  DNA is an attractive medium for digital data storage. When data is stored on
DNA, errors occur, which makes error-correcting coding techniques critical for
reliable DNA data storage. To reduce the errors, a common technique is to
include constraints that avoid homopolymers (consecutive repeated nucleotides)
and balance the GC content, as sequences with homopolymers and unbalanced GC
content are often associated with higher error rates. However, constrained
coding comes at the cost of an increase in redundancy. An alternative is to
control errors by randomizing the sequences, embracing errors, and paying for
them with additional coding redundancy. In this paper, we determine the error
regimes in which embracing substitutions is more efficient than constrained
coding for DNA data storage. Our results suggest that constrained coding for
substitution errors is inefficient for existing DNA data storage systems.
Theoretical analysis indicates that for constrained coding to be efficient, the
increase in substitution errors for nucleotides in homopolymers and sequences
with unbalanced GC content must be very large. Additionally, empirical results
show that the increase in substitution, deletion, and insertion rates for these
nucleotides is minimal in existing DNA storage systems.
