t4 rnl2  (New England Biolabs)


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  • 99
    Name:
    T4 RNA Ligase 2
    Description:
    T4 RNA Ligase 2 750 units
    Catalog Number:
    m0239l
    Price:
    312
    Size:
    750 units
    Category:
    RNA Ligases
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    Structured Review

    New England Biolabs t4 rnl2
    T4 RNA Ligase 2
    T4 RNA Ligase 2 750 units
    https://www.bioz.com/result/t4 rnl2/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    t4 rnl2 - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand"

    Article Title: Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkaa181

    Preparation of the ring of c-erbB-2-specific hammerhead ribozyme by Rnl2 through either the conventional ( A and B ) or present strategy ( C and D ). (A) Structure of conjugate between the original c-erB-2 hammerhead ribozyme (L-Rz (36,1) ) and 20-nt splint. The ligation site by Rnl2 is shown by dotted line. (B) 12% dPAGE analysis of the ligation products (P) using the original strategy. Lane 2, 16-nt splint; Lanes 3 and 6, [L-RNA] 0 = 2 μM; Lane 5, 20-nt splint; Lanes 4 and 7, [L-RNA] 0 = 10 μM. Here, ‘S’ refers to linear RNA (L-RNA). (C) Structure of precursor L-RNA (L-Rz (24,25) ) used for the present strategy. According to the prediction by Mfold, C-Rz was cut between C 24 and G 25 . (D) About 12% dPAGE analysis of the ligation products using the present strategy. Lane 2, [L-RNA] 0 = 2 μM; Lane 3, [L-RNA] 0 = 10 μM. Circularization conditions: [T4 Rnl2] = 0.2 U/μL, 1 × T4 Rnl2 buffer, [splint] / [L-RNA] = 2, 25°C. The reaction time is 2 h for [L-RNA] 0 = 2 μM, and 6 h for [L-RNA] 0 = 10 μM, respectively.
    Figure Legend Snippet: Preparation of the ring of c-erbB-2-specific hammerhead ribozyme by Rnl2 through either the conventional ( A and B ) or present strategy ( C and D ). (A) Structure of conjugate between the original c-erB-2 hammerhead ribozyme (L-Rz (36,1) ) and 20-nt splint. The ligation site by Rnl2 is shown by dotted line. (B) 12% dPAGE analysis of the ligation products (P) using the original strategy. Lane 2, 16-nt splint; Lanes 3 and 6, [L-RNA] 0 = 2 μM; Lane 5, 20-nt splint; Lanes 4 and 7, [L-RNA] 0 = 10 μM. Here, ‘S’ refers to linear RNA (L-RNA). (C) Structure of precursor L-RNA (L-Rz (24,25) ) used for the present strategy. According to the prediction by Mfold, C-Rz was cut between C 24 and G 25 . (D) About 12% dPAGE analysis of the ligation products using the present strategy. Lane 2, [L-RNA] 0 = 2 μM; Lane 3, [L-RNA] 0 = 10 μM. Circularization conditions: [T4 Rnl2] = 0.2 U/μL, 1 × T4 Rnl2 buffer, [splint] / [L-RNA] = 2, 25°C. The reaction time is 2 h for [L-RNA] 0 = 2 μM, and 6 h for [L-RNA] 0 = 10 μM, respectively.

