Petr M. Ponomarenko

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The following hypothesis has been proposed: IF an SNP can significantly increase the expression of an oncogene by increasing the affinity of the TATA-binding protein (TBP) to its promoter, THEN this SNP can also reduce the apparent bioactivity of inhibitors of this oncogene during antitumor chemotherapy and vice versa. In the context of this hypothesis, the(More)
The TATA-binding protein (TBP) is the subunit of basal transcription factor TFIID that recognizes the TATA boxes of TATA-containing promoters in class II genes, binds to them, and starts the assemblage of the RNA polymerase II basal transcription complex. The sequence of the TATA box with its flanking regions affects the levels of basal and activated(More)
We examined six regulatory SNPs (Single Nucleotide Polymorphisms) of two human genes, APC and MLH1 (rs75996864, rs76241113, rs78037487, rs80112297, rs80313086, and rs1800734), using the previously developed rSNP_Guide technology to calculate the significance of the changes in the binding of the SNP region to a set of 40 transcription factors. For each SNP,(More)
TATA-binding protein (TBP) is the first basal factor that recognizes and binds a TATA box on TATA-containing gene promoters transcribed by RNA polymerase II. Data available in the literature are indicative of admissible variability of the TATA box. The TATA box flanking sequences can influence TBP affinity as well as the level of basal and activated(More)
Mature miRNA of 20-24 nt in length are the endogenous sncRNA. They programs RISC to regulate functioning of mRNA with complimentary sites for these miRNAs. In case of Ago3 protein present in human RISC miRNAs direct inhibition of translation, whereas in case of Ago2 is in RISC, than mRNA cleavage in the middle of miRNA/mRNA heteroduplex is also possible.(More)
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variability in humans. Hereditary disorders in the hemoglobin synthesis caused by SNPs in the TATA boxes of the human β-globin gene promoter are associated with β-thalassemia of varying severity. The TATA-binding protein (TBP) is the first basal transcription factor that recognizes(More)
Among the main events of transcription initiation of TATA-containing genes in eukayotes are the recognition and binding of the TATA-box by the TATA-binding protein (TBP) to start the preinitiation complex formation on the nucleosomal DNA. Using the equilibrium equation for step-by-step TBP/TATA-binding, we have analyzed 69 experimental datasets on the(More)
We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1(More)
Single-nucleotide polymorphisms (SNPs) in the regulatory regions of human genes and, in particular, TATA boxes can alter the sensitivity to bacterial and viral infections and to drugs used for their treatment. These SNPs are associated with the risk of widespread multifactorial human diseases, such as arthritis, hypertension, cancer, Alzheimer’s disease,(More)