title: SPR Detection and Discrimination of the Oligonucleotides Related to the Normal and the Hybrid bcr-abl Genes by Two Stringency Control Strategies.
abstract: In this study, we applied two stringency control strategies for surface plasmon resonance (SPR) detection of DNA hybridization and discrimination of completely and partially complementary 24-mer sequences. These sequences are specific to the human normal bcr and the hybrid bcr-abl genes, protein products of which are responsible for some leukemia. SPR sensors based on resonance phenomena in nanoscale gold films are well suited for label-free, real-time investigations of the macromolecule interactions. Thermodynamic parameters obtained using the web server DINAMelt allowed supposing the possibility for realization (a) stringency control based on the ionic strength of the hybridization buffer and (b) stringency control based on the temperature elevation. The first one resulted in that the discrimination index of completely complementary and partially complementary oligonucleotides depending on the target concentration varied from 1.3 to 1.8 in 2 × SSC and from 2.0 to 2.9 in 0.5 × SSC. For implementation of the second stringency control strategy, SPR spectrometer measuring flow cell with built-in high-precision temperature control and regulation as well as corresponding software was created. It is shown that the duplexes formed by the immobilized probes mod-Ph and completely complementary oligonucleotides P1 remained without significant changes until ~50 °C, while the duplexes formed with partially complementary oligonucleotide Bcrex14 almost entirely disrupted at 40 °C. Thus, the absolutely effective thermodiscrimination of this pair of oligonucleotides was achieved in this temperature range (40-50 °C).
authors.affiliation: Institute of High Technologies, Taras Shevchenko Kyiv National University, 64 Volodymyrska Str., 01003, Kyiv, Ukraine. matsishinnicolas@gmail.com.|Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine. matsishinnicolas@gmail.com.
authors.forename: M J
authors.initials: MJ
authors.lastname: Matsishin
authors.affiliation: V. Ye. Lashkaryov Institute of Semiconductor Physics, NAS of Ukraine, 41, Prospect Nauki, Kyiv, 03028, Ukraine.
authors.forename: Iu V
authors.initials: IuV
authors.lastname: Ushenin
authors.affiliation: Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine.
authors.forename: A E
authors.initials: AE
authors.lastname: Rachkov
authors.affiliation: Institute of High Technologies, Taras Shevchenko Kyiv National University, 64 Volodymyrska Str., 01003, Kyiv, Ukraine.|Laboratory of Biomolecular Electronics, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo Str., 03680, Kyiv, Ukraine.
authors.forename: A P
authors.initials: AP
authors.lastname: Solatkin
keywords: Hybridization biosensor; Ionic strength; SPR; Stringency control; Thermodiscrimination