Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop

摘要

Forty thermodynamic parameters were estimated for DNA duplexes with a single bulge loop. In DNA computing, sequences need to form wanted structures, not unwanted structures. To achieve this, we should design sequences with low free energy (ΔG_(37)~0) in wanted structures and high free energy in unwanted structures. Conventional sequence design strategies have not prevented the formation of bulge loop structures completely. Estimation of the ΔG_(37)~0 of the bulge loop with the loop length from the chemical experimental data has not been enough to predict the ΔG_(37)~0 of the bulge loop structure. To investigate the effect of the type of bulged base and its flanking base pairs, we applied the nearest-neighbor model to DNA sequences with a single bulge loop. We also estimated the effect of loop position on the stability of a single bulge loop.