During duplex hybridisation of unmodified oligos, A-T base pairs have two hydrogen bonds, whereas G-C base pairs have three. One of the simplest methods of improving duplex stabilisation is the use of 2-Amino-dA phosphoramidite (2,6-diaminopurine) in place of dA.⁽¹⁾ This forms an additional hydrogen bond with thymidine. However, this product also destabilises A-G wobble mismatches, thus increasing specificity.

Ref:

1. Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their non-modified counterparts, Y. Lebedev, N. Akopyants, T. Azhikina, Y. Shevchenko, V. Potapov, D. Stecenko, D. Berg and E. Sverdlov, Genetic Analysis – Biomolecular Engineering, 13, 15-21, 1996.