PCILO INVESTIGATIONS ON THE CONFORMATION OF 2-BASE HAIRPIN LOOP IN DNA

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