Structured Review

Eurofins oligos
Reaction principle of db DNA-based rational HCR. ( a ) Schematic illustration of synthesis and inter-reaction of db DNA units. Two starting <t>oligonucleotides</t> (U1–1/U1–2 or U2–1/U2–2) possess the same sticky ends at 3′ and 5′ ends, as well as complementary midsequence segments, as indicated. For the process starting from U1 (left), the db DNA units (U1 or U2) hybridize (step 1). Similarly, the DNA synthesis process can also begin from U2 (right). The formed db DNA units (U2) can be combined to U1 during the rational HCR process (step 2), due to their exposed complementary sticky ends. Thus, by addition of U2 and U1 successively and repeatedly, these two units can bind to each other leading to an exponential growth of a packed complex 3D DNA structure (step n); ( b ) Evaluation of the product of db DNA-based rational HCR using gel electrophoresis. L lane was 100 bp ladder, lane 1 and 2 were U1 and U2, Lanes 3 and 4 were the hybridized products of U1 and U2 with stoichiometry ratio at 5:1 (and 1:5, respectively), and Lanes 5 and 6 were the product of stoichiometry ratio at 20:1 (and 1:20, respectively), the unit with a low concentration was kept at 0.1 μM. Bands from 90 to 225 bp (from lane 3 to 6) illustrate the expected products ratios, which are different to those from the smallest units (lane 1/2). For this concentration of single units, larger products are not formed efficiently (evidence of limited formation is shown by smears in the large sizes), since the single units become depleted as the reaction progresses.
Oligos, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 93 stars, based on 10 article reviews
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oligos - by Bioz Stars, 2020-09
93/100 stars

Images

1) Product Images from "Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis"

Article Title: Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis

Journal: ACS Nano

doi: 10.1021/acsnano.8b03183

Reaction principle of db DNA-based rational HCR. ( a ) Schematic illustration of synthesis and inter-reaction of db DNA units. Two starting oligonucleotides (U1–1/U1–2 or U2–1/U2–2) possess the same sticky ends at 3′ and 5′ ends, as well as complementary midsequence segments, as indicated. For the process starting from U1 (left), the db DNA units (U1 or U2) hybridize (step 1). Similarly, the DNA synthesis process can also begin from U2 (right). The formed db DNA units (U2) can be combined to U1 during the rational HCR process (step 2), due to their exposed complementary sticky ends. Thus, by addition of U2 and U1 successively and repeatedly, these two units can bind to each other leading to an exponential growth of a packed complex 3D DNA structure (step n); ( b ) Evaluation of the product of db DNA-based rational HCR using gel electrophoresis. L lane was 100 bp ladder, lane 1 and 2 were U1 and U2, Lanes 3 and 4 were the hybridized products of U1 and U2 with stoichiometry ratio at 5:1 (and 1:5, respectively), and Lanes 5 and 6 were the product of stoichiometry ratio at 20:1 (and 1:20, respectively), the unit with a low concentration was kept at 0.1 μM. Bands from 90 to 225 bp (from lane 3 to 6) illustrate the expected products ratios, which are different to those from the smallest units (lane 1/2). For this concentration of single units, larger products are not formed efficiently (evidence of limited formation is shown by smears in the large sizes), since the single units become depleted as the reaction progresses.
Figure Legend Snippet: Reaction principle of db DNA-based rational HCR. ( a ) Schematic illustration of synthesis and inter-reaction of db DNA units. Two starting oligonucleotides (U1–1/U1–2 or U2–1/U2–2) possess the same sticky ends at 3′ and 5′ ends, as well as complementary midsequence segments, as indicated. For the process starting from U1 (left), the db DNA units (U1 or U2) hybridize (step 1). Similarly, the DNA synthesis process can also begin from U2 (right). The formed db DNA units (U2) can be combined to U1 during the rational HCR process (step 2), due to their exposed complementary sticky ends. Thus, by addition of U2 and U1 successively and repeatedly, these two units can bind to each other leading to an exponential growth of a packed complex 3D DNA structure (step n); ( b ) Evaluation of the product of db DNA-based rational HCR using gel electrophoresis. L lane was 100 bp ladder, lane 1 and 2 were U1 and U2, Lanes 3 and 4 were the hybridized products of U1 and U2 with stoichiometry ratio at 5:1 (and 1:5, respectively), and Lanes 5 and 6 were the product of stoichiometry ratio at 20:1 (and 1:20, respectively), the unit with a low concentration was kept at 0.1 μM. Bands from 90 to 225 bp (from lane 3 to 6) illustrate the expected products ratios, which are different to those from the smallest units (lane 1/2). For this concentration of single units, larger products are not formed efficiently (evidence of limited formation is shown by smears in the large sizes), since the single units become depleted as the reaction progresses.

