PCILO investigations on the conformation of two-base hairpin loop in DNA Original Research Article

Hairpin loops are found in DNA and they are essential for various genetic processes. In general, four or five nucleotides are optimal to form a hairpin loop, but three-base loops are also observed. Recently, interest has grown to know the feasibility of formation of two-base hairpin loop in DNA. We have performed semi-emperical quantum mechanical PCILO calculations on the two previously proposed models (HA1 and HA2) with A and I bases in the loop. The results indicate that among the two structures, HA1 is energetically more stable than HA2. This result is supported by recent NMR observations of such hairpin loop. In addition, the decreasing order of the calculated upfield shifts of P atoms in the loop of HA1 structure also agrees well with the NMR experimental observations.