dna oligonucleotides  (Integrated DNA Technologies)


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    Name:
    RNA oligo
    Description:
    Long high quality RNA oligos up 120 bases Single stranded and duplexed RNA sequences are produced using proprietary technology that delivers industry leading RNA quality Specialized synthesis platforms deliver the highest fidelity guides for CRISPR duplexes for RNAi template switching oligos for NGS microRNAs aptamers and custom RNA oligos for other applications
    Catalog Number:
    ro-696512
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    Category:
    Nucleic acids
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    Structured Review

    Integrated DNA Technologies dna oligonucleotides
    The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR <t>RNA</t> at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), <t>DNA</t> cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.
    Long high quality RNA oligos up 120 bases Single stranded and duplexed RNA sequences are produced using proprietary technology that delivers industry leading RNA quality Specialized synthesis platforms deliver the highest fidelity guides for CRISPR duplexes for RNAi template switching oligos for NGS microRNAs aptamers and custom RNA oligos for other applications
    https://www.bioz.com/result/dna oligonucleotides/product/Integrated DNA Technologies
    Average 99 stars, based on 631 article reviews
    Price from $9.99 to $1999.99
    dna oligonucleotides - by Bioz Stars, 2021-01
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    Images

    1) Product Images from "Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence"

    Article Title: Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence

    Journal: bioRxiv

    doi: 10.1101/667758

    The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.
    Figure Legend Snippet: The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.

    Techniques Used: CRISPR, RNA Binding Assay, Purification, Recombinant, Variant Assay

    2) Product Images from "RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia"

    Article Title: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia

    Journal: Nature Communications

    doi: 10.1038/s41467-018-03513-4

    Differential expression of RNA:m 5 C, RCMTs and hnRNPK in 5-AZA-sensitive and 5-AZA-resistant leukaemia cells and the binding of hnRNPK to unmethylated and cytosine-methylated RNA. a Western blot analysis of expression of RCMTs, hnRNPK and other proteins in the 5-AZA-sensitive OCI-M2 and SC leukaemia cells and the 5-AZA-resistant M2AR and SCAR leukaemia cells. b Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from OCI-M2 and M2AR cells. c Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from SC and SCAR cells. d , e Visualization and measurement of the binding of purified recombinant hnRNPK to the unmethylated and cytosine-methylated fluorescein (FAM)-labelled RNA oligos by an antibody-coupled bead assay
    Figure Legend Snippet: Differential expression of RNA:m 5 C, RCMTs and hnRNPK in 5-AZA-sensitive and 5-AZA-resistant leukaemia cells and the binding of hnRNPK to unmethylated and cytosine-methylated RNA. a Western blot analysis of expression of RCMTs, hnRNPK and other proteins in the 5-AZA-sensitive OCI-M2 and SC leukaemia cells and the 5-AZA-resistant M2AR and SCAR leukaemia cells. b Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from OCI-M2 and M2AR cells. c Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from SC and SCAR cells. d , e Visualization and measurement of the binding of purified recombinant hnRNPK to the unmethylated and cytosine-methylated fluorescein (FAM)-labelled RNA oligos by an antibody-coupled bead assay

    Techniques Used: Expressing, Binding Assay, Methylation, Western Blot, Dot Blot, Purification, Recombinant

    3) Product Images from "Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex"

