1. A method of preparing a base sequence of 5′-cohesive end of linear nucleic acids for synthesis of a nucleic acid nanostructure, the method comprising: (a) selecting candidate groups of base sequences of 5′-cohesive end having guanine (G)-cytosine (C) content of 50 to 60%; (b) calculating Gibb's free energy values of the selected candidate groups of the step (a) to select candidates having maximum, median and minimum values, and performing ligation experiments on the candidates; (c) re-selecting the candidate groups having an approximation to the Gibb's free energy values of the candidates that are the most readily ligated based on the experimental results of step (b); and (d) selecting the candidate groups that have a sequence of 3 to 5 different successive bases among the base sequences from the re-selected candidate groups.