Data on G-quadruplex topology, and binding ability of G-quadruplex forming sequences found in the promoter region of biomarker proteins and those relations to the presence of nuclear localization signal in the proteins

Aptamer is a nucleic acid ligand which specifically binds to its target molecule. It is typically obtained by an in vitro screening process called SELEX (Sequential Evolution of Ligands by Exponential Enrichment) [1, 2]. However, it sometimes fails to obtain aptamers because of PCR bias [3, 4] and the limited diversity of the random library [5]. To overcome the problems, we previously designed a SELEX-free aptamer identification method called “G-quadruplex (G4) promoter-derived aptamer selection (G4PAS)” [6]. In G4PAS procedure, putative G4 forming sequences (PQS) were explored in a promoter region of a target biomarker protein in human genomic DNA through computational analysis, and the identified DNA sequences were characterized as aptamer candidates towards the gene product encoded in the downstream of the promoter. As the characterization, the identified PQSs were chemically synthesized, and the binding ability was investigated by surface plasmon resonance (SPR) measurement and gel-shift assay. Also, the G4 topology of the obtained PQSs was investigated by circular dichroism measurement. Additionally, the presence of nuclear localization signal in the target protein was predicted in silico using web tools (NLSdb [7] and cNLS Mapper [8]). This data set summarized all the DNA sequences of PQSs, the dissociation constant (KD) obtained by SPR measurement, the results of gel-shift assay, and the results of nuclear localization signal prediction to address the possibility of binding of these PQS region to the target proteins in vivo. Those data should contribute to increase the success rate of G4PAS. Moreover, considering the G4 motifs in genomic DNA are suggested to be involved in in vivo gene regulation [9, 10], this data set is also potentially beneficial for the cell biology field. [1] C. Tuerk, L. Gold L, Science 249 (1990) 505–510. [2] A.D. Ellington, J.W. Szostak, Nature 346 (1990) 818–822. [3] M. Polz, C. Cavanaugh, Applied and Environmental Microbiology 64 (1998) 3724–3730. [4] T. Kanagawa, Journal of Bioscience and Bioengineering 96 (2003) 317–323. [5] S.J. Klug, M. Famulok, Molecular Biology Reports 20 (1994) 97–107. [6] W. Yoshida, T. Saito, T. Yokoyama, S. Ferri, K. Ikebukuro, PLoS ONE, 8 (2013) e65497. [7] R. Nair, P. Carter, B. Rost, Nucleic acids research 31 (2003) 397-399. [8] S. Kosugi, M. Hasebe, M. Tomita, H. Yanagawa, Proceedings of the National Academy of Sciences of the United States of America, 106 (2009) 10171-10176 [9] H. J. Lipps, D. Rhodes, Trends in Cell Biology, 19 (2009) 414-422. [10] D. Varshney, J. Spiegel, K. Zyner, D. Tannahill, S. Balasubramanian. Nature Reviews Molecular Cell Biology, 21 (2020) 259-474.