ArticleNucleic acids research2007
T4 DNA ligase is more than an effective trap of cyclized dsDNA.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 31 citations in OpenAlex.
- Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick.Biomolecules · 2024Article
- Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens.Food and environmental virology · 2021Article
- Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand.Nucleic acids research · 2020Article
- The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis.Microbial cell factories · 2019Article
- The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining.Synthetic and systems biotechnology · 2019Article
- Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations.RSC advances · 2018Article
- Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration.Nucleic acids research · 2017Article
- Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.Angewandte Chemie (International ed. in English) · 2015Article
- Studying DNA looping by single-molecule FRET.Journal of visualized experiments : JoVE · 2014Article
- Probing transient protein-mediated DNA linkages using nanoconfinement.Biomicrofluidics · 2014Article
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
- Mechanical properties of DNA-like polymers.Nucleic acids research · 2013Article
- Measuring shape-dependent looping probability of DNA.Biophysical journal · 2013Article
- Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.Science (New York, N.Y.) · 2012Article
- Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA ligase.The Journal of biological chemistry · 2011Article
- Fluorescent DNA-based enzyme sensors.Chemical Society reviews · 2011Review
- Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.
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.