2018
DOI: 10.1093/dnares/dsy037
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3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA

Abstract: Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various genomic tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to insert 5′ phosphorylated blunt-end double-stranded DNA to DNA breaks at 3′-recessive ends, gaps, or nicks to form a Y-shaped 3′-branch structure. Therefore, this base pairing-independent ligation is termed 3′-branch ligation (3′BL). In … Show more

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Cited by 9 publications
(4 citation statements)
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“…The excess oligonucleotides and transposons were then digested with exonuclease and the transposase enzyme was denatured with sodium dodecyl sulfate. Next, the second adapter was introduced by a previously described 3′-branch ligation using T4 ligase [ 18 ]. Finally, PCR amplification was performed using primers annealing to the 5′ bead and 3′-branch adapter sequences.…”
Section: Methodsmentioning
confidence: 99%
“…The excess oligonucleotides and transposons were then digested with exonuclease and the transposase enzyme was denatured with sodium dodecyl sulfate. Next, the second adapter was introduced by a previously described 3′-branch ligation using T4 ligase [ 18 ]. Finally, PCR amplification was performed using primers annealing to the 5′ bead and 3′-branch adapter sequences.…”
Section: Methodsmentioning
confidence: 99%
“…Adapter ligation to the 5′ end of small RNAs is particularly well described and used in small RNA library construction involved in small RNA-Seq. Several comparative studies on 3′ or 5′ ligation of total RNA exist [ 26 , 27 , 28 ], but, to the best of our knowledge, none have been developed for the ligation to a specific small RNA sequence. Only a few studies used a (randomized) DNA splint to increase the ligation efficiency of an adapter [ 29 ], but, again, these approaches were not designed for a specific small RNA.…”
Section: Discussionmentioning
confidence: 99%
“…This can be achieved by mapping reads to miRNA isoforms or alternatively, by simply extending the 5′ end of canonical miRNA sequence a few nucleotides upstream of the reference position. Even though this recommendation is not tested in the current design of the study, it is well-known that T4 RNA ligase 1 prefers single stranded RNA as a substrate ( 36 , 37 ) and therefore, 5′ overhang of acceptor RNA in ‘blocked’ RNA:DNA hybrid might result in adapter ligation and in this way may reduce blocking efficiency of the oligonucleotides.…”
Section: Discussionmentioning
confidence: 99%