  Enzymatic DNA labeling is a powerful tool with applications in biochemistry,
molecular biology, biotechnology, medical science, and genomic research. This
paper contributes to the evolving field of DNA-based data storage by presenting
a formal framework for modeling DNA labeling in strings, specifically tailored
for data storage purposes. Our approach involves a known DNA molecule as a
template for labeling, employing patterns induced by a set of designed labels
to represent information. One hypothetical implementation can use CRISPR-Cas9
and gRNA reagents for labeling. Various aspects of the general labeling
channel, including fixed-length labels, are explored, and upper bounds on the
maximal size of the corresponding codes are given. The study includes the
development of an efficient encoder-decoder pair that is proven optimal in
terms of maximum code size under specific conditions.