    Techniques Used: Ligation

    Effects of ( A ) concentration of T4 Rnl2 buffer and ( B ) reaction temperature on the efficiency of circularization of L-miR-21c (2,3) . In (A), [L-RNA] = 10 μM, [T4 Rnl2] = 1 U/μl, 25°C, 12 h. In (B), [L-RNA] = 10 μM, [Rnl2] = 1 U/μl, 1 × Rnl2 buffer, 25°C or 37°C, 12 h. Note that 1 × ligase buffer contains 2 mM MgCl 2 , 400 μM ATP, 50 mM Tris–HCl (pH 7.5) and 1 mM DTT.
    Figure Legend Snippet: Effects of ( A ) concentration of T4 Rnl2 buffer and ( B ) reaction temperature on the efficiency of circularization of L-miR-21c (2,3) . In (A), [L-RNA] = 10 μM, [T4 Rnl2] = 1 U/μl, 25°C, 12 h. In (B), [L-RNA] = 10 μM, [Rnl2] = 1 U/μl, 1 × Rnl2 buffer, 25°C or 37°C, 12 h. Note that 1 × ligase buffer contains 2 mM MgCl 2 , 400 μM ATP, 50 mM Tris–HCl (pH 7.5) and 1 mM DTT.

    Techniques Used: Concentration Assay

    Effects of the numbers of terminal base pairs on the circularization efficiency by T4 Rnl2. ( A ) Proposed structures of L-miR-21c (3,4) , L-miR-21c (2,3) , L-miR-21c (1,2) and L-miR-21c (22,1) . The numbers of base pairs in the 3′-OH and 5′-phosphate sides of ligation site are (5,0), (4,1), (3,2) and (2,3), respectively. ( B ) 12% dPAGE for the cyclization products. Conditions: [L-RNA] = 10 μM, [T4 Rnl2] = 1 U/μl, 1 × T4 Rnl2 buffer, 25°C, 12 h.
    Figure Legend Snippet: Effects of the numbers of terminal base pairs on the circularization efficiency by T4 Rnl2. ( A ) Proposed structures of L-miR-21c (3,4) , L-miR-21c (2,3) , L-miR-21c (1,2) and L-miR-21c (22,1) . The numbers of base pairs in the 3′-OH and 5′-phosphate sides of ligation site are (5,0), (4,1), (3,2) and (2,3), respectively. ( B ) 12% dPAGE for the cyclization products. Conditions: [L-RNA] = 10 μM, [T4 Rnl2] = 1 U/μl, 1 × T4 Rnl2 buffer, 25°C, 12 h.

    Techniques Used: Ligation

    Predominant role of terminal base pairs on the preparation of C-siR-GAS by T4 Rnl2. ( A ) Proposed structures of L-siR-GAS (10,11) and L-siR-GAS (11,12) . The ligation sites by Rnl2 are shown by dotted lines. These two precursors are formed by hypothetically cutting C-siR-GAS. For example, L-siR-GAS (10,11) is formed by the scission between G 10 and A 11 . ( B ) Ligation of these L-RNAs by Rnl2. Lane 1, L-siR-GAS (10,11) only; lane 2, treatment of L-siR-GAS (10,11) with Rnl2; lane 3, L-siR-GAS (11,12) only; lane 4, treatment of L-siR-GAS (11,12) with Rnl2. Circularization conditions: [L-RNA] = 2 μM, [T4 Rnl2] = 0.2 U/μl, 1 × T4 Rnl2 buffer, 25°C, 2 h.
    Figure Legend Snippet: Predominant role of terminal base pairs on the preparation of C-siR-GAS by T4 Rnl2. ( A ) Proposed structures of L-siR-GAS (10,11) and L-siR-GAS (11,12) . The ligation sites by Rnl2 are shown by dotted lines. These two precursors are formed by hypothetically cutting C-siR-GAS. For example, L-siR-GAS (10,11) is formed by the scission between G 10 and A 11 . ( B ) Ligation of these L-RNAs by Rnl2. Lane 1, L-siR-GAS (10,11) only; lane 2, treatment of L-siR-GAS (10,11) with Rnl2; lane 3, L-siR-GAS (11,12) only; lane 4, treatment of L-siR-GAS (11,12) with Rnl2. Circularization conditions: [L-RNA] = 2 μM, [T4 Rnl2] = 0.2 U/μl, 1 × T4 Rnl2 buffer, 25°C, 2 h.

