysis of TFAM binding to DNA. ITC analyses of TFAM binding to ( A ) LSP DNA, ( B ) HSP DNA and ( C ) NS DNA. The top panels show the raw heats absorbed from injecting a 10 µl aliquot of 40 µM DNA into a 10 µM solution of TFAM. The bottom panels show the integrated absorbed heats with respect to time with the heat of mixing subtracted. Molar ratio is DNA:TFAM.

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques: Binding Assay

    Sequence of TFAM and promoter DNA sequences. ( A ) Schematic diagram of TFAM. Numbers below the diagram delineate the residues that form HMG box A (1–79), the linker region (80–110), HMG box B (111–179) and the C-terminal tail (180–204). ( B ) Sequences of the HSP1 and LSP promoter DNA, as well as a protein-coding region of the mitochondrial genome (NS DNA). The 25 bp regions of the promoters that were used here and where TFAM binds (−40 through −16 upstream of the start site) are depicted in bold italics. The NT and TS indicate the non-template, and template strand, respectively. The arrows indicate the POLRMT start site and direction of transcription. For FRET experiments, LSP, HSP1 or NS DNA was 3′-labeled with TAMRA as the acceptor for the template strand, and 3′-labeled with FAM as the donor for the non-template strand.

    Journal: Nucleic Acids Research

    Article Title: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

    doi: 10.1093/nar/gkr787

    Figure Lengend Snippet: Sequence of TFAM and promoter DNA sequences. ( A ) Schematic diagram of TFAM. Numbers below the diagram delineate the residues that form HMG box A (1–79), the linker region (80–110), HMG box B (111–179) and the C-terminal tail (180–204). ( B ) Sequences of the HSP1 and LSP promoter DNA, as well as a protein-coding region of the mitochondrial genome (NS DNA). The 25 bp regions of the promoters that were used here and where TFAM binds (−40 through −16 upstream of the start site) are depicted in bold italics. The NT and TS indicate the non-template, and template strand, respectively. The arrows indicate the POLRMT start site and direction of transcription. For FRET experiments, LSP, HSP1 or NS DNA was 3′-labeled with TAMRA as the acceptor for the template strand, and 3′-labeled with FAM as the donor for the non-template strand.

    Article Snippet: Forward and reverse single-stranded DNA oligomers of 25 nt corresponding to the LSP DNaseI LSP footprint of TFAM , HSP1 TFAM binding region ( , ) and NS protein coding region of the mitochondrial genome were purchased from Eurofins MWG Operon and purified on C18 Sep-Pak cartridges (Waters).

    Techniques: Sequencing, Labeling

    Detection of AAV2-specific small RNAs by Northern blot analysis. (A) Northern blot analysis of DNase treated total RNA extracts from HeLa cells, either none infected (Mock), or infected with AAV2, AAV2 and Ad2, AAV2 and HSV1, Ad2, or HSV1, harvested at the indicated time points. Total RNA extracts separated on 15% PAA-Urea gels, transferred to a positively charged membrane were hybridized with radiolabeled DNA probes directed against the depicted AAV2 small RNA sR-108, the human miRNA hsa-let-7a, or the cellular U6-snRNA, respectively. To the right detected small RNAs are indicated. (B) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA/LNA probe directed against the AAV2 small RNA sR-108. (C) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA probe directed against the AAV2 small RNA sR-271. (D) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA/LNA probe targeting the AAV2 small RNA sR-1862. To the left, the molecular sizes of the bands of the miRNA ladder and the ssRNA ladder, respectively, are depicted.

    Journal: PLoS ONE

    Article Title: Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation

    doi: 10.1371/journal.pone.0161454

    Figure Lengend Snippet: Detection of AAV2-specific small RNAs by Northern blot analysis. (A) Northern blot analysis of DNase treated total RNA extracts from HeLa cells, either none infected (Mock), or infected with AAV2, AAV2 and Ad2, AAV2 and HSV1, Ad2, or HSV1, harvested at the indicated time points. Total RNA extracts separated on 15% PAA-Urea gels, transferred to a positively charged membrane were hybridized with radiolabeled DNA probes directed against the depicted AAV2 small RNA sR-108, the human miRNA hsa-let-7a, or the cellular U6-snRNA, respectively. To the right detected small RNAs are indicated. (B) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA/LNA probe directed against the AAV2 small RNA sR-108. (C) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA probe directed against the AAV2 small RNA sR-271. (D) Experimental procedure as in (A) but RNAs were detected by a radiolabeled DNA/LNA probe targeting the AAV2 small RNA sR-1862. To the left, the molecular sizes of the bands of the miRNA ladder and the ssRNA ladder, respectively, are depicted.

    Article Snippet: DNA-oligonucleotides (MWG Eurofins) or DNA/LNA-oligonucleotides (Exiqon) [ ] with sequences complementary to sRNAs (see ) were 5’ end labeled with [γ-32 P]-ATP (Hartmann Analytic), and purified on a Bio-Gel P-10 column (Bio-Rad).

    Techniques: Northern Blot, Infection

    Visualization of Horse DNA nanostructure entry and lysosomal compartment localization in HL-60/ADR cells to induce cell death. (A) Cy3-labeled Horse DNA nanostructures (561 nm excitation) and Lysotracker Green fluorescent molecules (488 nm excitation)

    Journal: Small (Weinheim an der Bergstrasse, Germany)

    Article Title: Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug Resistance Mechanisms in a Leukemia Model

    doi: 10.1002/smll.201502118

    Figure Lengend Snippet: Visualization of Horse DNA nanostructure entry and lysosomal compartment localization in HL-60/ADR cells to induce cell death. (A) Cy3-labeled Horse DNA nanostructures (561 nm excitation) and Lysotracker Green fluorescent molecules (488 nm excitation)

    Article Snippet: In addition, Horse nanostructures were labeled with either YOYO-1 intercalating dye (Life Technologies), or Cy3-labeled oligonucleotides (Eurofins Genomics) for fluorescence imaging experiments.

    Techniques: Labeling