THE SOLUTION STRUCTURE OF A 3'-PHENAZINIUM (PZN) TETHERED DNA-RNA DUPLEX WITH A DANGLING ADENOSINE - R(5'GAUUGAA3')-D(5'TCAATC3'-PZN)

The 3'-Pzn group tethered to an oligo-DNA stabilizes a DNA-RNA hybrid duplex structure by 13 degrees C compared to the natural counterpart. This report constitutes the first full study of the conformational fea tures of a hybrid DNA-RNA duplex, which has been possible because of t he unique stabilization of this rather small duplex by the tethered 3' -Pzn moiety (T-m approximate to 40 degrees C from NMR). In this study, a total of 252 inter- and intra-strand torsional and distance constra ints along with the full NOE relaxation matrix, taking into account th e exchange process of imino and amino protons with water, have been us ed. The 3'-Pzn-promoted stabilization of the DNA-RNA hybrid duplex res ults in detailed local conformational characteristics such as the tors ion angles of the backbone and sugar moieties that are close to the fe atures of the other natural DNA-RNA hybrids (i.e. sugars of the RNA st rand are 3'-endo, but the sugars of the DNA strand are intermediate be tween A- and B-forms of DNA, 72 degrees < P < 180 degrees; note howeve r, that the sugars of our DNA strand have a C-1-exo conformation: 131 degrees < P < 154 degrees). This study suggests that 3'-Pzn-tethered s maller oligo-DNA should serve the same purpose as a larger oligo-DNA a s a antisense inhibitor of the viral mRNA. Additionally, these types o f tethered oligos have been found to be relatively more resistant to t he cellular nuclease. Moreover, they are taken up quite readily throug h the cellular membrane (14) compared to the natural counterparts.