SYNTHESIS AND PHYSICOCHEMICAL PROPERTIES OF ALTERNATING ALPHA,BETA-OLIGODEOXYRIBONUCLEOTIDES WITH ALTERNATING (3'-]3')-INTERNUCLEOTIDIC AND (5'-]5')-INTERNUCLEOTIDIC PHOSPHODIESTER LINKAGES

A simple and straightforward synthesis of alpha-2'-deoxycytidine and alpha-2'-deoxyadenosine derivatives 6a,b has been achieved from commercial N-4-benzoyl-beta-2'-deoxycytidine and N-6-benzoyl-beta-2'-deoxyadenosine, respectively. Properly protected alpha-2'-deoxyribonucleosides 8a-d were converted to the corresponding 5'-phosphoramidite derivatives 9a-d. These and commercial beta-2'-deoxyribonucleoside 3'-phosphoramidites were readily incorporated into alternating alpha,beta-oligodeoxyribonucleotides with alternating (3'-->3')- and (5'-->5')-internucleotidic phosphodiester linkages by standard solid-phase synthesis methods. The alpha,beta-oligodeoxyribonucleotide 12 (Scheme 3) was considerably more resistant to hydrolysis catalyzed by snake venom phosphodiesterase, calf spleen phosphodiesterase, and S1 nuclease than the parent unmodified oligonucleotide 17 (Table 2). Thermal stability of the complex composed of 12 and complementary unmodified beta-oligomer 18 was comparable to that measured for the hybrid composed of the beta-oligodeoxyribonucleoside phosphorothioate 20 and 18 but less than that of the native DNA duplex 17:18 (Table 3). The differences in thermal stability (Delta T-m) and free energy of dissociation (Delta Delta G(37)degrees) observed between the duplex 12:18 and the singly mismatched complex 12:19 (9 degrees C and -2.5 kcal/mol, respectively) (Tables 3 and 4) suggest that the sequence specificity;of 12 toward a complementary unmodified beta-DNA oligomer is comparable to that of 17. In addition, the CD spectrum of 12:18 at 22 degrees C resembles more closely that of the natural DNA duplex 17:18 than that of the alpha,beta-DNA duplex 12:13 (Figure 3). These findings indicate that the duplex 12:18 exhibits, at least to some extent, a B-type helicity. The alpha,beta-oligodeoxyribonucleotide 12 formed also a complex with the complementary beta-oligoribonucleotide 23 but with much reduced affinity (T-m = 35 degrees C) than that measured with the complementary DNA sequence 18 (T-m = 54 degrees C). CD spectroscopy indicated that the complex 12:23 adopted a conformation similar to that observed for duplex 17:23 at 22 degrees C. Unlike the DNA-RNA heteroduplex 17:23, the complex 12:23 was not a substrate for E. coli RNase H.