    Article Title: Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex

    Journal: bioRxiv

    doi: 10.1101/666776

    Stalling the translocation of helicase motor stimulates cleavage (A) Schematic representation of target DNA (100 bp) with PAM (TTC in red) end-labelled with 6-FAM at 5’ end of the non-target strand and biotinylated at 12 th nucleotide (Target I). A similar target DNA without biotin (Target II) is also represented. Indicated in red arrow are the prominent cleavage sites. (B) Target (I) (II) were incubated with streptavidin and Cascade/I-C to form interference complex. Cleavage was initiated by addition of Cas3 (0.2 and 0.5 μM) and 1 mM ATP/ADP/AMP-PNP. Prominent cleavages of the target (I) and (II) are indicated by a red arrow (approx. 60 nt and 40 nt). A 20% denaturing PAGE was used to assess the cleavage.
    Figure Legend Snippet: Stalling the translocation of helicase motor stimulates cleavage (A) Schematic representation of target DNA (100 bp) with PAM (TTC in red) end-labelled with 6-FAM at 5’ end of the non-target strand and biotinylated at 12 th nucleotide (Target I). A similar target DNA without biotin (Target II) is also represented. Indicated in red arrow are the prominent cleavage sites. (B) Target (I) (II) were incubated with streptavidin and Cascade/I-C to form interference complex. Cleavage was initiated by addition of Cas3 (0.2 and 0.5 μM) and 1 mM ATP/ADP/AMP-PNP. Prominent cleavages of the target (I) and (II) are indicated by a red arrow (approx. 60 nt and 40 nt). A 20% denaturing PAGE was used to assess the cleavage.

    Techniques Used: Translocation Assay, Incubation, Polyacrylamide Gel Electrophoresis

    Cascade and Cas3 form a stable complex during interference. (A) Schematic representation of 100 bp DNA substrates with biotin (black dot) at 5’ end of the nontarget strand (NTS), 6-FAM (fluorophore, green star) at 5 th nucleotide, Iowa Black ® FQ (quencher, brown dot) at 28 th nucleotide on target strand (TS) and PAM sequence TTC (depicted in red colour). (B) Substrate mentioned above was incubated with or without Cascade/I-C (1 μM) and increasing concentration of Cas3/I-C (0-5 μM). A significant decline in fluorescence intensity is evident when both Cascade/I-C and Cas3/I-C were present. There was no apparent quenching when dsDNA and ssDNA were used in the absence of Cascade/I-C (C) Fluorescence quenching was observed in the presence of ATP but not when ADP and AMP-PNP were used.
    Figure Legend Snippet: Cascade and Cas3 form a stable complex during interference. (A) Schematic representation of 100 bp DNA substrates with biotin (black dot) at 5’ end of the nontarget strand (NTS), 6-FAM (fluorophore, green star) at 5 th nucleotide, Iowa Black ® FQ (quencher, brown dot) at 28 th nucleotide on target strand (TS) and PAM sequence TTC (depicted in red colour). (B) Substrate mentioned above was incubated with or without Cascade/I-C (1 μM) and increasing concentration of Cas3/I-C (0-5 μM). A significant decline in fluorescence intensity is evident when both Cascade/I-C and Cas3/I-C were present. There was no apparent quenching when dsDNA and ssDNA were used in the absence of Cascade/I-C (C) Fluorescence quenching was observed in the presence of ATP but not when ADP and AMP-PNP were used.

    Techniques Used: Sequencing, Incubation, Concentration Assay, Fluorescence

    Roadblock in the translocation of Cas3/I-C stimulates cleavage (A) (D) A schematic representation of 60 nt 5’ 6-FAM labelled ssDNA with biotin at 12 th (Target A) and 20th nucleotide (Target B), respectively. (B) (E) ssDNA mentioned above was incubated with 200 nM of Cas3/I-C for several time points and anisotropy measurements were recorded. With time, the decrease in anisotropy values was observed for ssDNA with a biotin roadblock. (C) (F) ssDNA was pre-incubated with streptavidin before the addition of Cas3/I-C. Prominent DNA cleavage products were observed in the presence of ATP at ~40 nt in target A and ~50 nt in target B, indicated with a red arrow. In the presence of AMP-PNP higher Cas3 concentration was required for the cleavage. A 20% denaturing PAGE was used to study the cleavage pattern.
    Figure Legend Snippet: Roadblock in the translocation of Cas3/I-C stimulates cleavage (A) (D) A schematic representation of 60 nt 5’ 6-FAM labelled ssDNA with biotin at 12 th (Target A) and 20th nucleotide (Target B), respectively. (B) (E) ssDNA mentioned above was incubated with 200 nM of Cas3/I-C for several time points and anisotropy measurements were recorded. With time, the decrease in anisotropy values was observed for ssDNA with a biotin roadblock. (C) (F) ssDNA was pre-incubated with streptavidin before the addition of Cas3/I-C. Prominent DNA cleavage products were observed in the presence of ATP at ~40 nt in target A and ~50 nt in target B, indicated with a red arrow. In the presence of AMP-PNP higher Cas3 concentration was required for the cleavage. A 20% denaturing PAGE was used to study the cleavage pattern.

