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deaza gtp  (New England Biolabs)


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    Structured Review

    New England Biolabs deaza gtp
    Deaza Gtp, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 104 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/deaza+gtp/7-deaza/pm41643021-463-76-80
    Average 95 stars, based on 104 article reviews
    deaza gtp - by Bioz Stars, 2026-10
    95/100 stars

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    Related Articles

    Sequencing:

    Article Title: Discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus Gyrovirus.
    Article Snippet: A 2.4-kb phi29 polymerase amplification product from serum of a diseased chicken was cloned and sequenced.. The 2383-nucleotide sequence showed about 40% identity to a representative genome of chicken anemia virus (CAV), the only member of the genus Gyrovirus, family Circoviridae.. The new genome had an organization similar to that of CAV: a putative 50 untranscribed region of about 400 nt followed by three partially overlapping open reading frames encoding VP1, VP2 and VP3 homologs.

    Article Title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil
    Article Snippet: .. The impossibility to achieve the complete sequencing of virus DNA from clusters I and V was probably due to the high GC-rich content present in the 3 ́ IGR GC region, even though attempts on PCR amplification before sequencing were made without much success by varying the concentrations of DMSO and/or in the presence of 50% 7-deaza-GTP and 50% dGTP (New England Biolabs), as performed by Rijsewijk et al. [ ]. ..

    Polymerase Chain Reaction:

    Article Title: Discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus Gyrovirus.
    Article Snippet: A 2.4-kb phi29 polymerase amplification product from serum of a diseased chicken was cloned and sequenced.. The 2383-nucleotide sequence showed about 40% identity to a representative genome of chicken anemia virus (CAV), the only member of the genus Gyrovirus, family Circoviridae.. The new genome had an organization similar to that of CAV: a putative 50 untranscribed region of about 400 nt followed by three partially overlapping open reading frames encoding VP1, VP2 and VP3 homologs.

    Article Title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil
    Article Snippet: .. The impossibility to achieve the complete sequencing of virus DNA from clusters I and V was probably due to the high GC-rich content present in the 3 ́ IGR GC region, even though attempts on PCR amplification before sequencing were made without much success by varying the concentrations of DMSO and/or in the presence of 50% 7-deaza-GTP and 50% dGTP (New England Biolabs), as performed by Rijsewijk et al. [ ]. ..

    Article Title: Blocking RAN translation without altering repeat RNAs rescues C9ORF72 -related ALS and FTD phenotypes.
    Article Snippet: INTRODUCTION: GGGGCC (G4C2) hexanucleotide repeat expansions within the first intron of the C9ORF72 gene represent the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two devastating neurodegenerative disorders.. The repeat is bidirectionally transcribed into sense G4C2 and antisense C2G4 repeat–containing RNAs, which are subsequently translated into five dipeptide repeat proteins (DPRs): polyGA, polyGP, polyGR, polyPA, and polyPR.. Repeatcontaining RNAs also accumulate into socalled RNA foci that are proposed to participate in the pathology through sequestration of RNA binding proteins.

    Amplification:

    Article Title: Discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus Gyrovirus.
    Article Snippet: A 2.4-kb phi29 polymerase amplification product from serum of a diseased chicken was cloned and sequenced.. The 2383-nucleotide sequence showed about 40% identity to a representative genome of chicken anemia virus (CAV), the only member of the genus Gyrovirus, family Circoviridae.. The new genome had an organization similar to that of CAV: a putative 50 untranscribed region of about 400 nt followed by three partially overlapping open reading frames encoding VP1, VP2 and VP3 homologs.

    Article Title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil
    Article Snippet: .. The impossibility to achieve the complete sequencing of virus DNA from clusters I and V was probably due to the high GC-rich content present in the 3 ́ IGR GC region, even though attempts on PCR amplification before sequencing were made without much success by varying the concentrations of DMSO and/or in the presence of 50% 7-deaza-GTP and 50% dGTP (New England Biolabs), as performed by Rijsewijk et al. [ ]. ..

    Virus:

    Article Title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil
    Article Snippet: .. The impossibility to achieve the complete sequencing of virus DNA from clusters I and V was probably due to the high GC-rich content present in the 3 ́ IGR GC region, even though attempts on PCR amplification before sequencing were made without much success by varying the concentrations of DMSO and/or in the presence of 50% 7-deaza-GTP and 50% dGTP (New England Biolabs), as performed by Rijsewijk et al. [ ]. ..

