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Shortreed, M.R., Chang, S.B., Hong, D.,. Phillips, M, Campion, B., Tulpan, D.C., Andronescu, M., Condon, A., Hoos, H.H. and Smith, L.M. (2005) A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research, 33, 4965-4977. doi:10.1093/nar/gki812

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• TITLE: Analytical consideration of the selectivity of oligonucleotide hybridization

  AUTHORS: M. R. Kabilov, D. V. Pyshnyi

  KEYWORDS: Allele Specific Hybridization; Duplex Stability; Oligonucleotide Probes; SNP Discrimination; Specificity; Thermodynamics

  JOURNAL NAME: Journal of Biophysical Chemistry, Vol.2 No.2, May 31, 2011

  ABSTRACT: Systematic analysis of factors determining efficiency in discrimination of a point substitution (SNP) within specific DNA sequences was carried out in the context of hybridization approach. There are two types of selectivity that are critical for the rational design of highly specific oligonucleotides probes. The first type is the real selectivity of hybridization (fa) that is the ratio of association degrees of targets with an oligonucleotide probe upon the perfect and imperfect complex formation. This type of selectivity reflects the level of discrimination between matched and mismatched signals, which is determined both by experimental conditions and the thermodynamics of oligonucleotide hybridization. The second parameter characterizing the efficiency of SNP discrimination is the limit selectivity of hybridization, which determines the utmost value of fa at a given temperature. This value can be calculated as the ratio of corresponding equilibrium association constants of perfect and imperfect complex formation determined purely by thermodynamics. We have shown that the fa function is the most reliable characteristic describing the hybridization selectivity. For the analytical system designed to reveal any type of perturbation in DNA (e.g. SNP or modification), there is usually a temperature at which fa has its maximum value. The dependency of the fa maximum on different experimental parameters as well as the structural characteristics of a probe are described in details. The results allowed us to postulate points of principle to rationally design the most selective probes on the basis of oli- gonucleotides or their derivatives.