ArticleNucleic acids research2007
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
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 21 papers.
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Who cites it
21 citing papers in PubMed.
- Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.Nucleic acids research · 2019Article
- Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a.Molecular cell · 2018Article
- UbaLAI is a monomeric Type IIE restriction enzyme.Nucleic acids research · 2017Article
- Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.Nucleic acids research · 2015Article
- Base flipping in open complex formation at bacterial promoters.Biomolecules · 2015Review
- Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.Nucleic acids research · 2013Article
- Quadruplex formation as a molecular switch to turn on intrinsically fluorescent nucleotide analogs.Nucleic acids research · 2013Article
- Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.Nucleic acids research · 2012Article
- Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system.The EMBO journal · 2011Article
- DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.Nucleic acids research · 2010Article
- Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not.Protein science : a publication of the Protein Society · 2010Article
- Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.Nucleic acids research · 2009Article
- Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.Nucleic acids research · 2009Article
- Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease.The Journal of biological chemistry · 2009Article
- Article
- Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.Journal of molecular biology · 2009Article
- How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.Nucleic acids research · 2008Article
- Central base pair flipping and discrimination by PspGI.Nucleic acids research · 2008Article
- DNA base flipping by both members of the PspGI restriction-modification system.Nucleic acids research · 2008Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.
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