    Clone Assay:

    Article Title: Blocking RAN translation without altering repeat RNAs rescues C9ORF72 -related ALS and FTD phenotypes.
    Article Snippet: INTRODUCTION: GGGGCC (G4C2) hexanucleotide repeat expansions within the first intron of the C9ORF72 gene represent the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two devastating neurodegenerative disorders.. The repeat is bidirectionally transcribed into sense G4C2 and antisense C2G4 repeat–containing RNAs, which are subsequently translated into five dipeptide repeat proteins (DPRs): polyGA, polyGP, polyGR, polyPA, and polyPR.. Repeatcontaining RNAs also accumulate into socalled RNA foci that are proposed to participate in the pathology through sequestration of RNA binding proteins.



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    a, pUG RNA is unfolded by <t>7</t> <t>deaza</t> G substitution. Native gel analysis of (GU)12 electrophoretic mobility. Lane1: (AC)12 was used as a marker for single stranded RNA (ssRNA). Lane 2: 7 deaza G substitution of (GU)12 produces ssRNA with the same electrophoretic mobility as (AC)12. Lane 3: (GU)12 RNA runs with anomalously slow electrophoretic mobility. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results. b, CD analysis of unfolded 7 deaza G substituted (GU)12 compared to (GU)12. c, The pUG fold electrophoretic mobility is concentration independent. Lane 1: double stranded RNA (dsRNA) was enforced by heat annealing (GU)12 to excess (AC)12 complementary ssRNA. Lane 2: ssRNA maker (AC)12. Lanes 3–6: (GU)12 at 10, 5, 1, and 0.5 μM, respectively. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results.
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    a, pUG RNA is unfolded by <t>7</t> <t>deaza</t> G substitution. Native gel analysis of (GU)12 electrophoretic mobility. Lane1: (AC)12 was used as a marker for single stranded RNA (ssRNA). Lane 2: 7 deaza G substitution of (GU)12 produces ssRNA with the same electrophoretic mobility as (AC)12. Lane 3: (GU)12 RNA runs with anomalously slow electrophoretic mobility. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results. b, CD analysis of unfolded 7 deaza G substituted (GU)12 compared to (GU)12. c, The pUG fold electrophoretic mobility is concentration independent. Lane 1: double stranded RNA (dsRNA) was enforced by heat annealing (GU)12 to excess (AC)12 complementary ssRNA. Lane 2: ssRNA maker (AC)12. Lanes 3–6: (GU)12 at 10, 5, 1, and 0.5 μM, respectively. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results.
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    Image Search Results


    a, pUG RNA is unfolded by 7 deaza G substitution. Native gel analysis of (GU)12 electrophoretic mobility. Lane1: (AC)12 was used as a marker for single stranded RNA (ssRNA). Lane 2: 7 deaza G substitution of (GU)12 produces ssRNA with the same electrophoretic mobility as (AC)12. Lane 3: (GU)12 RNA runs with anomalously slow electrophoretic mobility. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results. b, CD analysis of unfolded 7 deaza G substituted (GU)12 compared to (GU)12. c, The pUG fold electrophoretic mobility is concentration independent. Lane 1: double stranded RNA (dsRNA) was enforced by heat annealing (GU)12 to excess (AC)12 complementary ssRNA. Lane 2: ssRNA maker (AC)12. Lanes 3–6: (GU)12 at 10, 5, 1, and 0.5 μM, respectively. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results.

    Journal: Nature structural & molecular biology

    Article Title: An atypical RNA quadruplex marks RNAs as vectors for gene silencing

    doi: 10.1038/s41594-022-00854-z

    Figure Lengend Snippet: a, pUG RNA is unfolded by 7 deaza G substitution. Native gel analysis of (GU)12 electrophoretic mobility. Lane1: (AC)12 was used as a marker for single stranded RNA (ssRNA). Lane 2: 7 deaza G substitution of (GU)12 produces ssRNA with the same electrophoretic mobility as (AC)12. Lane 3: (GU)12 RNA runs with anomalously slow electrophoretic mobility. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results. b, CD analysis of unfolded 7 deaza G substituted (GU)12 compared to (GU)12. c, The pUG fold electrophoretic mobility is concentration independent. Lane 1: double stranded RNA (dsRNA) was enforced by heat annealing (GU)12 to excess (AC)12 complementary ssRNA. Lane 2: ssRNA maker (AC)12. Lanes 3–6: (GU)12 at 10, 5, 1, and 0.5 μM, respectively. A representative gel is shown from experiments that were performed in triplicate, all of which produced the same results.

