ArticleNucleic acids research2008
Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 37 citations in OpenAlex.
- Oriented Soft DNA Curtains for Single-Molecule Imaging.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand.Nucleic acids research · 2020Article
- Electrochemiluminescent determination of the activity of uracil-DNA glycosylase: Combining nicking enzyme assisted signal amplification and catalyzed hairpin assembly.Mikrochimica acta · 2019Article
- Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival.Nucleic acids research · 2018Article
- Efficient modification of λ-DNA substrates for single-molecule studies.Scientific reports · 2017Article
- Mapping the nicking efficiencies of nickase R.BbvCI for side-specific LNA-substituted substrates using rolling circle amplification.Scientific reports · 2016Article
- Article
- Nicking enzyme-based internal labeling of DNA at multiple loci.Nature protocols · 2012Article
- Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase.Cell · 2011Article
- Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA.Nanoscale · 2011Review
- Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Efficient preparation of internally modified single-molecule constructs using nicking enzymes.Nucleic acids research · 2011Article
- Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.Nucleic acids research · 2011Review
- Peptide nucleic acids as tools for single-molecule sequence detection and manipulation.Nano letters · 2010Article
- Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.Nucleic acids research · 2010Article
- Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.Nucleic acids research · 2009Article
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
We describe a new approach for labeling of unique sequences within dsDNA under nondenaturing conditions. The method is based on the site-specific formation of vicinal nicks, which are created by nicking endonucleases (NEases) at specified DNA sites on the same strand within dsDNA. The oligomeric segment flanked by both nicks is then substituted, in a strand displacement reaction, by an oligonucleotide probe that becomes covalently attached to the target site upon subsequent ligation. Monitoring probe hybridization and ligation reactions by electrophoretic mobility retardation assay, we show that selected target sites can be quantitatively labeled with excellent sequence specificity. In these experiments, predominantly probes carrying a target-independent 3' terminal sequence were employed. At target labeling, thus a branched DNA structure known as 3'-flap DNA is obtained. The single-stranded terminus in 3'-flap DNA is then utilized to prime the replication of an externally supplied ssDNA circle in a rolling circle amplification (RCA) reaction. In model experiments with samples comprised of genomic lambda-DNA and human herpes virus 6 type B (HHV-6B) DNA, we have used our labeling method in combination with surface RCA as reporter system to achieve both high sequence specificity of dsDNA targeting and high sensitivity of detection. The method can find applications in sensitive and specific detection of viral duplex DNA.
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