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Nucleic Acids Research, 1992, Vol. 20, No. 1 55-61
© 1992

CHEMISTRY

7-Deazapurine containing DNA: efficiency of c7Gd TP, c7Ad TP and c7ld TP incorporation during PCR amplification and protection from endodeoxyribonuclease hydrolysis

Frank Seela and Angelika Röling

Laboratorium für Organische und Bioorganische Chemie, Fachbereich Biologie/Chemie, Universität Osnabrück Barbarastraße 7, D-4500 Osnabrück, FRG

Received October 23, 1991. Revised December 2, 1991. Accepted December 2, 1991.

The enzymatic synthesis of 7-deazapurine nucleoside containing DNA (501 bp) is performed by PCR-amplification (Taq polymerase) using a pUC18 plasmid DNA as template and the triphosphates of 7-deaza-2'-deoxyguanosine (c7Gd), -adenosine (c7Ad) and -inosine (c7ld). c7GdTP can fully replace dGTP resulting in a completely modified DNA-fragment of defined size and sequence. The other two 7-deazapurine triphosphates (c7AdTP) and (c7IdTP) require the presence of the parent purine 2'-deoxyribonucleotides. In purine/7-deazapurine nucleotide mixtures Taq polymerase prefers purine over 7-deazapurine nucleotides but accepts c7GdTP much better than c7AdTP or c7ldTP. As incorporation of 7-deazapurine nucleotides represents a modification of the major groove of DNA it can be used to probe DNA/protein interaction. Regioselective phospho-diester hydrolysis of the modified DNA-fragments was studied with 28 endodeoxyribonucleases. c7Gd is able to protect the DNA from the phosphodiester hydrolysis in more than 20 cases, only a few enzymes (Mae lll, lRsa l, Hind lll, Pvu ll or Taq l) do still hydrolyze the modified DNA. c7Ad protects DNA less efficiency, as this DNA could only be modified in part. The absence of N-7 as potential binding position or a geometric distortion of the recognition duplex caused by the 7-deazapurine base can account for protection of hydrolysis.


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