    Techniques Used: Translocation Assay, Incubation, Concentration Assay, Polyacrylamide Gel Electrophoresis

    4) Product Images from "Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence"

    Article Title: Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence

    Journal: bioRxiv

    doi: 10.1101/667758

    The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.
    Figure Legend Snippet: The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.

    Techniques Used: CRISPR, RNA Binding Assay, Purification, Recombinant, Variant Assay

    The Cas6 ribonuclease cleaves the Mtb CRISPR repeat sequence to generate crRNA. ( A ) Cas6 (0.5 µM) was incubated with 50 nM 5’-FAM CRISPR repeat RNA at 37 °C for 5, 15, 45 min in 20 mM Tris, 100 mM potassium glutamate, pH 7.5 in the absence or presence of 5 mM divalent metal ions as indicated. Reactions were stopped by phenol-chloroform extraction. ( B ) Cas6 cleavage leaves a 3’-(cyclic) phosphate group. CRISPR repeat RNA (crRepeat, 5’-FAM labeled, 400 nM) was digested with 2 µM Cas6 for 1 h in the presence of Mg 2+ using the same reaction conditions as before. Phenol-chloroform followed by chloroform extraction provided the substrate for the E. coli Poly(A) polymerase (PAP, New England Biolabs) reaction. Polyadenylation was performed according to the manufacturer’s instructions. In a parallel experiment, Cas6 was omitted. The CRISPR repeat RNA but not the Cas6 product can be 3’-polyadenylated by PAP. This suggests that the reaction product has a cyclic 2’,3’-phosphate, as observed for other Cas6 enzymes. This observation, together with the observation that calcium supports enhanced cleavage of the CRISPR repeat, suggests that the metal ion does not participate directly in catalysis but rather plays a role in stabilisation of the RNA substrate or RNA:protein complex.
    Figure Legend Snippet: The Cas6 ribonuclease cleaves the Mtb CRISPR repeat sequence to generate crRNA. ( A ) Cas6 (0.5 µM) was incubated with 50 nM 5’-FAM CRISPR repeat RNA at 37 °C for 5, 15, 45 min in 20 mM Tris, 100 mM potassium glutamate, pH 7.5 in the absence or presence of 5 mM divalent metal ions as indicated. Reactions were stopped by phenol-chloroform extraction. ( B ) Cas6 cleavage leaves a 3’-(cyclic) phosphate group. CRISPR repeat RNA (crRepeat, 5’-FAM labeled, 400 nM) was digested with 2 µM Cas6 for 1 h in the presence of Mg 2+ using the same reaction conditions as before. Phenol-chloroform followed by chloroform extraction provided the substrate for the E. coli Poly(A) polymerase (PAP, New England Biolabs) reaction. Polyadenylation was performed according to the manufacturer’s instructions. In a parallel experiment, Cas6 was omitted. The CRISPR repeat RNA but not the Cas6 product can be 3’-polyadenylated by PAP. This suggests that the reaction product has a cyclic 2’,3’-phosphate, as observed for other Cas6 enzymes. This observation, together with the observation that calcium supports enhanced cleavage of the CRISPR repeat, suggests that the metal ion does not participate directly in catalysis but rather plays a role in stabilisation of the RNA substrate or RNA:protein complex.

