ArticleThe Biochemical journal2006
Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4.
Article in The Biochemical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 112 citations in OpenAlex.
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- A simple, fast, and cost-efficient protocol for ultra-sensitive ribosome profiling.Nucleic acids research · 2025Article
- Exploring the Potential and Advancements of Circular RNA Therapeutics.Exploration (Beijing, China) · 2025Review
- Rapid generation of long, chemically modified pegRNAs for prime editing.Nature biotechnology · 2025Article
- Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger.Genome research · 2025Article
- The therapeutic potential of circular RNAs.Nature reviews. Genetics · 2025Review
- One-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation.Nucleic acids research · 2025Article
- Quantitative and spatially resolved detection of multiplexed microRNA from plant tissue via hybridization to hydrogel-bound DNA probes in nanoliter well arrays.Microsystems & nanoengineering · 2024Article
- Template-dependent DNA ligation for the synthesis of modified oligonucleotides.Nature communications · 2024Article
- Advances in methods for tRNA sequencing and quantification.Trends in genetics : TIG · 2024Review
- A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection.Frontiers in oncology · 2024Review
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- Review
- Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP.Nucleic acids research · 2023Article
- Profiling DNA Ligase Substrate Specificity with a Pacific Biosciences Single-Molecule Real-Time Sequencing Assay.Current protocols · 2023Article
- Enzymatic Conjugation of Modified RNA Fragments by Ancestral RNA Ligase AncT4_2.Applied and environmental microbiology · 2022Article
6 more citing papers are in PubMed but not listed here.
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
The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-stranded oligonucleotides containing a single-strand break was determined. Between 4 and 37 degrees C, all proteins ligated substrates containing various combinations of DNA and RNA. The RNA ligases ligated a more diverse set of substrates than T4Dnl and, generally, T4Rnl1 had 50-1000-fold lower activity than T4Rnl2. In assays using identical conditions, optimal ligation of all substrates was at pH 8 for T4Dnl and T4Rnl1 and pH 7 for T4Rnl2, demonstrating that the protein dictates the pH optimum for ligation. All proteins ligated a substrate containing DNA as the unbroken strand, with the nucleotides at the nick of the broken strand being RNA at the 3'-hydroxy group and DNA at the 5'-phosphate. Since this RNA-DNA hybrid was joined at a similar maximal rate by T4Dnl and T4Rnl2 at 37 degrees C, we consider the possibility that this could be an unexpected physiological substrate used during some pathways of 'DNA repair'.
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