Abstract
Abstract DNA has many properties that cannot be attained with other molecules. The ability of DNA to form base pairing and its structural polymorphism allow the formation of distinct secondary and tertiary structures and may have further catalytic or aptamer function. It is also of great advantage that the base pairing of a short oligonucleotide sequence can be well predicted and designed with the thermodynamic parameters of Watson–Crick base pairs, mismatch pairs, and noncanonical base pairs based on the nearest-neighbor model. We have investigated the thermodynamics of various types of oligonucleotide structures, and obtained the nearest-neighbor parameters for Watson–Crick base pair formations and fundamental information regarding the nucleotide interactions. The data of the DNA interaction energy were also applied for molecular design of a DNA logic gate and DNA nanowire. I will further discuss the importance of quantitative data of DNA interaction energy toward the rational design of artificial DNAs carried out by our laboratory, such as base pair-mimic nucleosides and DNA containing bipyridine units, useful as nanobiodevices and nanobiomaterial.
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