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This paper presents constructions of DNA codes that satisfy biological and combinatorial constraints for DNA-based data storage systems. We introduce an algorithm that generates DNA blocks containing sequences that meet the required constraints for DNA codes. The constructed DNA sequences satisfy biological constraints: balanced GC-content, avoidance of secondary structures, and prevention of homopolymer runs.

DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards system, which introduces nicks (cuts) in the DNA backbone, encodes only one bit per nicking site, limiting density. We propose DNA Tails, a storage paradigm that encodes nonbinary symbols at nicking sites by growing enzymatically synthesized single-stranded DNA of varied lengths.

The number of zeros and the number of ones in a binary string are referred to as the composition of the string, and the prefix-suffix compositions of a string are a multiset formed by the compositions of the prefixes and suffixes of all possible lengths of the string. In this work, we present binary codes of length n in which every codeword can be efficiently reconstructed from its erroneous prefix-suffix compositions with at most t composition errors.