    Techniques Used: CRISPR, Sequencing, Incubation, Labeling

    5) Product Images from "RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia"

    Article Title: RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia

    Journal: Nature Communications

    doi: 10.1038/s41467-018-03513-4

    Differential expression of RNA:m 5 C, RCMTs and hnRNPK in 5-AZA-sensitive and 5-AZA-resistant leukaemia cells and the binding of hnRNPK to unmethylated and cytosine-methylated RNA. a Western blot analysis of expression of RCMTs, hnRNPK and other proteins in the 5-AZA-sensitive OCI-M2 and SC leukaemia cells and the 5-AZA-resistant M2AR and SCAR leukaemia cells. b Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from OCI-M2 and M2AR cells. c Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from SC and SCAR cells. d , e Visualization and measurement of the binding of purified recombinant hnRNPK to the unmethylated and cytosine-methylated fluorescein (FAM)-labelled RNA oligos by an antibody-coupled bead assay
    Figure Legend Snippet: Differential expression of RNA:m 5 C, RCMTs and hnRNPK in 5-AZA-sensitive and 5-AZA-resistant leukaemia cells and the binding of hnRNPK to unmethylated and cytosine-methylated RNA. a Western blot analysis of expression of RCMTs, hnRNPK and other proteins in the 5-AZA-sensitive OCI-M2 and SC leukaemia cells and the 5-AZA-resistant M2AR and SCAR leukaemia cells. b Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from OCI-M2 and M2AR cells. c Dot blot analysis of 5-methylcytosine (m 5 C) in RNA and DNA from SC and SCAR cells. d , e Visualization and measurement of the binding of purified recombinant hnRNPK to the unmethylated and cytosine-methylated fluorescein (FAM)-labelled RNA oligos by an antibody-coupled bead assay

    Techniques Used: Expressing, Binding Assay, Methylation, Western Blot, Dot Blot, Purification, Recombinant

    6) Product Images from "Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence"

    Article Title: Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence

    Journal: bioRxiv

    doi: 10.1101/667758

    The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.
    Figure Legend Snippet: The CRISPR system of M. tuberculosis A. The CRISPR locus of M. tuberculosis includes genes encoding Cas6 (crRNA processing), Csm1-5 (type III-A interference complex), Csm6 (ancillary ribonuclease), Cas1 and Cas2 (Adaptation). Cas6 cleaves the CRISPR RNA at the base of a short hairpin to generate mature crRNA that is bound by the Csm complex. On target RNA binding, the Csm complex is expected to display three enzymatic activities: target RNA cleavage ( 1 ), DNA cleavage by the HD domain ( 2 ) and cOA production by the cyclase domain ( 3 ). B. Purified, recombinant CRISPR-associated proteins of M. tuberculosis . M: PageRuler Unstained (Thermo Scientific); 1: Csm1-5 interference complex; 2: Csm1-5, Csm1 D630A, D631A (Cy variant); 3: Csm1-5, Csm3 D35A (C3 variant); 4: Csm6; 5: Cas6.

    Techniques Used: CRISPR, RNA Binding Assay, Purification, Recombinant, Variant Assay

