title: Cleavage of functionalized DNA containing 5-modified pyrimidines by type II restriction endonucleases.
abstract: A series of six pyrimidine-modified dNTPs--5-ethynyl-, 5-phenyl-, and 5-(3-nitrophenyl)deoxycitidine and -deoxyuridine triphosphates--were prepared and incorporated by primer extension with Vent (exo-)polymerase to specific DNA sequences within or next to the recognition sequences of selected restriction endonucleases. The cleavage of these pyrimidine-modified DNA sequences by 13 restriction enzymes was then studied. Whereas the presence of any modified C within the target sequence completely prevented any restriction cleavage, most enzymes tolerated the presence of 5-ethynylU and two of them even the presence of 5-phenyl- and 5-(3-nitrophenyl)U. Modifications outside the recognition sequence were tolerated except in the case of phenyl derivatives with the PvuII enzyme. 5-EthynylC was used for protection of the recognition sequence from cleavage in the presence of the second unmodified copy of the same sequence that was cleaved.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo náměstí 2, Prague 6, 16610, Czech Republic.
authors.forename: Hana
authors.initials: H
authors.lastname: Macíčková-Cahová
authors.forename: Radek
authors.initials: R
authors.lastname: Pohl
authors.forename: Michal
authors.initials: M
authors.lastname: Hocek
mesh_terms: D004247:DNA / Q000378:metabolism*; D053837:DNA Cleavage; D004262:DNA Restriction Enzymes / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D011743:Pyrimidines; D004247:DNA; D004262:DNA Restriction Enzymes; D015252:Deoxyribonucleases, Type II Site-Specific