Techniques Used: DNA Synthesis, Nucleic Acid Electrophoresis, Concentration Assay

2) Product Images from "Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation"

Article Title: Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkt312

RecFACS to create producers with genetic diversity at codon 81 of murE in the genome of C. glutamicum wild-type. A mixture of oligonucleotides murE1 to murE20 was used for ssDNA recombineering, and recombinants with productive mutations were selected via FACS. Thirteen of the 20 possible recombinants were obtained (table), exhibiting l -lysine formation to different degrees (black bar).
Figure Legend Snippet: RecFACS to create producers with genetic diversity at codon 81 of murE in the genome of C. glutamicum wild-type. A mixture of oligonucleotides murE1 to murE20 was used for ssDNA recombineering, and recombinants with productive mutations were selected via FACS. Thirteen of the 20 possible recombinants were obtained (table), exhibiting l -lysine formation to different degrees (black bar).

Techniques Used: FACS

Related Articles

High Performance Liquid Chromatography:

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. ..

Clone Assay:

Article Title: Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation
Article Snippet: .. Primers used for cloning and oligos used for recombineering were purchased from Eurofins MWG Operon (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.

Positive Control:

Article Title: Chloroquine efficacy studies confirm drug susceptibility of Plasmodium vivax in Chennai, India
Article Snippet: .. Forward (5′-3′) oligonucleotides were labeled with the phosphoramidite conjugate 6-FAM (Eurofins MWG Operon, Huntsville, AL) and the P. vivax laboratory strain Salvador I was used as a positive control. .. PCR amplicons were analyzed on an ABI 3730xl sequencer using GeneScan-500 LIZ size standard (Applied Biosystems, Foster City, CA) for size determination.

Synthesized:

Article Title: Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis
Article Snippet: .. The oligos were commercially synthesized, PAGE purified (Eurofins, UK), and dissolved in TE buffer (10 mM Tris, 1 mM ethylenediaminetetraacetic acid (EDTA), pH = 8.0) to a final concentration of 100 μM. .. Two db DNA units were constructed by mixing two specific oligonucleotide components (1:1 molar ratio) in 2× SSC buffer with a final concentration of 2 μM for each oligonucleotide.

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: 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.

Labeling:

Article Title: Chloroquine efficacy studies confirm drug susceptibility of Plasmodium vivax in Chennai, India
Article Snippet: .. Forward (5′-3′) oligonucleotides were labeled with the phosphoramidite conjugate 6-FAM (Eurofins MWG Operon, Huntsville, AL) and the P. vivax laboratory strain Salvador I was used as a positive control. .. PCR amplicons were analyzed on an ABI 3730xl sequencer using GeneScan-500 LIZ size standard (Applied Biosystems, Foster City, CA) for size determination.

Purification:

Article Title: Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis
Article Snippet: .. The oligos were commercially synthesized, PAGE purified (Eurofins, UK), and dissolved in TE buffer (10 mM Tris, 1 mM ethylenediaminetetraacetic acid (EDTA), pH = 8.0) to a final concentration of 100 μM. .. Two db DNA units were constructed by mixing two specific oligonucleotide components (1:1 molar ratio) in 2× SSC buffer with a final concentration of 2 μM for each oligonucleotide.

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. ..

