Chemical mapping of cytosines enzymatically flipped out of the DNA helix | Zendy

D. Daujotyte | Zendy; Zita Liutkevičiūtė | Zendy; Gintautas Tamulaitis | Zendy; Saulius Klimašauskas | Zendy

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Chemical mapping of cytosines enzymatically flipped out of the DNA helix

Author(s) -

D. Daujotyte,

Zita Liutkevičiūtė,

Gintautas Tamulaitis,

Saulius Klimašauskas

Publication year - 2008

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkn200

Subject(s) - cytosine , dna , biology , methyltransferase , restriction enzyme , biochemistry , base pair , enzyme , genetics , microbiology and biotechnology , methylation

Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in protein-DNA complexes. The generality of this method was verified with two other DNA cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes. Our results thus offer a simple and convenient laboratory tool for detection and mapping of flipped-out cytosines in protein-DNA complexes.

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