    The Cas6 ribonuclease cleaves the Mtb CRISPR repeat sequence to generate crRNA. ( A ) Cas6 (0.5 µM) was incubated with 50 nM 5’-FAM CRISPR repeat RNA at 37 °C for 5, 15, 45 min in 20 mM Tris, 100 mM potassium glutamate, pH 7.5 in the absence or presence of 5 mM divalent metal ions as indicated. Reactions were stopped by phenol-chloroform extraction. ( B ) Cas6 cleavage leaves a 3’-(cyclic) phosphate group. CRISPR repeat RNA (crRepeat, 5’-FAM labeled, 400 nM) was digested with 2 µM Cas6 for 1 h in the presence of Mg 2+ using the same reaction conditions as before. Phenol-chloroform followed by chloroform extraction provided the substrate for the E. coli Poly(A) polymerase (PAP, New England Biolabs) reaction. Polyadenylation was performed according to the manufacturer’s instructions. In a parallel experiment, Cas6 was omitted. The CRISPR repeat RNA but not the Cas6 product can be 3’-polyadenylated by PAP. This suggests that the reaction product has a cyclic 2’,3’-phosphate, as observed for other Cas6 enzymes. This observation, together with the observation that calcium supports enhanced cleavage of the CRISPR repeat, suggests that the metal ion does not participate directly in catalysis but rather plays a role in stabilisation of the RNA substrate or RNA:protein complex.
    Figure Legend Snippet: The Cas6 ribonuclease cleaves the Mtb CRISPR repeat sequence to generate crRNA. ( A ) Cas6 (0.5 µM) was incubated with 50 nM 5’-FAM CRISPR repeat RNA at 37 °C for 5, 15, 45 min in 20 mM Tris, 100 mM potassium glutamate, pH 7.5 in the absence or presence of 5 mM divalent metal ions as indicated. Reactions were stopped by phenol-chloroform extraction. ( B ) Cas6 cleavage leaves a 3’-(cyclic) phosphate group. CRISPR repeat RNA (crRepeat, 5’-FAM labeled, 400 nM) was digested with 2 µM Cas6 for 1 h in the presence of Mg 2+ using the same reaction conditions as before. Phenol-chloroform followed by chloroform extraction provided the substrate for the E. coli Poly(A) polymerase (PAP, New England Biolabs) reaction. Polyadenylation was performed according to the manufacturer’s instructions. In a parallel experiment, Cas6 was omitted. The CRISPR repeat RNA but not the Cas6 product can be 3’-polyadenylated by PAP. This suggests that the reaction product has a cyclic 2’,3’-phosphate, as observed for other Cas6 enzymes. This observation, together with the observation that calcium supports enhanced cleavage of the CRISPR repeat, suggests that the metal ion does not participate directly in catalysis but rather plays a role in stabilisation of the RNA substrate or RNA:protein complex.

    Techniques Used: CRISPR, Sequencing, Incubation, Labeling

    Related Articles

    High Performance Liquid Chromatography:

    Article Title: A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation
    Article Snippet: .. Helicase assay Fluorescent reporter and loading RNA oligonucleotides were chemically synthesized, modified and HPLC-purified by Integrated DNA Technologies (IDT). .. The reporter strand was modified with cyanine 3 (Cy3) on its 5′-end, and the loading strand was modified with a spectrally paired black hole quencher (BHQ) on its 3′-end.

    Helicase Assay:

    Article Title: A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation
    Article Snippet: .. Helicase assay Fluorescent reporter and loading RNA oligonucleotides were chemically synthesized, modified and HPLC-purified by Integrated DNA Technologies (IDT). .. The reporter strand was modified with cyanine 3 (Cy3) on its 5′-end, and the loading strand was modified with a spectrally paired black hole quencher (BHQ) on its 3′-end.

    Synthesized:

    Article Title: Proximal disruptor aided ligation (ProDAL) of kilobase-long RNAs
    Article Snippet: .. All DNA and RNA oligonucleotides were synthesized by Integrated DNA Technologies. .. Oligonucleotides used for ProDAL of kb-long RNAs are listed in Supplementary Table 1.

    Article Title: A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation
    Article Snippet: .. Helicase assay Fluorescent reporter and loading RNA oligonucleotides were chemically synthesized, modified and HPLC-purified by Integrated DNA Technologies (IDT). .. The reporter strand was modified with cyanine 3 (Cy3) on its 5′-end, and the loading strand was modified with a spectrally paired black hole quencher (BHQ) on its 3′-end.

