Generally, the DNA binding protein of most DNA viruses showed DNA binding activity with no sequence specificity. In this study, VP1 showed DNA binding characteristics with no sequence specificity similar to other DNA viruses, such as human papillomavirus and polyomavirus [27, 28]. Therefore, some other strategy of VP1 binding to the CAV viral genome should be adopted by the virus. With respect to the binding preferences of the VP1 protein to different DNA molecule conformations, VP1 was found to interact with circular ssDNA and exhibit a higher preference for this conformation, as shown in Table 1. This outcome might truly reflect the conditions of viral encapsidation for coating circular ssDNA of the CAV genome. Actually, circular ssDNA is prone to forming secondary structures with a high probability. This possibility was examined and confirmed with a computational prediction from the Mfold program (http://unafold.rna.albany.edu/?q=mfold/DNA-Folding-Form) (Additional file 1: Figure S1A, B). Similarly, linear ssDNA also has a high probability for forming secondary DNA structures (Additional file 1: Figure S2A, B). Thus, the binding preference of VP1 to linear ssDNA is surpassed only by the preference for circular ssDNA (Table 1). This difference truly meets our expectations. In fact, the sequence of linear ssDNA(−) was complemented with linear ssDNA(+). Then, linear ssDNA(+) was found to have significant VP1-DNA interaction in terms of the results of the DNA migration assay. The binding preference of VP1 to the linear plus-strand of ssDNA(+) is slightly lower than the linear plus-strand of ssDNA(−) (53.1% for 300 μg of VP1) (Additional file 1: Figure S3A, B). Other DNA molecules, such as supercoiled dsDNA, linearized ds DNA and opened dsDNA, displayed lower binding preferences to VP1, which might be a mechanism for VP1 protein to competitively bind various DNA molecules during different stages of the life cycle.