    Techniques Used: Ligation

    Highly selective preparative-scale circularization of L-Rz (24,25) . Lane 1, L-Rz (24,25)  only; lanes 2–4, circularization by Rnl2 for 1, 6 and 10 h. Reaction conditions: [L-RNA] = 20 μM, [T4 Rnl2] = 2 U/μl, [ATP] = 400 μM, 0.1 × Rnl2 buffer ([Mg 2+ ] = 200 μM), 37°C.
    Figure Legend Snippet: Highly selective preparative-scale circularization of L-Rz (24,25) . Lane 1, L-Rz (24,25) only; lanes 2–4, circularization by Rnl2 for 1, 6 and 10 h. Reaction conditions: [L-RNA] = 20 μM, [T4 Rnl2] = 2 U/μl, [ATP] = 400 μM, 0.1 × Rnl2 buffer ([Mg 2+ ] = 200 μM), 37°C.

    Techniques Used:

    Circularization of L-RNA having smaller number of terminal base pairs. ( A ) Proposed structures of L-siR-GAS (12,13) , L-siR-GAS (8,9) , L-siR-GAS (7,8) , L-siR-GAS (21,1) , L-siR-GAS (20,21)  and L-siR-GAS (9,10) . These structures are some possible structures, which we propose to be formed due to Rnl2 binding for ligation. ( B ) About 12% denaturing PAGE. In lanes 2, 5, 8, 11, 14 and 17, [L-RNA] = 2 μM and [T4 Rnl2] = 0.2 U/μl, 25°C, 2 h, 1 × buffer; in lanes 3, 6, 9, 12, 15 and 18, [L-RNA] = 10 μM and [T4 Rnl2] = 1 U/μl, 12 h, 1 × buffer. Lanes 1, 4, 7, 10, 13 and 16 refer to the substrates alone.
    Figure Legend Snippet: Circularization of L-RNA having smaller number of terminal base pairs. ( A ) Proposed structures of L-siR-GAS (12,13) , L-siR-GAS (8,9) , L-siR-GAS (7,8) , L-siR-GAS (21,1) , L-siR-GAS (20,21)  and L-siR-GAS (9,10) . These structures are some possible structures, which we propose to be formed due to Rnl2 binding for ligation. ( B ) About 12% denaturing PAGE. In lanes 2, 5, 8, 11, 14 and 17, [L-RNA] = 2 μM and [T4 Rnl2] = 0.2 U/μl, 25°C, 2 h, 1 × buffer; in lanes 3, 6, 9, 12, 15 and 18, [L-RNA] = 10 μM and [T4 Rnl2] = 1 U/μl, 12 h, 1 × buffer. Lanes 1, 4, 7, 10, 13 and 16 refer to the substrates alone.

    Techniques Used: Binding Assay, Ligation, Polyacrylamide Gel Electrophoresis

    Highly selective preparative-scale circularization of L-miR-21c (2,3) by employing ‘terminal base-pair strategy’ in 0.1 × T4 Rnl2 buffer at 37°C. Lane 1, L-miR-21c (2,3) only; lane 2, [L-RNA] = 1 μM, [Rnl2] = 0.2 U/μl; lane 4, [L-RNA] = 20 μM, [Rnl2] = 2 U/μl; lane 6, [L-RNA] = 50 μM, [Rnl2] = 2 U/μl. [ATP (supplied by 0.1 × Rnl2 buffer)] = 40 μM. The reaction time was 12 h. In Ianes 3, 5 and 7, the products in lanes 2, 4 and 6 were treated with Exonuclease T.
    Figure Legend Snippet: Highly selective preparative-scale circularization of L-miR-21c (2,3) by employing ‘terminal base-pair strategy’ in 0.1 × T4 Rnl2 buffer at 37°C. Lane 1, L-miR-21c (2,3) only; lane 2, [L-RNA] = 1 μM, [Rnl2] = 0.2 U/μl; lane 4, [L-RNA] = 20 μM, [Rnl2] = 2 U/μl; lane 6, [L-RNA] = 50 μM, [Rnl2] = 2 U/μl. [ATP (supplied by 0.1 × Rnl2 buffer)] = 40 μM. The reaction time was 12 h. In Ianes 3, 5 and 7, the products in lanes 2, 4 and 6 were treated with Exonuclease T.