    Construct:

    Article Title: A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides
    Article Snippet: .. Oligonucleotide Synthesis and Purification The DNA and RNA oligonucleotides used to assemble the conditional RNA/DNA constructs, including those that were fluorescently labeled, were purchased from Integrated DNA Technologies (IDT, Coralville, IA, USA) and reconstituted in nuclease-free water (Quality Biological, Gaithersburg, MD, USA) for use. .. All AlexaFluor546, AlexaFluor488 and 6-carboxyfluorescein (6-FAM) fluorescently labeled oligonucleotides were purchased from IDT.

    Purification:

    Article Title: A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides
    Article Snippet: .. Oligonucleotide Synthesis and Purification The DNA and RNA oligonucleotides used to assemble the conditional RNA/DNA constructs, including those that were fluorescently labeled, were purchased from Integrated DNA Technologies (IDT, Coralville, IA, USA) and reconstituted in nuclease-free water (Quality Biological, Gaithersburg, MD, USA) for use. .. All AlexaFluor546, AlexaFluor488 and 6-carboxyfluorescein (6-FAM) fluorescently labeled oligonucleotides were purchased from IDT.

    Article Title: Chromosome fusions triggered by noncoding RNA
    Article Snippet: .. Microinjection of synthetic oligonucleotides 27 nt DNA and RNA oligonucleotides were purchased from IDT DNA with standard desalting and used without further purification. .. Prior to each injection, 3μL of an oligonucleotide in nuclease free water (Ambion) (15μg /μL ) was heated at 65 °C for 2 min, and chilled on ice for at least 2 min, then injected (Narishige IM 300) into the cytoplasm of mating cells 10–15 hours post mixing of mating types.

    Oligonucleotide Synthesis:

    Article Title: A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides
    Article Snippet: .. Oligonucleotide Synthesis and Purification The DNA and RNA oligonucleotides used to assemble the conditional RNA/DNA constructs, including those that were fluorescently labeled, were purchased from Integrated DNA Technologies (IDT, Coralville, IA, USA) and reconstituted in nuclease-free water (Quality Biological, Gaithersburg, MD, USA) for use. .. All AlexaFluor546, AlexaFluor488 and 6-carboxyfluorescein (6-FAM) fluorescently labeled oligonucleotides were purchased from IDT.

    Activity Assay:

    Article Title: Bioinspired Fabrication of DNA–Inorganic Hybrid Composites Using Synthetic DNA
    Article Snippet: .. RNase Activity Test The ribonucleotic activity of RNase A was evaluated using a synthetic RNA oligonucleotide, which has a fluorescein dye and quencher at both ends (RNase Alert substrate, Integrated DNA Technology). .. Before testing, the protein concentration of each sample was measured by Qubit protein reagent (Thermo Fisher Scientific), based on the standard curve using free RNase A with known concentrations (0, 200, and 400 ng μL–1 ).

    Labeling:

    Article Title: Crystal Structure of Human Nocturnin Catalytic Domain
    Article Snippet: .. Preparation of labeled oligonucleotides RNA oligonucleotides were purchased from Integrated DNA Technologies. .. 2 pmol of nucleic acid were 5′ radiolabeled with T4 polynucleotide kinase (New England BioLabs) and γ−32P ATP (Perkin Elmer) in 1 × T4 polynucleotide kinase buffer for 30 min at 37 °C.

    Article Title: A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides
    Article Snippet: .. Oligonucleotide Synthesis and Purification The DNA and RNA oligonucleotides used to assemble the conditional RNA/DNA constructs, including those that were fluorescently labeled, were purchased from Integrated DNA Technologies (IDT, Coralville, IA, USA) and reconstituted in nuclease-free water (Quality Biological, Gaithersburg, MD, USA) for use. .. All AlexaFluor546, AlexaFluor488 and 6-carboxyfluorescein (6-FAM) fluorescently labeled oligonucleotides were purchased from IDT.

