In this paper, we propose a first dynamic slidingwindow encoding (DSWE) for storing encrypted data in a DNAform taking into account biological constraints and prohibitednucleotide motifs used for data indexing. Its originality is twofold.First, it takes advantage of variable length DNA codewords toavoid homopolymers longer than N bases when encoding binarydata. Second, it relies on a sliding window to prevent the creationof prohibited motifs of nucleotides, adding non-coding bases whennecessary. Contrarily to existing schemes, scaling DSWE to highvalues of N and of numbers of prohibited motifs is extremelysimple. It is furthermore independent of the cryptosystem. Weprovide the theoretical information rate of our proposal for agiven number of prohibited motifs and a maximum homopolymerlength. Experiments show that in general, it offers much higherperformances than existing schemes.