Base modified oligothymidylates d(T)(12) containing one or more 5-(o-carboran-1-yl)-2’-deoxyuridine (CDU) instead of thymidine were synthesized using an automated beta-cyanoethyl phosphoramidite approach. The thermostability of duplexes formed by these new oligonucleotides with natural complementary strand d(A)(12) and poly(rA) was affected by the location of the carboranyl nucleotide within the chain. CDUd(T)(11) oligomer modified at the 5’-terminus displayed a melting temperature (T-m = 28 degrees C) similar to natural d(T)(12) ((T)m = 29 degrees C), whereas 3’-modified d(T)(10)CDUd(T) and centrally modified d(T)(6)CDUd(T)(5) oligonucleotide had lower T-m values (Tm = 20.5 and 15.3 degrees C, respectively). The T-m studies were supported by molecular modeling of a duplex containing d(T)(6)CDUd(T)(5), which showed steric interactions between the boron cage and 5’-adjacent base. As an added benefit, CDU modification at the 3’-terminus of the oligomers markedly increased their resistance toward 5’-exonuclease activity, as determined by half-life (t(1/2)) measurements. The t(1/2) increased in the order d(T)(12) < d(T)(10)CDUd(T) << d(T)(9)CDU(2)d(T). The presence of one or more carborane clusters in these new compounds increases their lipophilicity and makes them potential candidates for boron neutron capture therapy (BNCT) and antisense oligonucleotide technology (AOT).