    Techniques Used:

    Related Articles

    Incubation:

    Article Title: A general and efficient approach for the construction of RNA oligonucleotides containing a 5?-phosphorothiolate linkage
    Article Snippet: .. The 5-nt RNA 5′-CUCUU-3′ (40 nmol) and phosphorylated dinucleotide 24 (pC2′-X G5′-Y ) (20 nmol) were incubated together with 200 U of T4 RNA ligase (NEB), 10 µl DMSO, and 1× T4 RNA ligase buffer (50 mM Tris–HCl, pH 7.78, 10 mM MgCl2 , 10 mM dithiothreitol, 1 mM ATP) in a 100 μl reaction volume at 37°C for 6 h. The reaction mixture was worked up by PCI and ether extraction of the aqueous layers. .. The ligated product was purified by high pressure liquid chromatography on a C18 reversed-phase column (Vydac 201SP54) (6% acetonitrile/94% 0.1 M triethylammonium acetate, pH 7.0, for 5 min; then 6–16% acetonitrile/94–84% 0.1 M triethylammonium acetate, pH 7.0, over 30 min) and evaporated to dryness before further use.

    other:

    Article Title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast
    Article Snippet: To this end, DNA ‘anchor’ oligonucleotide (W242) was ligated with T4 RNA ligase to total RNA from untreated and treated W303 cells to prepare cDNA using a primer specific for the anchor (W243).

    Article Title: Addition of non-genomically encoded nucleotides to the 3?-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA
    Article Snippet: T4 RNA ligase is reported to require a single unpaired nucleotide at the 3′-terminus.

    Ligation:

    Article Title: A general and efficient approach for the construction of RNA oligonucleotides containing a 5?-phosphorothiolate linkage
    Article Snippet: .. T4 RNA ligase catalyzes the ligation of an oligonucleotide bearing a 5′ phosphate group (the donor) to a second oligonucleotide bearing a free 3′-OH group (the acceptor). ..

    Article Title: Cloning and characterization of the extreme 5?-terminal sequences of the RNA genomes of GB virus C/hepatitis G virus
    Article Snippet: .. The ligation solution contained 5 pg of the synthetic oligonucleotide adapter, 50 mM Tris·HCl (pH 7.8), 10 mM MgCl2 , 1 mM 2-mercaptoethanol, 1 mM ATP, 20 units of human placenta ribonuclease inhibitor (RNasin, Promega), and 20 units of T4 RNA ligase (New England BioLabs). ..

    Article Title: A fast, efficient and sequence-independent method for flexible multiple segmental isotope labeling of RNA using ribozyme and RNase H cleavage
    Article Snippet: .. A typical large-scale ligation reaction using T4 RNA ligase was 40 μM in both RNA fragments in 1× NEB ligation buffer (50 mM Tris–HCl pH = 7.8, 1 mM ATP, 10 mM MgCl2 , 10 mM DTT), 1x in BSA using 5 U T4 RNA ligase per nmol of RNA to be ligated. .. A typical large-scale ligation reaction using T4 DNA ligase was 10 μM in RNA fragments, 15 μM in DNA splint oligo, 10% PEG-4000 in 40 mM Tris–HCl pH = 7.8, 0.5 mM ATP, 10 mM MgCl2 , 10 mM DTT using 50 U T4 DNA ligase (fermentas) per nmol of RNA to be ligated or 2 μM final concentration of in-house produced T4 DNA ligase.