    Article Snippet: To incorporate 7-deaza-G or 7-deaza-A into pUG RNAs, GTP or ATP was substituted with equal molar concentrations of 7-deaza-GTP (TriLink, N-1044–1) or 7-deaza-ATP (TriLink, N-1061–1) during in vitro transcription using an MEGAscript T7 transcription kit (Invitrogen, cat. no. AM1334).

    Techniques: Marker, Produced, Concentration Assay

    a, Injection of 250 μM NMM into the germlines of rde-1(ne219);oma-1(zu405ts) animals does not affect embryo hatching at 15 °C, showing that NMM does not impact rde-1(ne219);oma-1(zu405ts) embryonic viability. Data are presented as mean ± s.d. Number of independent experiments (injected animals), n = 13 (no injection) and 13 (250 μM NMM). b, oma-1 pUG RNAs consisting of the first 541 nt of oma-1 mRNA and 18.5 GU repeat tails were pretreated with or without the indicated concentrations of NMM and injected into the germlines of adult rde-1(ne219);oma-1(zu405ts) animals (Methods). The percentage of embryonic arrest of the progeny of injected animals was scored at 20 °C. Data are presented as mean ± s.d. Numbers of independent experiments (injected animals): n = 6 (no injection), 19 (no treatment), 20 (25 μM NMM) and 18 (250 μM NMM). **P < 0.005 (P = 6.71 × 10−4 (25 μM) and 8.95 × 10−6 (250 μM)) (two-sided Student’s t-test). c, Incorporation of 7-deaza-G blocks the silencing activity of oma-1 pUG RNAs, while control pUG RNAs containing 7-deaza-A substitutions remain functional. Adult rde-1(ne219);oma-1(zu405ts) animals were injected in the germline with oma-1 pUG RNAs consisting of the first 541 nt of oma-1 mRNA and 18.5 GU repeat tails. The percentage of embryonic arrest of the progeny of injected animals was scored at 20 °C. Data are presented as mean ± s.d. Panels below the x axis show RNAs run on 6% polyacrylamide gel to assess RNA integrity. Numbers of independent experiments (injected animals): n = 3 (no injection), 10 (no modification), 9 (7-deaza-G) and 10 (7-deaza-A). **P < 0.005 (P = 7.01 × 10−4 (no modification) and 1.82 × 10−3 (7-deaza-A)) (two-sided Student’s t-test). d, pUG RNAs synthesized with 7-deaza-G failed to silence gfp, while control pUG RNAs containing 7-deaza-A substitutions remained functional. The percentage of progeny with gfp::h2b silenced (mean ± s.d.) is shown. Numbers of independent experiments (injected animals): n = 5 (no injection), 8 (no modification), 8 (7-deaza-G) and 8 (7-deaza-A). The fluorescence micrographs show −1, −2 and −3 oocytes of adult progeny of rde-1(ne219);gfp::h2b animals after germline injection of in vitro-transcribed gfp pUG RNAs, consisting of the first 369 nt of gfp mRNA and 18.5 GU repeat tails. Scale bar, 10 μm.

    Journal: Nature structural & molecular biology

    Article Title: An atypical RNA quadruplex marks RNAs as vectors for gene silencing

