ArticleNucleic acids research2011
Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 34 citations in OpenAlex.
- Use of a Dihydroxyacetone Derivative as Protecting Reagent to Phosphorylate Oligonucleotides.Current protocols · 2025Article
- Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus.Nucleic acids research · 2024Article
- Functional biology and biotechnology of thermophilic viruses.Essays in biochemistry · 2023Review
- Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP.Nucleic acids research · 2023Article
- Application of microfluidic chip electrophoresis for high-throughput nucleic acid fluorescence fragment analysis assays.NAR genomics and bioinformatics · 2023Article
- Article
- Direct adenylation from 5'-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase.Nucleic acids research · 2022Article
- Strategies and Best Practice in Cloning Small RNAs.Gene technology · 2020Article
- Small RNA-seq: The RNA 5'-end adapter ligation problem and how to circumvent it.Journal of biological methods · 2019Article
- High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.RNA biology · 2017Article
- Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation.RNA biology · 2017Article
- Capture and sequencing of NAD-capped RNA sequences with NAD captureSeq.Nature protocols · 2017Article
- Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.Nucleic acids research · 2016Article
- Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I.RNA (New York, N.Y.) · 2016Article
- Efficient synthesis of stably adenylated DNA and RNA adapters for microRNA capture using T4 RNA ligase 1.Scientific reports · 2015Article
- Polynucleotide 3'-terminal phosphate modifications by RNA and DNA ligases.The Journal of biological chemistry · 2014Article
- Biases in small RNA deep sequencing data.Nucleic acids research · 2014Review
- Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase - engineering a thermostable ATP independent enzyme.BMC molecular biology · 2012Article
- Article
- Structural bias in T4 RNA ligase-mediated 3'-adapter ligation.Nucleic acids research · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We report a simple method of enzymatic synthesis of pre-adenylated DNA linkers/adapters for next-generation sequencing using thermostable RNA ligase from Methanobacterium thermoautotrophicum (MthRnl). Using RNA ligase for the reaction instead of the existing chemical or T4 DNA ligase-based methods allows quantitative conversion of 5'-phosphorylated single-stranded DNA (ssDNA) to the adenylated form. The MthRnl adenylation reaction is specific for ATP and either ssDNA or RNA. In the presence of Mg(+2), the reaction has a pH optimum of 6.0-6.5. Unlike reactions that use T4 DNA ligase, this protocol does not require synthesis of a template strand for adenylation. The high yield of the reaction simplifies isolation and purification of the adenylated product. Conducting the adenylation reaction at the elevated temperature (65°C) reduces structural constraints, while increased ATP concentrations allow quantitative adenylation of DNA with a 3'-unprotected end.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.