Synthesis and purification of oligoribonucleotides using T4 RNA ligase and reverse-phase chromatography

Middleton, Tim; Herlihy, Walter C.; Schimmel, Paul; Munro, Hamish N.

doi:10.1016/0003-2697(85)90091-0

Cited by 14 publications

(5 citation statements)

References 22 publications

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“…At the same time, PAP was added to polyadenylate the 3′ end of cfRNAs 42 . Then, 5′ RNA adaptor was ligated by T4 RNA ligase 1 43 . TD with RNase H and DNase I was designed to remove abundant rRNA, vtRNA and Y RNA.…”

Section: Resultsmentioning

confidence: 99%

“…42 Then, 5′ RNA adaptor was ligated by T4 RNA ligase 1. 43 TD with RNase H and DNase I was designed to remove abundant rRNA, vtRNA and Y RNA. In contrast to 3′ DNA adaptor used in common small RNA-Seq, 3′ polyadenylation and 5′ RNA adaptor could keep intact in the following RNase H-based targeted RNA depletion 28 and make it possible to eliminate abundant RNA and prevent DNA contamination.…”

Section: Design Of Palm-seq For Cf-mrna and Cf-lncrna Sequencingmentioning

confidence: 99%

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Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

Liu

Wang

Yang

et al. 2022

Clinical & Translational Med

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Section: Resultsmentioning

confidence: 99%

Section: Design Of Palm-seq For Cf-mrna and Cf-lncrna Sequencingmentioning

confidence: 99%

Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

Liu

Wang

Yang

et al. 2022

Clinical & Translational Med

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“…Because T4 PNK and PAP could work in the same buffer with ATP, separate step of pretreatment for cfRNA with T4 PNK was unnecessary. Then, 5' adaptor was then ligated by T4 RNA Ligase 1 19 . In contrast to 3' DNA adaptor used in common small RNA seq, 3' polyadenylation could not be degraded by DNase I which was necessary for RNase H method 20 .…”

Section: Principle Of Palm-seqmentioning

confidence: 99%

PALM-Seq: integrated sequencing of cell-free long RNA and small RNA

Yang

Wang

Zhu

et al. 2019

Preprint

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Cell-free RNA, including both long RNA and small RNA, has been considered important for its biological functions and potential clinical usage, but the major challenge is to effectively sequence them at the same time. Here we present PolyAdenylation Ligation Mediated-Seq (PALM-Seq), an integrated sequencing method for cell-free long and small RNA. Through terminal modification and addition of 3' polyadenylation and 5' adaptor, we could get mRNA, long non-coding RNA, microRNA, tRNA, piRNA and other RNAs in a single library. With target RNA depletion, all these RNAs could be sequenced with relatively low depth. Using PALM-Seq, we identified pregnant-related mRNAs, long non-coding RNAs and microRNAs in female plasma. We also applied PALM-Seq to sequence RNA from amniotic fluids, leukocytes and placentas, and could find RNA signatures associated with specific sample type. PALM-Seq provides an integrated, cost-effective and simple method to characterize the landscape of cell-free RNA, and can stimulate further progress in cell-free RNA study and usage.

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“…The enzyme, in the presence of ATP as cofactor, supports the ligation of single stranded nucleic acids, and accepts DNA and RNA fragments as substrates. 46 T4 RNA ligase is useful for joining RNA to RNA, provided that the donor contains a 5-phosphate and the acceptor a 3 0 -OH (Fig. 1a).…”

Section: Enzymatic Strategiesmentioning

confidence: 99%

In vitro circularization of RNA

Müller

Appel

2016

RNA Biology

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Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.Abbreviations: AMP, adenosine monophosphate; AppRNA, 5 0 -adenylated RNA; ATP, adenosine triphosphate; bp, base pair; CEV-A, citrus exocortis viroid strain A; circRNA, circular RNA; ciRNA, circular intronic RNA; CuAAC, cupper catalyzed azide alkyne cycloaddition; EDC, ethyl-3-(3 0 -dimethylaminopropyl)-carbodiimide; HIV, human immunodeficiency virus; IEciRNA, intron-exon circular RNA; nt, nucleotide; PIE, permuted intron exon; T4 Dnl, T4 DNA Ligase; T4 Rnl, T4 RNA Ligase

show abstract

Synthesis and purification of oligoribonucleotides using T4 RNA ligase and reverse-phase chromatography

Cited by 14 publications

References 22 publications

Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

Polyadenylation ligation‐mediated sequencing (PALM‐Seq) characterizes cell‐free coding and non‐coding RNAs in human biofluids

PALM-Seq: integrated sequencing of cell-free long RNA and small RNA

In vitro circularization of RNA

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