Concentration Assay:

Article Title: Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis
Article Snippet: .. The oligos were commercially synthesized, PAGE purified (Eurofins, UK), and dissolved in TE buffer (10 mM Tris, 1 mM ethylenediaminetetraacetic acid (EDTA), pH = 8.0) to a final concentration of 100 μM. .. Two db DNA units were constructed by mixing two specific oligonucleotide components (1:1 molar ratio) in 2× SSC buffer with a final concentration of 2 μM for each oligonucleotide.

Polyacrylamide Gel Electrophoresis:

Article Title: Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis
Article Snippet: .. The oligos were commercially synthesized, PAGE purified (Eurofins, UK), and dissolved in TE buffer (10 mM Tris, 1 mM ethylenediaminetetraacetic acid (EDTA), pH = 8.0) to a final concentration of 100 μM. .. Two db DNA units were constructed by mixing two specific oligonucleotide components (1:1 molar ratio) in 2× SSC buffer with a final concentration of 2 μM for each oligonucleotide.

Sequencing:

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.

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.

Plasmid Preparation:

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.

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  • 93
    Eurofins pde8a intron 9 specific primers
    Editing sites in the <t>intron</t> 9 of <t>PDE8A</t> pre-mRNA from human brain. Putative PDE8A intron 9 mRNA secondary structure as predicted by Vienna RNA Websuite. The mRNA positions where significant editing events have been detected are highlighted with arrows. Editing Sites A to G have been previously described in T cells 32 . Newly identified sites in the brain are highlighted in red. Most of the editing sites are in close proximity to each other. All bases are annotated on chromosome 15 according to the last GRCh38 genebuild
    Pde8a Intron 9 Specific Primers, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pde8a intron 9 specific primers/product/Eurofins
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    88
    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: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bp oligo/product/Eurofins
    Average 88 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
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    88
    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: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/single stranded dna oligomers/product/Eurofins
    Average 88 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
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    84
    Eurofins 5 cy3b cy5 functionalized oligonucleotides oligonucleotides
    MinDE spatially sorts cargo according to effective size. a , Schematic of the experimental setup. MinDE self-organization was performed in presence of two different cargo species with distinct fluorescent labels, cargo-2 with <t>Cy3B</t> and cargo-42 with <t>Cy5</t> (1 μM MinD (30% EGFP-MinD), 1.5 μM MinE-His, 50 pM origami-Cy3b with 2, and 50 pM origami-Cy5 with 42 biotinylated oligonucleotides, non-labeled streptavidin). b , Representative images of individual and overlayed channels, and c line plot of indicated selection of MinDE-induced sorting of cargo species. Scale bars: 50 μm. Experiment was performed three times under identical conditions. d , Spatial distribution of two cargo species in response to the (imposed) MinD profile, corresponding to the cross-correlation functions in b. The Maxwell-Stefan type model allows for stronger reorganization of cargo molecules than the Flory-Huggins type model. In particular, the Maxwell-Stefan type model predicts that cargo-2 accumulates between cargo-42 and MinD. Model parameters: average coverage of MinD proteins , streptavidin , cargo-2 and cargo-42 ; interaction parameter (in terms of MinD coverage) of cargo-2 and cargo-42 . Surface coverages θ = a c and surface densities c are connected by the particle size a .
    5 Cy3b Cy5 Functionalized Oligonucleotides Oligonucleotides, supplied by Eurofins, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/5 cy3b cy5 functionalized oligonucleotides oligonucleotides/product/Eurofins
    Average 84 stars, based on 1 article reviews
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    Editing sites in the intron 9 of PDE8A pre-mRNA from human brain. Putative PDE8A intron 9 mRNA secondary structure as predicted by Vienna RNA Websuite. The mRNA positions where significant editing events have been detected are highlighted with arrows. Editing Sites A to G have been previously described in T cells 32 . Newly identified sites in the brain are highlighted in red. Most of the editing sites are in close proximity to each other. All bases are annotated on chromosome 15 according to the last GRCh38 genebuild

