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. Previously, we have designed an identification method of aptamer called “G-quadruplex (G4) promoter-derived aptamer selection (G4PAS)” . In G4PAS procedure, putative G4 forming sequences (PQS) were explored in a promoter region of a target protein in human gene through computational analysis, and evaluated binding ability towards the gene product encoded in the downstream of the promoter. We investigated the topology of the obtained PQSs by circular dichroism measurement, as well as their binding ability against its target protein by surface plasmon resonance measurement and gel-shift assay. Additionally, the presence of nuclear localization signal in the target protein was predicted in silico. This data set summarized all the PQS sequences, these biochemical characteristics, and the presence of nuclear localization signal to address the possibility of binding of these PQS region to the target proteins in vivo. hese data should contribute to increase the success rate of G4PAS, and potentially beneficial for the cell biology field as G4 is supposed to participate in vivo gene regulation.  W. Yoshida, T. Saito, T. Yokoyama, S. Ferri, K. Ikebukuro, Aptamer selection based on G4-forming promoter region. PLoS ONE, 8(6) (2013) e65497. http://doi.org/10.1371/journal.pone.0065497
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Known biomarker proteins were chosen as the target, and G-quadruplex-forming DNA sequences were picked up from a genomic region around the transcription start site of the proteins the criterion of G2 < N1-7G2 < N1-7G2 < N1-7 G2 <, where “G” is guanine base and “N” can be any bases. The binding between the DNA sequences towards the target protein, and the topology of the G-quadruplex-structure were performed with or without 100 mM KCl in Tris-based buffer (pH 7.4) at 25 °C. The search of G-quadruplex-forming sequence in genomic DNA, and the nuclear localization signal prediction in the target proteins were performed by web tools (NLSDB and cNLS Mapper). The binding between the G-quadruplex-forming DNA and the target proteins was investigated by gel shift assay, surface plasmon resonance measurement. The topology of G-quadruplex-forming sequence was analyzed by Circular dichroism spectroscopy.