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Mohammadi-Kambs M, Hölz K, Somoza MM, et al. Hamming Distance as a Concept in DNA Molecular Recognition. ACS Omega. 2017;2(4):1302-1308doi: 10.1021/acsomega.7b00053.
Mohammadi-Kambs, M., Hölz, K., Somoza, M. M., & Ott, A. (2017). Hamming Distance as a Concept in DNA Molecular Recognition. ACS omega, 2(4), 1302-1308. https://doi.org/10.1021/acsomega.7b00053
Mohammadi-Kambs, Mina, et al. "Hamming Distance as a Concept in DNA Molecular Recognition." ACS omega vol. 2,4 (2017): 1302-1308. doi: https://doi.org/10.1021/acsomega.7b00053
Mohammadi-Kambs M, Hölz K, Somoza MM, Ott A. Hamming Distance as a Concept in DNA Molecular Recognition. ACS Omega. 2017 Apr 30;2(4):1302-1308. doi: 10.1021/acsomega.7b00053. Epub 2017 Apr 05. PMID: 28474009; PMCID: PMC5410656.
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ACS Omega. 2017 Apr 30;2(4):1302-1308. doi: 10.1021/acsomega.7b00053. Epub 2017 Apr 05.

Hamming Distance as a Concept in DNA Molecular Recognition.

ACS omega

Mina Mohammadi-Kambs, Kathrin Hölz, Mark M Somoza, Albrecht Ott

Affiliations

  1. Biological Experimental Physics, Saarland University, Campus B2.1, 66123 Saarbrücken, Germany.
  2. Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.

PMID: 28474009 PMCID: PMC5410656 DOI: 10.1021/acsomega.7b00053

Abstract

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.

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