    Modification:

    Article Title: A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation
    Article Snippet: .. Helicase assay Fluorescent reporter and loading RNA oligonucleotides were chemically synthesized, modified and HPLC-purified by Integrated DNA Technologies (IDT). .. The reporter strand was modified with cyanine 3 (Cy3) on its 5′-end, and the loading strand was modified with a spectrally paired black hole quencher (BHQ) on its 3′-end.

    Binding Assay:

    Article Title: Identification of motifs that function in the splicing of non-canonical introns
    Article Snippet: .. U2AF65 binding RNA oligonucleotides (listed in Figure , IDT, Integrated DNA Technologies, San Diego, CA, USA) for U2AF65 binding assays were 5' end-labeled with γ-32 P ATP using T4 polynucleotide kinase (NEB, Ipswich, MA, USA) for 30 minutes at 37°C. .. The RNAs were then gel purified using an 8% denaturing gel, eluted from the gel in 0.3M Na acetate and ethanol precipitated.

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    Integrated DNA Technologies 6 fam labelled oligonucleotides
    Stalling the translocation of helicase motor stimulates cleavage (A) Schematic representation of target DNA (100 bp) with PAM (TTC in red) end-labelled with <t>6-FAM</t> at 5’ end of the non-target strand and biotinylated at 12 th nucleotide (Target I). A similar target DNA without biotin (Target II) is also represented. Indicated in red arrow are the prominent cleavage sites. (B) Target (I) (II) were incubated with streptavidin and Cascade/I-C to form interference complex. Cleavage was initiated by addition of Cas3 (0.2 and 0.5 μM) and 1 mM ATP/ADP/AMP-PNP. Prominent cleavages of the target (I) and (II) are indicated by a red arrow (approx. 60 nt and 40 nt). A 20% denaturing PAGE was used to assess the cleavage.
    6 Fam Labelled Oligonucleotides, supplied by Integrated DNA Technologies, used in various techniques. Bioz Stars score: 80/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/6 fam labelled oligonucleotides/product/Integrated DNA Technologies
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    6 fam labelled oligonucleotides - by Bioz Stars, 2021-01
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    Stalling the translocation of helicase motor stimulates cleavage (A) Schematic representation of target DNA (100 bp) with PAM (TTC in red) end-labelled with 6-FAM at 5’ end of the non-target strand and biotinylated at 12 th nucleotide (Target I). A similar target DNA without biotin (Target II) is also represented. Indicated in red arrow are the prominent cleavage sites. (B) Target (I) (II) were incubated with streptavidin and Cascade/I-C to form interference complex. Cleavage was initiated by addition of Cas3 (0.2 and 0.5 μM) and 1 mM ATP/ADP/AMP-PNP. Prominent cleavages of the target (I) and (II) are indicated by a red arrow (approx. 60 nt and 40 nt). A 20% denaturing PAGE was used to assess the cleavage.

    Journal: bioRxiv

    Article Title: Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex

    doi: 10.1101/666776

    Figure Lengend Snippet: Stalling the translocation of helicase motor stimulates cleavage (A) Schematic representation of target DNA (100 bp) with PAM (TTC in red) end-labelled with 6-FAM at 5’ end of the non-target strand and biotinylated at 12 th nucleotide (Target I). A similar target DNA without biotin (Target II) is also represented. Indicated in red arrow are the prominent cleavage sites. (B) Target (I) (II) were incubated with streptavidin and Cascade/I-C to form interference complex. Cleavage was initiated by addition of Cas3 (0.2 and 0.5 μM) and 1 mM ATP/ADP/AMP-PNP. Prominent cleavages of the target (I) and (II) are indicated by a red arrow (approx. 60 nt and 40 nt). A 20% denaturing PAGE was used to assess the cleavage.

    Article Snippet: 6-FAM labelled oligonucleotides were obtained from IDT.

