M.A. Livshits, and A.D. Mirzabekov
Argonne National Laboratory (U.S.A.) and Engelhardt Institute of Molecular Biology (Moscow)-Joint Human Genome Program.
The goal of a DNA hybridization test with a set of octanucleotides is to reveal the eight-letter words present in the DNA text. The straightforward identification of perfect duplexes is subject to a number of inevitable random errors. To diminish the errors, one can use, instead of statistics of repeated measurements, rather large statistics of data provided by a single hybridization experiment with the complete octanucleotide matrix. To this end, one should take into account also mismatched duplexes. The presence of a given word in the DNA sequence is confirmed not only by the perfect duplex formed with the octanucleotide strictly complementary to the word, but also by the obligatory formation of single-mismatch duplexes with all 24 related single-substitution octanucleotides. If, on the other hand, the octanucleotide fixed in a given hybridization cell forms with DNA a single-mismatch duplex, then in most of related single-substitution cells (21 or 24), double-mismatch duplexes with the same DNA site will be formed. Because of this, the "family test" evaluating the signal from a given hybridization cell together with the signals from 24 related single-substitution cells deals in fact with the difference in stability of single- and double-mismatch duplexes rather than with identification of a perfect duplex. Importantly in such a test, a much higher discrimination power can be achieved due to the fact that the ratio of standard deviation to mean value is considerably lower (by 4.6 times) for the "family" signal than for the individual cell signals.
* Work supported in part by the U.S. Department of Energy, Office of Health and Environmental Research, under Contract No. W-31-109-ENG-38 and Russian Human Genome Program.
The submitted manuscript has been authorized by a contractor of the U.S. Government under contract No. W-31-109-ENG-38. Accordingly, the U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes.