%0 Journal Article %A Mohammadi-Kambs, Mina %A Hölz, Kathrin %A Somoza, Mark M. %A Ott, Albrecht %D 2017 %T Hamming Distance as a Concept in DNA Molecular Recognition %U https://acs.figshare.com/articles/journal_contribution/Hamming_Distance_as_a_Concept_in_DNA_Molecular_Recognition/4817995 %R 10.1021/acsomega.7b00053.s001 %2 https://acs.figshare.com/ndownloader/files/7987753 %K sequence length %K throughput experiments %K signal propagation %K graph-theoretical method %K Hamming Distance %K hybridization processes %K Hamming distance %K DNA Molecular Recognition DNA microarrays %K candidate sequences %K orthogonal sets %K recognition environment %K example system %X 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. %I ACS Publications