Volume 12, June 2017, Pages 351–357

Open Access
Data Article

Synthesis of practical red fluorescent probe for cytoplasmic calcium ions with greatly improved cell-membrane permeability

  • a Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
  • b Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
  • c Drug Discovery Initiative, The University of Tokyo, Tokyo 113-0033, Japan
  • d Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
  • e CREST, AMED, Saitama 332-0012, Japan

Abstract

In this data article, we described the detailed synthetic procedure and the experimental data for the synthesis of a red-fluorescent probe for calcium ions (Ca2+) with improved water solubility. This Ca2+ red-fluorescent probe CaTM-3 AM could be applied to fluorescence imaging of physiological Ca2+ concentration changes in not only live cells, but also brain slices, with high cell-membrane permeability leading to bright fluorescence in biosamples. The data provided herein are in association with the research article “The Development of Practical Red Fluorescent Probe for Cytoplasmic Calcium Ions with Greatly Improved Cell-membrane Permeability” in Cell Calcium (Hirabayashi et al., 2016) [1].

Specifications table

Subject areaChemistry
More specific subject areaSynthesis of fluorescent probes
Type of dataSynthetic schemes, experimental synthesis protocols, NMR and MS spectra, HPLC chromatogram
How data was acquiredNMR: JNM-LA300 (JEOL) or JNM-LA400 (JEOL), mass spectroscopy: JMS-T100LC AccuTOF (JEOL), HPLC analyses: Inertsil ODS-3 (4.6 ×250 mm) column (GL Sciences Inc.) using a HPLC system composed of a pump (PU-2080, JASCO) and a detector (MD-2018 or FP-2025, JASCO)
Data formatAnalyzed
Experimental factorsStarting compounds were either purchased or synthesized using already published synthetic protocols
Experimental featuresCompounds were synthesized and their structures were identified by NMR and mass spectrometry
Data source locationTokyo, Japan
Data accessibilityData are provided with this article
Full-size table

Value of the data

The data allows to reproduce the experiments described in the research article Ref. [1].

The synthesized compound, CaTM-3 AM, could be used to fluorescence imaging of the physiological Ca2+ concentration change.

The data provides an opportunity to synthesize red fluorescent probes based on TokyoMagenta (TM) derivatives.

1. Data

NMR spectra were recorded on a JEOL JNM-LA300 instrument at 300 MHz for 1H NMR and at 75 MHz for 13C NMR or JEOL JNM-LA400 instrument at 100 MHz for 13C NMR. Mass spectra (ESI+) were measured with a JEOL JMS-T100LC AccuTOF for ESI. HPLC analyses were performed on an Inertsil ODS-3 (4.6×250 mm) column (GL Sciences Inc.) using a HPLC system composed of a pump (PU-2080, JASCO) and a detector (MD-2018 or FP-2025, JASCO).

2. Experimental design, materials and methods

2.1. Synthetic materials and instrumentation

General chemicals were of the best grade available, supplied by Tokyo Chemical Industries, Wako Pure Chemical, Aldrich Chemical Co., Kanto Chemical Co., Inc., Toronto Research Chemicals Inc., Watanabe Chemical Industries, Applied Biosystems, Dojindo and Invitrogen Corp., and were used without further purification. All solvents were used after appropriate distillation or purification. Preparative HPLC were performed on an Inertsil ODS-3 (10×250 mm) column (GL Sciences Inc.) using a HPLC system composed of a pump (PU-2080, JASCO) and a detector (MD-2015 or FP-2025, JASCO) or a HPLC system composed of a pump (PU-2086, JASCO) and a detector (MD-2018, JASCO).

2.2. Synthesis and characterization of compounds

2.2.1. Synthesis of compound 1

This compound was synthesized according to Ref. [2].