2-Amino-dA 1000 nmol scale, 1 modification

While 2-amino-dA forms a very stable base pair with T containing three hydrogen bonds, the stability of the base pair with 2-thio-dT is greatly diminished. Model building suggests that steric interactions between the 2-thiol group of thymidine and the 2-amino group of adenine tilt the bases relative to each other yielding a base pair that contains only a single hydrogen bond. However, 2-thio-dT base pairs perfectly well with A. Oligonucleotides in which A has been replaced with 2-amino-dA and T with 2-thio-dT represent an excellent example of electively Binding Complementary (SBC) oligonucleotides, able to simultaneously bind to both the sense and antisense strands of a DNA or RNA duplex. SBC 20 bases annealed against a DNA 20mer target exhibited Tm values 10°C higher than the corresponding DNA-DNA hybrid, whereas the SBC-SBC hybrid yielded Tm values 30°C lower.