Analytical consideration of the selectivity of oligonucleotide hybridization英文文献资料.docVIP

Vol.2, No.2, 75-91 (2011) Journal of Biophysical Chemistry doi:10.4236/jbpc.2011.22011 Analytical consideration of the selectivity of oligonucleotide hybridization Marsel R. Kabilov , Dmitril V. Pyshnyi * Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia; Corresponding Author: kabilov@niboch.nsc.ru * Received 7 February 2010; revised 1 May 2010; accepted 27 December 2010. ABSTRACT Discrimination; Specificity; Thermodynamics Systematic analysis of factors determining effi- ciency in discrimination of a point substitution (SNP) within specific DNA sequences was car- ried out in the context of hybridization approach. There are two types of selectivity that are criti- cal for the rational design of highly specific oligonucleotides probes. The first type is the real selectivity of hybridization (f?) that is the ratio of association degrees of targets with an oligonucleotide probe upon the perfect and imperfect complex formation. This type of se- lectivity reflects the level of discrimination be- tween matched and mismatched signals, which is determined both by experimental conditions and the thermodynamics of oligonucleotide hy- bridization. The second parameter character- izeing the efficiency of SNP discrimination is the limit selectivity of hybridization, which deter- mines the utmost value of f? at a given tem- perature. This value can be calculated as the ratio of corresponding equilibrium association constants of perfect and imperfect complex formation determined purely by thermodynam- ics. We have shown that the f? function is the most reliable characteristic describing the hy- bridization 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 f? has its maximum value. The dependency of the f? maximum on