The analysis of data on genomic DNA sequences in the binding sites of human ribosomal protein uS3 in vivo, obtained earlier by ChIP-Seq method, was carried out; the presence of significant content of TGGAA repeats, belonging to the type III of human satellites, was found. The dependence of the affinity of the corresponding recombinant protein uS3 to single-stranded DNA and its AP lyase activity on the DNA sequence in vitro, in particular on the presence of TGGAA pentamer repeats, was investigated. It was shown that the presence of these repeats in the model DNAs did not provide an increased affinity to the isolated ribosomal protein uS3. The presence of TCC and TTC motifs in DNA complementary to the corresponding pentamer triplets only slightly increased the affinity of DNA to this protein. It was established that the AP lyase activity of the uS3 protein was also not increased when DNA containing abasic (AP) site contained TGGAA repeats and was independent on the position of the AP site in it. It was shown that the efficiency of single-stranded DNA cleavage at the AP site as a whole correlated with the affinity of uS3 protein to this DNA. It was concluded that the high content of the above repeats in the ribosomal protein uS3 binding sites on chromatin relate to high content of (TGGAA)n repeats in single-stranded DNA regions physically accessible for the protein binding but not to its higher affinity to the pentamer or DNA motifs complementary to it.
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Ochkasova, A.S., Kabilov, M.R., Karpova, G.G. et al. Exploring the Interaction of Human Ribosomal Protein uS3 with Single-Stranded DNAs Having Different Sequences. Russ J Bioorg Chem 45, 619–624 (2019). https://doi.org/10.1134/S106816201906030X
- ribosomal uS3 protein
- single-stranded DNA
- protein binding to DNA
- abasic site in DNA
- AP lyase activity
- satellite DNA