10.1021/acsomega.7b00053.s001 Mina Mohammadi-Kambs Mina Mohammadi-Kambs Kathrin Hölz Kathrin Hölz Mark M. Somoza Mark M. Somoza Albrecht Ott Albrecht Ott Hamming Distance as a Concept in DNA Molecular Recognition American Chemical Society 2017 sequence length throughput experiments signal propagation graph-theoretical method Hamming Distance hybridization processes Hamming distance DNA Molecular Recognition DNA microarrays candidate sequences orthogonal sets recognition environment example system 2017-04-05 08:18:26 Journal contribution https://acs.figshare.com/articles/journal_contribution/Hamming_Distance_as_a_Concept_in_DNA_Molecular_Recognition/4817995 DNA microarrays constitute an in vitro example system of a highly crowded molecular recognition environment. Although they are widely applied in many biological applications, some of the basic mechanisms of the hybridization processes of DNA remain poorly understood. On a microarray, cross-hybridization arises from similarities of sequences that may introduce errors during the transmission of information. Experimentally, we determine an appropriate distance, called minimum Hamming distance, in which the sequences of a set differ. By applying an algorithm based on a graph-theoretical method, we find large orthogonal sets of sequences that are sufficiently different not to exhibit any cross-hybridization. To create such a set, we first derive an analytical solution for the number of sequences that include at least four guanines in a row for a given sequence length and eliminate them from the list of candidate sequences. We experimentally confirm the orthogonality of the largest possible set with a size of 23 for the length of 7. We anticipate our work to be a starting point toward the study of signal propagation in highly competitive environments, besides its obvious application in DNA high throughput experiments.