DNA Labeling with Composite Symbols

DNA labeling is an important tool in molecular biology and biotechnology to visualize, detect, and support the study of DNA at the molecular level. Existing literature has focused primarily on using standard labels, where each label is defined by a fixed q-ary pattern whose occurrences are detected along the sequence. Such schemes, however, impose limitations on the achievable labeling capacity and often require a large label set to approach the maximum possible capacity of log2q bits per symbol for q-ary sequences (and 2 bits per symbol in the quaternary DNA alphabet).In this work, we propose a novel approach for DNA labeling using composite labels, in which each composite symbol can store a mixture of the standard letters, consequently, allowing multiple patterns to be recognized by a single composite label. We show that composite labels strictly increase the achievable labeling capacity compared with standard labels, and substantially reduce the minimum number of labels required to attain the maximum labeling capacity.