    Journal: Translational Psychiatry

    Article Title: Brain region-specific alterations of RNA editing in PDE8A mRNA in suicide decedents

    doi: 10.1038/s41398-018-0331-3

    Figure Lengend Snippet: Editing sites in the intron 9 of PDE8A pre-mRNA from human brain. Putative PDE8A intron 9 mRNA secondary structure as predicted by Vienna RNA Websuite. The mRNA positions where significant editing events have been detected are highlighted with arrows. Editing Sites A to G have been previously described in T cells 32 . Newly identified sites in the brain are highlighted in red. Most of the editing sites are in close proximity to each other. All bases are annotated on chromosome 15 according to the last GRCh38 genebuild

    Article Snippet: The set of fluorescent, PDE8A intron 9-specific primers was as follows: forward 5′P-FAM-CTAGGGAACCCTGTTTAGTCC-3′OH (Eurofins MWG operons) and reverse 5′P- VIC-CAATGGGCACCAAAAAAGGG-3′OH (Applied Biosystems).

    Techniques:

    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

    MinDE spatially sorts cargo according to effective size. a , Schematic of the experimental setup. MinDE self-organization was performed in presence of two different cargo species with distinct fluorescent labels, cargo-2 with Cy3B and cargo-42 with Cy5 (1 μM MinD (30% EGFP-MinD), 1.5 μM MinE-His, 50 pM origami-Cy3b with 2, and 50 pM origami-Cy5 with 42 biotinylated oligonucleotides, non-labeled streptavidin). b , Representative images of individual and overlayed channels, and c line plot of indicated selection of MinDE-induced sorting of cargo species. Scale bars: 50 μm. Experiment was performed three times under identical conditions. d , Spatial distribution of two cargo species in response to the (imposed) MinD profile, corresponding to the cross-correlation functions in b. The Maxwell-Stefan type model allows for stronger reorganization of cargo molecules than the Flory-Huggins type model. In particular, the Maxwell-Stefan type model predicts that cargo-2 accumulates between cargo-42 and MinD. Model parameters: average coverage of MinD proteins , streptavidin , cargo-2 and cargo-42 ; interaction parameter (in terms of MinD coverage) of cargo-2 and cargo-42 . Surface coverages θ = a c and surface densities c are connected by the particle size a .

    Journal: bioRxiv

    Article Title: ATP driven diffusiophoresis: active cargo transport without motor proteins

    doi: 10.1101/2020.05.01.072744

    Figure Lengend Snippet: MinDE spatially sorts cargo according to effective size. a , Schematic of the experimental setup. MinDE self-organization was performed in presence of two different cargo species with distinct fluorescent labels, cargo-2 with Cy3B and cargo-42 with Cy5 (1 μM MinD (30% EGFP-MinD), 1.5 μM MinE-His, 50 pM origami-Cy3b with 2, and 50 pM origami-Cy5 with 42 biotinylated oligonucleotides, non-labeled streptavidin). b , Representative images of individual and overlayed channels, and c line plot of indicated selection of MinDE-induced sorting of cargo species. Scale bars: 50 μm. Experiment was performed three times under identical conditions. d , Spatial distribution of two cargo species in response to the (imposed) MinD profile, corresponding to the cross-correlation functions in b. The Maxwell-Stefan type model allows for stronger reorganization of cargo molecules than the Flory-Huggins type model. In particular, the Maxwell-Stefan type model predicts that cargo-2 accumulates between cargo-42 and MinD. Model parameters: average coverage of MinD proteins , streptavidin , cargo-2 and cargo-42 ; interaction parameter (in terms of MinD coverage) of cargo-2 and cargo-42 . Surface coverages θ = a c and surface densities c are connected by the particle size a .

    Article Snippet: Staple oligonucleotides, 5’-Cy3B/Cy5-functionalized oligonucleotides oligonucleotides (Both: High purity salt free, Eurofins MWG Operon, Ebersberg, Germany) and 5’-biotin-TEG functionalized (Sigma-Aldrich, St. Louis, USA) were purchased or diluted in Milli-Q ultrapure water at a concentration of 100 μM.

    Techniques: Labeling, Selection