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  • 99
    New England Biolabs t4 rna ligase
    Ligation scheme for constructing a 29-nt VS ribozyme substrate 23 . ( A ) Phosphorylation of dinucleotide 18a with T4 PNK and ATP. ( B ) <t>T4</t> RNA ligase-mediated ligation of phosphorylated dinucleotide 19 with 5′ flanking oligonucleotide 20 to yield 21 . ( C ) Splint- and T4 DNA ligase-mediated ligation of 21 and 18-nt oligonucleotide 22 to yield full-length VS ribozyme substrate 23 .
    T4 Rna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 rna ligase/product/New England Biolabs
    Average 99 stars, based on 30 article reviews
    Price from $9.99 to $1999.99
    t4 rna ligase - by Bioz Stars, 2020-09
    99/100 stars
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    Ligation scheme for constructing a 29-nt VS ribozyme substrate 23 . ( A ) Phosphorylation of dinucleotide 18a with T4 PNK and ATP. ( B ) T4 RNA ligase-mediated ligation of phosphorylated dinucleotide 19 with 5′ flanking oligonucleotide 20 to yield 21 . ( C ) Splint- and T4 DNA ligase-mediated ligation of 21 and 18-nt oligonucleotide 22 to yield full-length VS ribozyme substrate 23 .

    Journal: Nucleic Acids Research

    Article Title: A general and efficient approach for the construction of RNA oligonucleotides containing a 5?-phosphorothiolate linkage

    doi: 10.1093/nar/gkq1265

    Figure Lengend Snippet: Ligation scheme for constructing a 29-nt VS ribozyme substrate 23 . ( A ) Phosphorylation of dinucleotide 18a with T4 PNK and ATP. ( B ) T4 RNA ligase-mediated ligation of phosphorylated dinucleotide 19 with 5′ flanking oligonucleotide 20 to yield 21 . ( C ) Splint- and T4 DNA ligase-mediated ligation of 21 and 18-nt oligonucleotide 22 to yield full-length VS ribozyme substrate 23 .

    Article Snippet: T4 RNA ligase catalyzes the ligation of an oligonucleotide bearing a 5′ phosphate group (the donor) to a second oligonucleotide bearing a free 3′-OH group (the acceptor).

    Techniques: Ligation

    Amplification of anchor-ligated cDNAs is dependent on T4 RNA ligase. Maize mitochondrial RNA (1–2 µg) was incubated with 40 pmol of anchor oligonucleotide in the presence or absence of T4 RNA ligase. Anchor-ligated RNAs were reverse transcribed and amplified by PCR and the cDNA products were electrophoresed on agarose gels. Lanes marked M show the migration of commercial DNA size markers. PCR products for the following cDNAs are shown: ( A ) atp9 , lanes 1 and 2; ( B ) cox2 , lanes 3 and 4; ( C ) rps12 , lanes 5 and 6, and trnS , lanes 7 and 8. Amplification of anchor-ligated atp9 . Odd numbered lanes (1, 3, 5 and 7) included T4 RNA ligase and even numbered lanes (2, 4, 6 and 8) omitted T4 RNA ligase.

    Journal: Nucleic Acids Research

    Article Title: Addition of non-genomically encoded nucleotides to the 3?-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA

    doi:

    Figure Lengend Snippet: Amplification of anchor-ligated cDNAs is dependent on T4 RNA ligase. Maize mitochondrial RNA (1–2 µg) was incubated with 40 pmol of anchor oligonucleotide in the presence or absence of T4 RNA ligase. Anchor-ligated RNAs were reverse transcribed and amplified by PCR and the cDNA products were electrophoresed on agarose gels. Lanes marked M show the migration of commercial DNA size markers. PCR products for the following cDNAs are shown: ( A ) atp9 , lanes 1 and 2; ( B ) cox2 , lanes 3 and 4; ( C ) rps12 , lanes 5 and 6, and trnS , lanes 7 and 8. Amplification of anchor-ligated atp9 . Odd numbered lanes (1, 3, 5 and 7) included T4 RNA ligase and even numbered lanes (2, 4, 6 and 8) omitted T4 RNA ligase.