    Techniques: Translocation Assay, Incubation, Polyacrylamide Gel Electrophoresis

    Cascade and Cas3 form a stable complex during interference. (A) Schematic representation of 100 bp DNA substrates with biotin (black dot) at 5’ end of the nontarget strand (NTS), 6-FAM (fluorophore, green star) at 5 th nucleotide, Iowa Black ® FQ (quencher, brown dot) at 28 th nucleotide on target strand (TS) and PAM sequence TTC (depicted in red colour). (B) Substrate mentioned above was incubated with or without Cascade/I-C (1 μM) and increasing concentration of Cas3/I-C (0-5 μM). A significant decline in fluorescence intensity is evident when both Cascade/I-C and Cas3/I-C were present. There was no apparent quenching when dsDNA and ssDNA were used in the absence of Cascade/I-C (C) Fluorescence quenching was observed in the presence of ATP but not when ADP and AMP-PNP were used.

    Journal: bioRxiv

    Article Title: Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex

    doi: 10.1101/666776

    Figure Lengend Snippet: Cascade and Cas3 form a stable complex during interference. (A) Schematic representation of 100 bp DNA substrates with biotin (black dot) at 5’ end of the nontarget strand (NTS), 6-FAM (fluorophore, green star) at 5 th nucleotide, Iowa Black ® FQ (quencher, brown dot) at 28 th nucleotide on target strand (TS) and PAM sequence TTC (depicted in red colour). (B) Substrate mentioned above was incubated with or without Cascade/I-C (1 μM) and increasing concentration of Cas3/I-C (0-5 μM). A significant decline in fluorescence intensity is evident when both Cascade/I-C and Cas3/I-C were present. There was no apparent quenching when dsDNA and ssDNA were used in the absence of Cascade/I-C (C) Fluorescence quenching was observed in the presence of ATP but not when ADP and AMP-PNP were used.

    Article Snippet: 6-FAM labelled oligonucleotides were obtained from IDT.

    Techniques: Sequencing, Incubation, Concentration Assay, Fluorescence

    Roadblock in the translocation of Cas3/I-C stimulates cleavage (A) (D) A schematic representation of 60 nt 5’ 6-FAM labelled ssDNA with biotin at 12 th (Target A) and 20th nucleotide (Target B), respectively. (B) (E) ssDNA mentioned above was incubated with 200 nM of Cas3/I-C for several time points and anisotropy measurements were recorded. With time, the decrease in anisotropy values was observed for ssDNA with a biotin roadblock. (C) (F) ssDNA was pre-incubated with streptavidin before the addition of Cas3/I-C. Prominent DNA cleavage products were observed in the presence of ATP at ~40 nt in target A and ~50 nt in target B, indicated with a red arrow. In the presence of AMP-PNP higher Cas3 concentration was required for the cleavage. A 20% denaturing PAGE was used to study the cleavage pattern.

    Journal: bioRxiv

    Article Title: Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex

    doi: 10.1101/666776

    Figure Lengend Snippet: Roadblock in the translocation of Cas3/I-C stimulates cleavage (A) (D) A schematic representation of 60 nt 5’ 6-FAM labelled ssDNA with biotin at 12 th (Target A) and 20th nucleotide (Target B), respectively. (B) (E) ssDNA mentioned above was incubated with 200 nM of Cas3/I-C for several time points and anisotropy measurements were recorded. With time, the decrease in anisotropy values was observed for ssDNA with a biotin roadblock. (C) (F) ssDNA was pre-incubated with streptavidin before the addition of Cas3/I-C. Prominent DNA cleavage products were observed in the presence of ATP at ~40 nt in target A and ~50 nt in target B, indicated with a red arrow. In the presence of AMP-PNP higher Cas3 concentration was required for the cleavage. A 20% denaturing PAGE was used to study the cleavage pattern.

    Article Snippet: 6-FAM labelled oligonucleotides were obtained from IDT.

    Techniques: Translocation Assay, Incubation, Concentration Assay, Polyacrylamide Gel Electrophoresis