A method of preparing a base sequence for synthesis of a nucleic acid nanostructure, a method of synthesizing a nucleic acid nanostructure, a candidate base sequence pair, and a nucleic acid nanostructure are provided. A method of preparing a base sequence includes selecting candidate groups of base sequences of 5′-cohesive end having at least 50% GC content, calculating Gibb's free energy values of the selected candidate groups to re-select the candidate groups, and selecting the candidate groups, that have a sequence of 3 different successive bases among the base sequences from the re-selected candidate groups.