    Article Snippet: T4 RNA ligase is reported to require a single unpaired nucleotide at the 3′-terminus.

    Techniques: Amplification, Incubation, Polymerase Chain Reaction, Migration

    Small RNA Northern blot screen reveals a population of tRNA-derived 21–22-nt small RNAs that are 5′-phosphorylated and 3′-hydroxylated. ( A ) Northern blot screen candidate sequences. T4 RNA ligase-sensitive small RNAs in bold, except

    Journal: RNA

    Article Title: Human tRNA-derived small RNAs in the global regulation of RNA silencing

    doi: 10.1261/rna.2000810

    Figure Lengend Snippet: Small RNA Northern blot screen reveals a population of tRNA-derived 21–22-nt small RNAs that are 5′-phosphorylated and 3′-hydroxylated. ( A ) Northern blot screen candidate sequences. T4 RNA ligase-sensitive small RNAs in bold, except

    Article Snippet: Amounts of enzymes used: 15 units (U) of T4 PNK, 3′ phophatase ± (NEB M0201/m0236); 8 U of Tobacco Acid Pyrophosphatase (Epicentre Biotechnologies); 3 U of Terminator Exonuclease (Epicentre Biotechnologies); 4 U polyA polymerase (PAP; Ambion); and 15 U T4 RNA ligase (NEB).

    Techniques: Northern Blot, Derivative Assay

    The RNA-ligase-mediated 5′-RACE procedure to clone the 5′ terminus of a viral RNA genome. Viral RNA is converted to cDNA with random primers by reverse transcription. A phosphorylated synthetic oligodeoxynucleotide adapter is ligated to the 3′ end of cDNA by using T4 RNA ligase, and then two rounds of PCR amplification are performed. The first-round PCR is done with the adapter primer (AP-1), complementary to the 3′ end of the adapter, and the viral-specific primer 1 (VS-1). The second-round nested PCR is done with the other adapter primer (AP-2), complementary to the 5′ portion of the adapter, and the viral-specific primer 2 (VS-2). The PCR products are subjected to cloning and then sequencing. The RNA molecule is represented as a wavy line, cDNA molecules are straight lines, adapters are thick lines, and primers are short arrows.

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

    Article Title: Cloning and characterization of the extreme 5?-terminal sequences of the RNA genomes of GB virus C/hepatitis G virus

    doi:

    Figure Lengend Snippet: The RNA-ligase-mediated 5′-RACE procedure to clone the 5′ terminus of a viral RNA genome. Viral RNA is converted to cDNA with random primers by reverse transcription. A phosphorylated synthetic oligodeoxynucleotide adapter is ligated to the 3′ end of cDNA by using T4 RNA ligase, and then two rounds of PCR amplification are performed. The first-round PCR is done with the adapter primer (AP-1), complementary to the 3′ end of the adapter, and the viral-specific primer 1 (VS-1). The second-round nested PCR is done with the other adapter primer (AP-2), complementary to the 5′ portion of the adapter, and the viral-specific primer 2 (VS-2). The PCR products are subjected to cloning and then sequencing. The RNA molecule is represented as a wavy line, cDNA molecules are straight lines, adapters are thick lines, and primers are short arrows.

    Article Snippet: The ligation solution contained 5 pg of the synthetic oligonucleotide adapter, 50 mM Tris·HCl (pH 7.8), 10 mM MgCl2 , 1 mM 2-mercaptoethanol, 1 mM ATP, 20 units of human placenta ribonuclease inhibitor (RNasin, Promega), and 20 units of T4 RNA ligase (New England BioLabs).

    Techniques: Polymerase Chain Reaction, Amplification, Nested PCR, Clone Assay, Sequencing