The pace of growth in information technology stimulates the information security field to rival to keep up at the same pace. One of the most common encryption techniques is the Advanced Encryption Standard and, despite its` good reputation, the analysis in this work showed some limitations in its procedures. Indeed, as a response to this scarcity, many approaches have been proposed, and many other exertions have been spent. One promising consequence is bio-inspired cryptography that emerged with the progress of the DNA computing field. In this paper, a new enhanced method will be proposed using properties of bio-inspired cryptography, bioinformatics, and conventional cryptography to produce a more complex, robust, and less prone to attacks procedures. The contribution presented in this work can be epitomized in three main aspects. First, making the AES internal steps dynamic and key dependent. Second, modifying the Shift-Row step in the AES by involving the Sequence Alignment algorithm. Third, a key exchange technique inherited from the process of DNA fingerprint. The presented algorithm has been built on a DNA basis to demonstrate the capability of applying such a complex system on a promising biological environment such as a molecular computer. It must be clarified that the perception is not to negate or replace the mathematical and theoretical basis of the traditional cryptography, but to combine it with the sophisticated biological characteristics to produce a more powerful cryptographic technique, also to create a bridge between the existing and the new technologies. The experimental analysis showed remarkable enhancement in testing the modified Shift-Row function detached and the encryption strength added by the multi-model layer. Theoretically, the overall modified algorithm showed a significant advance over the classical AES in the resistance against linear and differential cryptanalysis which reveals a promising future of bio-inspired cryptographic techniques.