Hamming Distance as a Concept in DNA Molecular Recognition
- Author(s)
- Mina Mohammadi-Kambs, Kathrin Hölz, Mark Manuel Somoza, Albrecht Ott
- 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.
- Organisation(s)
- Department of Inorganic Chemistry
- External organisation(s)
- Universität des Saarlandes
- Journal
- ACS Omega
- Volume
- 2
- Pages
- 1302-1308
- No. of pages
- 7
- ISSN
- 2470-1343
- DOI
- https://doi.org/10.1021/acsomega.7b00053
- Publication date
- 04-2017
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106006 Biophysics, 104004 Chemical biology
- ASJC Scopus subject areas
- General Chemical Engineering, General Chemistry
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/fd78b52b-d0b3-4ecd-abca-59260203fd39