    doi: 10.1038/s41594-022-00854-z

    Figure Lengend Snippet: a, Injection of 250 μM NMM into the germlines of rde-1(ne219);oma-1(zu405ts) animals does not affect embryo hatching at 15 °C, showing that NMM does not impact rde-1(ne219);oma-1(zu405ts) embryonic viability. Data are presented as mean ± s.d. Number of independent experiments (injected animals), n = 13 (no injection) and 13 (250 μM NMM). b, oma-1 pUG RNAs consisting of the first 541 nt of oma-1 mRNA and 18.5 GU repeat tails were pretreated with or without the indicated concentrations of NMM and injected into the germlines of adult rde-1(ne219);oma-1(zu405ts) animals (Methods). The percentage of embryonic arrest of the progeny of injected animals was scored at 20 °C. Data are presented as mean ± s.d. Numbers of independent experiments (injected animals): n = 6 (no injection), 19 (no treatment), 20 (25 μM NMM) and 18 (250 μM NMM). **P < 0.005 (P = 6.71 × 10−4 (25 μM) and 8.95 × 10−6 (250 μM)) (two-sided Student’s t-test). c, Incorporation of 7-deaza-G blocks the silencing activity of oma-1 pUG RNAs, while control pUG RNAs containing 7-deaza-A substitutions remain functional. Adult rde-1(ne219);oma-1(zu405ts) animals were injected in the germline with oma-1 pUG RNAs consisting of the first 541 nt of oma-1 mRNA and 18.5 GU repeat tails. The percentage of embryonic arrest of the progeny of injected animals was scored at 20 °C. Data are presented as mean ± s.d. Panels below the x axis show RNAs run on 6% polyacrylamide gel to assess RNA integrity. Numbers of independent experiments (injected animals): n = 3 (no injection), 10 (no modification), 9 (7-deaza-G) and 10 (7-deaza-A). **P < 0.005 (P = 7.01 × 10−4 (no modification) and 1.82 × 10−3 (7-deaza-A)) (two-sided Student’s t-test). d, pUG RNAs synthesized with 7-deaza-G failed to silence gfp, while control pUG RNAs containing 7-deaza-A substitutions remained functional. The percentage of progeny with gfp::h2b silenced (mean ± s.d.) is shown. Numbers of independent experiments (injected animals): n = 5 (no injection), 8 (no modification), 8 (7-deaza-G) and 8 (7-deaza-A). The fluorescence micrographs show −1, −2 and −3 oocytes of adult progeny of rde-1(ne219);gfp::h2b animals after germline injection of in vitro-transcribed gfp pUG RNAs, consisting of the first 369 nt of gfp mRNA and 18.5 GU repeat tails. Scale bar, 10 μm.

    Article Snippet: To incorporate 7-deaza-G or 7-deaza-A into pUG RNAs, GTP or ATP was substituted with equal molar concentrations of 7-deaza-GTP (TriLink, N-1044–1) or 7-deaza-ATP (TriLink, N-1061–1) during in vitro transcription using an MEGAscript T7 transcription kit (Invitrogen, cat. no. AM1334).

    Techniques: Injection, Activity Assay, Functional Assay, Modification, Synthesized, Fluorescence, In Vitro

    7- a, RNA oligonucleotides consisting of a random 30-nt sequence followed by 12 GU repeats were synthesized with or without 7-deaza-G and conjugated to streptavidin beads using a 3′ biotinylated DNA adapter (Methods). RNA-conjugated beads were then incubated with extracts from animals expressing HA::TagRFP::RRF-1. Bead-bound material (pulldown) and supernatant were analyzed by western blot (WB) using anti-HA antibodies. Data are representative of two biologically independent experiments. b, NMM treatment prevented interactions between GU repeats and RRF-1. 5′-biotinylated RNA oligonucleotides of the indicated UG repeat length were conjugated with streptavidin beads with or without pretreatment with 250 μM NMM. RNA-conjugated beads were then incubated with extracts from animals expressing HA::TagRFP::RRF-1. Bead-bound material (pulldown) and supernatant were analyzed by immunoblotting with HA antibody. Data are representative of two biologically independent experiments.

    Journal: Nature structural & molecular biology

    Article Title: An atypical RNA quadruplex marks RNAs as vectors for gene silencing

    doi: 10.1038/s41594-022-00854-z

    Figure Lengend Snippet: 7- a, RNA oligonucleotides consisting of a random 30-nt sequence followed by 12 GU repeats were synthesized with or without 7-deaza-G and conjugated to streptavidin beads using a 3′ biotinylated DNA adapter (Methods). RNA-conjugated beads were then incubated with extracts from animals expressing HA::TagRFP::RRF-1. Bead-bound material (pulldown) and supernatant were analyzed by western blot (WB) using anti-HA antibodies. Data are representative of two biologically independent experiments. b, NMM treatment prevented interactions between GU repeats and RRF-1. 5′-biotinylated RNA oligonucleotides of the indicated UG repeat length were conjugated with streptavidin beads with or without pretreatment with 250 μM NMM. RNA-conjugated beads were then incubated with extracts from animals expressing HA::TagRFP::RRF-1. Bead-bound material (pulldown) and supernatant were analyzed by immunoblotting with HA antibody. Data are representative of two biologically independent experiments.

    Article Snippet: To incorporate 7-deaza-G or 7-deaza-A into pUG RNAs, GTP or ATP was substituted with equal molar concentrations of 7-deaza-GTP (TriLink, N-1044–1) or 7-deaza-ATP (TriLink, N-1061–1) during in vitro transcription using an MEGAscript T7 transcription kit (Invitrogen, cat. no. AM1334).

    Techniques: Sequencing, Synthesized, Incubation, Expressing, Western Blot