ArticleThe Journal of biological chemistry2011
Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase.
Article in The Journal of biological chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- Cloning and Functional Characterization of AhyAP-T65Lig, an ATP-Dependent DNA Ligase from Trabzonvirus AP-T65.Molecular biotechnology · 2026Article
- Enhanced Golden Gate Assembly: evaluating overhang strength for improved ligation efficiency.Nucleic acids research · 2024Article
- Mismatch discrimination and sequence bias during end-joining by DNA ligases.Nucleic acids research · 2022Article
- Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase.Biopolymers · 2021Article
- Interplay between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation.Journal of molecular biology · 2019Review
- Temperature adaptation of DNA ligases from psychrophilic organisms.Extremophiles : life under extreme conditions · 2019Article
- A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining.Nucleic acids research · 2018Article
- Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement.Scientific reports · 2018Article
- Article
- Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA).Nucleic acids research · 2016Article
- Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes.Nucleic acids research · 2016Article
- A high-throughput assay for the comprehensive profiling of DNA ligase fidelity.Nucleic acids research · 2016Article
- The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase.PloS one · 2016Article
- Coevolution of RtcB and Archease created a multiple-turnover RNA ligase.RNA (New York, N.Y.) · 2015Article
- Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology.Archaea (Vancouver, B.C.) · 2015Review
- Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay.Nucleic acids research · 2014Article
- A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation.Nucleic acids research · 2014Article
- Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase.Nucleic acids research · 2014Article
- Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3'-OH base mispairs and damaged base lesions.RNA (New York, N.Y.) · 2013Article
- Universal labeling of 5'-triphosphate RNAs by artificial RNA ligase enzyme with broad substrate specificity.Chemical communications (Cambridge, England) · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
T4 DNA ligase catalyzes phosphodiester bond formation between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA in three steps: 1) enzyme-adenylylate formation by reaction with ATP; 2) adenylyl transfer to a 5'-phosphorylated polynucleotide to generate adenylylated DNA; and 3) phosphodiester bond formation with release of AMP. This investigation used synthetic, nicked DNA substrates possessing either a 5'-phosphate or a 5'-adenylyl phosphate. Steady state experiments with a nicked substrate containing juxtaposed dC and 5'-phosphorylated dT deoxynucleotides (substrate 1) yielded kcat and kcat/Km values of 0.4±0.1 s(-1) and 150±50 μm(-1) s(-1), respectively. Under identical reaction conditions, turnover of an adenylylated version of this substrate (substrate 1A) yielded kcat and kcat/Km values of 0.64±0.08 s(-1) and 240±40 μm(-1) s(-1). Single turnover experiments utilizing substrate 1 gave fits for the forward rates of Step 2 (k2) and Step 3 (k3) of 5.3 and 38 s(-1), respectively, with the slowest step ∼10-fold faster than the rate of turnover seen under steady state conditions. Single turnover experiments with substrate 1A produced a Step 3 forward rate constant of 4.3 s(-1), also faster than the turnover rate of 1A. Enzyme self-adenylylation was confirmed to also occur on a fast time scale (∼6 s(-1)), indicating that the rate-limiting step for T4 DNA ligase nick sealing is not a chemical step but rather is most likely product release. Pre-steady state reactions displayed a clear burst phase, consistent with this conclusion.
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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.