Coding for Efficient DNA Synthesis

Abstract

For DNA data storage to become a feasible technology, all aspects of the encoding and decoding pipeline must be optimized. Writing the data into DNA, which is known as DNA synthesis, is currently the most costly part of existing storage systems. As a step toward more efficient synthesis, we study the design of codes that minimize the time and number of required materials needed to produce the DNA strands. We consider a popular synthesis process that builds many strands in parallel in a step-by-step fashion using a fixed supersequence S. The machine iterates through S one nucleotide at a time, and in each cycle, it adds the next nucleotide to a subset of the strands. The synthesis time is determined by the length of S. We show that by introducing redundancy to the synthesized strands, we can significantly decrease the number of synthesis cycles. We derive the maximum amount of information per synthesis cycle assuming S is an arbitrary periodic sequence. To prove our results, we exhibit new connections to cost-constrained codes.