ArticleNucleic acids research2004
Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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Who cites it
8 citing papers in PubMed, 16 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
- Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration.Nucleic acids research · 2017Article
- Defining the functional footprint for recognition and repair of deaminated DNA.Nucleic acids research · 2012Article
- The DNA-binding domain of human PARP-1 interacts with DNA single-strand breaks as a monomer through its second zinc finger.Journal of molecular biology · 2011Article
- Nonspecific DNA binding and coordination of the first two steps of base excision repair.Biochemistry · 2010Article
- Synthesis and evaluation of new spacers for use as dsDNA end-caps.Bioconjugate chemistry · 2010Article
- Selectivity of Enzymatic Conversion of Oligonucleotide Probes during Nucleotide Polymorphism Analysis of DNA.Acta naturae · 2010Article
- Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.Biophysical journal · 2006Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oligodeoxyribonucleotides (5'-phosphorylated) of varying lengths were capped using a polyamide linker to form thermodynamically stable, endcapped DNA duplexes containing 8-14 bp. We have employed these endcapped DNA duplexes as tools to determine the DNA footprint of T4 DNA ligase. By high-performance liquid chromatography and PAGE analysis of the ligation mixtures of the endcapped DNA duplexes, we have found that by varying the lengths and the position of the nick, we can determine the minimal DNA-binding site as well as the mode of binding (symmetrical or asymmetrical binding) by the enzyme. The results of the study revealed that a 11 bp endcapped duplex was the shortest duplex effectively ligated. Dependence of ligation efficiency on nick position demonstrates that T4 DNA ligase bound asymmetrically to its DNA substrate. The use of a set of thermodynamically stable endcapped deoxyribonucleoside duplexes as a tool to elucidate the DNA footprint provides an efficient strategy for footprinting, which avoids ambiguities associated with chemical and biochemical footprinting methods.
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Registered trials
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