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Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S., Podkolodny, N.L., Savinkova, L.K., Kolchanov, N.A. and Overton, G.C. (1999) Identification of sequence dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics, 15, 687-703. doi:10.1093/bioinformatics/15.7.687

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• TITLE: In vitro examining the existing prognoses how TBP binds to TATA with SNP associated with human diseases

  AUTHORS: Irina A. Drachkova, Petr M. Ponomarenko, Tatyana V. Arshinova, Мikhail P. Ponomarenko, Valentin V. Suslov, Ludmila K. Savinkova, Nikolay А. Kolchanov

  KEYWORDS: Disease; Polymorphism; ТАТА Box; TATA-Binding Protein; Affinity; In Vitro; In Silico

  JOURNAL NAME: Health, Vol.3 No.9, September 23, 2011

  ABSTRACT: We in vitro examined the existing prognoses of the dissociation constant, KD, between ТАТА- Binding Protein (TBP) and ТАТА box with single nucleotide polymorphism (SNP) associated with human diseases. Five SNPs of the genes for cytochrome P450 2A6 (associated with lung cancer), β-globin (associated with β-thalassemia), mannose binding lectin (associated with variable immunodeficiency), superoxide dismutase 1 (associated with amyotrophic lateral sclerosis) and triosephosphate isomerase (associated with anemia) fell within the range of –ln(KD;M/KD;WT) between –1.5 and –1 (here KD;WT and KD;M denote the normal ТАТА box and with SNP). The mea-surements using EMSA demonstrated that: 1) all the predictions stating that the affinity between ТВР and ТАТА boxes with SNPs would be reduced were correct; 2) the departures of three predictions from the measurements fell within the confidence interval; 3) all the predictions consistently underestimated actual mutational damage caused to ТАТА boxes with SNPs (a