Codes with Biochemical Constraints and Single Error Correction for DNA-Based Data Storage

Abstract

In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary structures which may cause chemical inactivity. Homopolymer run-length limit and GC-balanced limit also help to reduce the error probability of DNA sequences during synthesizing and sequencing. In this letter, based on a recent work \cite{bib7}, we construct DNA codes free of secondary structures of stem length $\geq m$ and have homopolymer run-length $\leq\ell$ for odd $m\leq11$ and $\ell\geq3$ with rate $1+\log_2\rho_m-3/(2^{\ell-1}+\ell+1)$, where $\rho_m$ is in Table \ref{tm}. In particular, when $m=3$, $\ell=4$, its rate tends to 1.3206 bits/nt, beating a previous work by Benerjee {\it et al.}. We also construct DNA codes with all of the above three constraints as well as single error correction. At last, codes with GC-locally balanced constraint are presented.