Dipyrido[3,2-a :2',3'-c]phenazine-Tethered Oligo-DNA: Synthesis and Thermal Stability of Their DNA ́ DNA and DNA ́ RNA Duplexes and DNA ́ DNA ́ DNA Triplexes

Dipyrido[3,2-a :2',3'-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA (ODN) at a site without nucleobase, either at the 5'or 3'-end or at a internucleotide position, via linkers of 7, 12, or 18 atoms lengths. These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites: Glycerol, serving as artificial nucleoside without nucleobase, was modified to amines 10, 23, and 24, which were suitable for the subsequent key reaction with dppz-carboxylic acid 3 (Schemes 2 and 3). The products of these reactions (see 5 ± 7) were then transformed to the standard phosphoramidite derivatives (see 27, 29, and 30) or used for loading on a CPG support (see 28, 31, and 32). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis. The 9-mer ODN-dppz conjugates 35 ± 43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11 (60) or R11 (61)), while the 18-mer ODN-dppz conjugates 48 ± 56 were tested for their ability to form stable triplexes with a DNA target duplex D24 ́ D24 (62) (see Tables 1 and 2). The presence of the conjugated dppz derivative increases the stability of DNA ́ DNA and DNA ́ RNA duplexes, typically by a DTm of 7.3 ± 10.98 and 4.5 ± 7.48, respectively, when the dppz is tethered at the 5'or 3'-terminal (Table 2). The dppz derivatives also stabilize triplexes when attached to the 5'or 3'-end, with a DTm varying from 3.8 ± 11.18 (Table 3). The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA ́ DNA duplexes (DTmˆ 0.5 to 4.28) and DNA ́ RNA duplexes (DTmˆÿ1.5 to 0.98), while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all. Different types of modifications in the middle of the 18-mer ODN, in general, do not lead to any triplex formation, except when the dppz derivative is tethered to the ODN through a 12-atom-long linker (Entry 9 in Table 3).