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Nucleic Acids Research, 1985, Vol. 13, No. 24 8749-8764
© 1985

Articles

The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA

John W. Taylor1, Walter Schmidt, Richard Cosstick2, Andrzej Okruszek3 and Fritz Eckstein

Max-Planck-Institut für experimentelle Medizin Abteilung Chemie, Hermann-Rein-Strasse 3, D-3400 Göttingen, FRG

Received October 7, 1985. Revised November 26, 1985. Accepted November 26, 1985.

The RF IV form of M13 DNA was synthesized enzymatically in vitro, using the viral (+)strand as template, to contain phosphorothioate-modified inter-nucleotidic linkages of the Rp configuration on the 5' side of avery base of a particular type in the nawly-synthesizad (–)strand. Twenty nine restriction enzymes were then tested for their reactions with the appropriate modified DNA types having a phosphorothioate linkage placed exactly at the cleavage site(s) of these enzymes in the (–)strand. Eleven of the seventeen restriction enzymes tested that had recognition sequences of five bases or more could be used to convert the phosphorothioate DNA entirely into the nicked form, either by simply allowing the reaction to go to completion with axcess enzyme (Ava I, Ava II, Ban II, Hind II, Nci I, Pst I or Pvu I) or by stopping the reaction at the appropriate time before the nicked DNA is linearized (Bam HI, Bgl I, Eco RI or Hind III). Only modification of the axact cleavage site in the (–)strand could block linearization by the first class of enzymes. The results presented imply that the restriction enzyme-directed nicking of phosphorothioate M13 DNA occurs exclusively in the (+)strand.

1Present address: Laboratory of Bioorganic Chemistry and Biochemistiy, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA

2Present address: Liverpool University, Department of Organic Chemistiy, Robert Robinson Laboratory, P.O. Box 147, Liverpool L69 3BX, UK

3Present address: Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Boczna, 90-362 Lódz, Poland


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