THE PARALLEL AND ANTIPARALLEL TRIPLEX FORMATION AND STABILITY OF SELF-COMPLEMENTARY OLIGONUCLEOTIDES CONTAINING 2'-FLUORO-ARABINOSYL THYMINE AND 5-METHYL-2'-DEOXYCYTIDINE

We examined the effects of -(2-deoxy-2-fluoro-beta-D-arabinofuranosyl) thymine (or FMAU, a potent antiviral nucleoside) on the stability of d uplex and triplexes. When compared the stability of the self-complemen tary 5'-A(5)T(5) duplex with 5'-A(5)X(5) (X = FMAU), duplex containing FMAU has much higher melting temperature (T-m). 5'-A(6)T(5)T(3)X(3)T( 5)F(3)X(3) and T(3)X(3)T(5)A(6)T(5)F(3)X(3) form the parallel and anti parallel triplexes T3X3:A(6):X3T3, respectively. The former exhibited the typical T:A:T tripler behavior with only one melting temperature a t 70 degrees C and 45 degrees C in 1.0 M and 0.2 M NaCl solution, resp ectively, whereas the latter has two T-m values at 56 degrees C and 28 degrees C in 1.0 M solution. FMAU clearly stabilize the tripler struc ture as A(6)T(22) which forms the parallel tripler T-6:A(6):T-6 has al so only one T-m at 54 degrees C and 37 degrees C in high and low salt concentration solutions, respectively. A 31mer 5'-TCCTCCTTTTTTAGGAGGAT TTTTTGGTGGT and 5'-TCCTCCTTTTTTAGGAGGATTTTTTX'X'TX'X'T (X' = 2'-deoxy- 5-methylcytidine) were prepared to study their tripler forming potenti al. The former was found to have a week interaction of the Watson-Cric k duplex with the mismatched third-strand at all pH. The latter formed a stable tripler at lower pH consistent with required protonation on the 5-methylcytosine base. For these studies we developed a simple Pc desktop spreadsheet program to calculate the first derivative profile of the melting curve data.