Energetics of Formation of Sixteen Triple Helical Complexes Which Vary at a Single Position within a Pyrimidine Motif

The association constants for the formation of 16 pyrimidine•purine•pyrimidine triple helical complexes which vary at a single common position (Z.XY where Z = A, G, ^(Me)C, T and XY = AT, GC, CG, TA) were determined by quantitative affinity cleavage titration. The sequence context in which the 16 pairings Z•XY were studied is 5'-d(AAAAAGAGAXAGAGA)-3' within a 242 base pair DNA fragment. The association constants of four pyrimidine rich oligodeoxyribonucleotides, 5'-d(TTTTT^(Me)CT^(Me)CTZT^(Me)CT^(Me)CT)-3', ranged from 3.8 x 10^4 M^(-1) (Z•XY = A.CG) to 5.6 x 10^7 M^(-1) (Z•XY = T•AT) at 22 °C, pH 7.0; 10 mM bis-tris, 100 mM NaCl, 250 µM spermine. For the sequences studied, T.AT is more stable than T•GC, T•CG, or T•TA by greater than or equal to 2.3 kcal mol^(-1); ^(Me)C•GC is more stable than ^(Me)C•AT, ^(Me)C•CG, or ^(Me)C•TA by greater than or equal to 1.4 kcal mol^(-1); G•TA is more stable than G•AT, G•CG, or G•GC by greater than or equal to 0.8 kcal mol^(-1)