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 a lpha-2'-deoxyadenosine derivatives 6a,b has been achieved from commerc ial N-4-benzoyl-beta-2'-deoxycytidine and N-6-benzoyl-beta-2'-deoxyade nosine, respectively. Properly protected alpha-2'-deoxyribonucleosides 8a-d were converted to the corresponding 5'-phosphoramidite derivativ es 9a-d. These and commercial beta-2'-deoxyribonucleoside 3'-phosphora midites were readily incorporated into alternating alpha,beta-oligodeo xyribonucleotides with alternating (3'-->3')- and (5'-->5')-internucle otidic phosphodiester linkages by standard solid-phase synthesis metho ds. The alpha,beta-oligodeoxyribonucleotide 12 (Scheme 3) was consider ably more resistant to hydrolysis catalyzed by snake venom phosphodies terase, calf spleen phosphodiesterase, and S1 nuclease than the parent unmodified oligonucleotide 17 (Table 2). Thermal stability of the com plex composed of 12 and complementary unmodified beta-oligomer 18 was comparable to that measured for the hybrid composed of the beta-oligod eoxyribonucleoside phosphorothioate 20 and 18 but less than that of th e native DNA duplex 17:18 (Table 3). The differences in thermal stabil ity (Delta T-m) and free energy of dissociation (Delta Delta G(37)degr ees) observed between the duplex 12:18 and the singly mismatched compl ex 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 u nmodified 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 o f 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 exhibi ts, at least to some extent, a B-type helicity. The alpha,beta-oligode oxyribonucleotide 12 formed also a complex with the complementary beta -oligoribonucleotide 23 but with much reduced affinity (T-m = 35 degre es C) than that measured with the complementary DNA sequence 18 (T-m = 54 degrees C). CD spectroscopy indicated that the complex 12:23 adopt ed a conformation similar to that observed for duplex 17:23 at 22 degr ees C. Unlike the DNA-RNA heteroduplex 17:23, the complex 12:23 was no t a substrate for E. coli RNase H.