Palindromic octa- and dodecanucleotides containing 2'-deoxytubercidin: synthesis, hairpin formation, and recognition by the endodeoxyribonuclease EcoRI

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Abstract
Octa- and dodecanucleotides containing 2''-deoxytubericidin within the endodeoxyribonuclease EcoRI recognition fragment d(GAATTC) have been prepared by solid-phase synthesis. Whereas octamers as well as dodecamers with a "random" flanking region formed duplexes in aqueous solution, the dodecamer d(CGCGAATTCGCG) and isosterically modified oligomers thereof showed a strong tendency of hairpin formation. Due to this, cleavage with the endodeoxyribonuclease EcoRI was strongly decreased. In contrast, d(GTAGAATTCTAC) was easily cleaved by the enzyme. Single replacement of one of the dA residues by 2''-deoxytubericidin within the recognition sequence decreased the cleavage velocity but retained specificity. Twofold modification prevents cleavage of the oligomer. This implies that both N-7 purine nitrogens are proton acceptor sites for the endodeoxyribonuclease EcoRI.