Triplex Formation of Oligonucleotides Containing 2′‐O‐Methylurldine, 5‐Bromo‐2′‐OMethyluridine and 2′‐0‐Methycytidine

The influence of 5‐bromo and 2′‐ O ‐methyl substitution of pyrimidine bases on nucleic acid triplex formation was examined by thermal denaturation and circular dichroism spectra with the following oligomers: 5′‐(U m ) (I, U m = 2′‐ O ‐methyluridine), 5′‐( B U m ) 15 T (II, B U m = 5‐bromo2′‐ O ‐metnyluridine), 5′‐(C m U m ) 6 C m ‐T (III, C m = 2′‐ O ‐methylcytidine), and 5′‐(C m U m ) 6 C m T (IV). Both I and II form triplexes with dA 16 (A) or 5′‐d(C 2 A 16 C 2 )‐5′‐d(G 2 T 16 G 2 ) (D), but III and IV form triplexes with 5′‐d(AG) 8 (G). Triplex formation involving two unmodified oligomers, dT 16 (T) and 5′‐d(CT) 7 (C), was used for comparison. The orders of melting temperatures (T m ) of triplexes were II A II (T m = 48 °C) > I A I (34 °C) > T A T (22 °C); II D (T m = 30 °C) > I D (22 °) > T D (12 °C); and IV G IV (T m = 82 °C) > III G III (72 °C) > C G C (55 °C). The pKa of IVG IV, III G III, and C G C were determined by CD to be 6.5,6.3, and 6.2, respectively. Triplexes formed by oligonucleotides containing both 2′‐ O ‐methyl and 5‐bromo substitutions are more stable and have a greater pKa than those formed by oligonucleotides with 2′‐ O ‐methyl substitution only; which in turn are more stable and have a greater pKa than those formed by unmodified oligonucleotides.