Systems and methods for timing recovery in DNA storage systems is described. In one embodiment, the present systems and methods include generating a unique pattern of DNA bases and use the unique pattern for a phase-locked loop (PLL) field of a data layout, generating a multidimensional mapping, configuring the multidimensional mapping to include one or more prohibited sequences of DNA bases, identifying a prohibited sequence from the multidimensional mapping and use the prohibited sequence for one or more synch-mark (SM) fields of the data layout, prohibiting a User Data field from using any of the prohibited sequences of DNA bases when converting binary data to DNA bases, identifying random insertion and/or deletion of DNA bases in the User Data field, and repairing the random insertion and/or deletion of DNA bases in the User Data field.