Abstract
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°) 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° of the bulge loop with the loop length from the chemical experimental data has not been enough to predict the ΔG 37° 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.
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Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A. (2004). Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_16
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DOI: https://doi.org/10.1007/978-3-540-24628-2_16
Publisher Name: Springer, Berlin, Heidelberg
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