A Facile Combinatorial Approach to Construct a Ratiometric Fluorescent Sensor: Application for the Real-time Sensing of Cellular PH Changes

Overview

Journal Chem Sci

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2021 Jul 1

PMID 34194714

Citations 2

Authors

Eiji Nakata

Hisaaki Hirose

Khongorzul Gerelbaatar

Jan Vincent V Arafiles

Zhengxiao Zhang

Shiroh Futaki

Takashi Morii

Affiliations

Soon will be listed here.

Abstract

Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.

Citing Articles

Controlled Assembly of Fluorophores inside a Nanoliposome.

Konishi H, Nakata E, Komatsubara F, Morii T Molecules. 2023; 28(2).

PMID: 36677968 PMC: 9864194. DOI: 10.3390/molecules28020911.

Fully Automated Computational Approach for Precisely Measuring Organelle Acidification with Optical pH Sensors.

Chandra A, Prasad S, Alemanno F, De Luca M, Rizzo R, Romano R ACS Appl Mater Interfaces. 2022; 14(16):18133-18149.

PMID: 35404562 PMC: 9052195. DOI: 10.1021/acsami.2c00389.

References

Lavis L, Raines R . Bright ideas for chemical biology. ACS Chem Biol. 2008; 3(3):142-55. PMC: 2802578. DOI: 10.1021/cb700248m. View

Yuan L, Lin W, Zheng K, Zhu S . FRET-based small-molecule fluorescent probes: rational design and bioimaging applications. Acc Chem Res. 2013; 46(7):1462-73. DOI: 10.1021/ar300273v. View

Weiss S . Shattering the diffraction limit of light: a revolution in fluorescence microscopy?. Proc Natl Acad Sci U S A. 2000; 97(16):8747-9. PMC: 34005. DOI: 10.1073/pnas.97.16.8747. View

Zhang X, Lin Y, Gillies R . Tumor pH and its measurement. J Nucl Med. 2010; 51(8):1167-70. PMC: 4351768. DOI: 10.2967/jnumed.109.068981. View

Huang X, Song J, Yung B, Huang X, Xiong Y, Chen X . Ratiometric optical nanoprobes enable accurate molecular detection and imaging. Chem Soc Rev. 2018; 47(8):2873-2920. PMC: 5926823. DOI: 10.1039/C7CS00612H. View

Demchenko A . The concept of λ-ratiometry in fluorescence sensing and imaging. J Fluoresc. 2010; 20(5):1099-128. DOI: 10.1007/s10895-010-0644-y. View

Modi S, M G S, Goswami D, Gupta G, Mayor S, Krishnan Y . A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat Nanotechnol. 2009; 4(5):325-30. DOI: 10.1038/nnano.2009.83. View

Rothemund P . Folding DNA to create nanoscale shapes and patterns. Nature. 2006; 440(7082):297-302. DOI: 10.1038/nature04586. View

Hell S . Toward fluorescence nanoscopy. Nat Biotechnol. 2003; 21(11):1347-55. DOI: 10.1038/nbt895. View

10.

Jun J, Chenoweth D, Petersson E . Rational design of small molecule fluorescent probes for biological applications. Org Biomol Chem. 2020; 18(30):5747-5763. PMC: 7453994. DOI: 10.1039/d0ob01131b. View

11.

Linko V, Nummelin S, Aarnos L, Tapio K, Toppari J, Kostiainen M . DNA-Based Enzyme Reactors and Systems. Nanomaterials (Basel). 2017; 6(8). PMC: 5224616. DOI: 10.3390/nano6080139. View

12.

Demchenko A . Optimization of fluorescence response in the design of molecular biosensors. Anal Biochem. 2005; 343(1):1-22. DOI: 10.1016/j.ab.2004.11.041. View

13.

Han J, Burgess K . Fluorescent indicators for intracellular pH. Chem Rev. 2009; 110(5):2709-28. DOI: 10.1021/cr900249z. View

14.

Sigaeva A, Ong Y, Damle V, Morita A, van der Laan K, Schirhagl R . Optical Detection of Intracellular Quantities Using Nanoscale Technologies. Acc Chem Res. 2019; 52(7):1739-1749. PMC: 6639779. DOI: 10.1021/acs.accounts.9b00102. View

15.

Steinegger A, Wolfbeis O, Borisov S . Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications. Chem Rev. 2020; 120(22):12357-12489. PMC: 7705895. DOI: 10.1021/acs.chemrev.0c00451. View

16.

Yue Y, Huo F, Lee S, Yin C, Yoon J . A review: the trend of progress about pH probes in cell application in recent years. Analyst. 2016; 142(1):30-41. DOI: 10.1039/c6an01942k. View

17.

Kolanowski J, Liu F, New E . Fluorescent probes for the simultaneous detection of multiple analytes in biology. Chem Soc Rev. 2017; 47(1):195-208. DOI: 10.1039/c7cs00528h. View

18.

Arafiles J, Hirose H, Akishiba M, Tsuji S, Imanishi M, Futaki S . Stimulating Macropinocytosis for Intracellular Nucleic Acid and Protein Delivery: A Combined Strategy with Membrane-Lytic Peptides To Facilitate Endosomal Escape. Bioconjug Chem. 2020; 31(3):547-553. DOI: 10.1021/acs.bioconjchem.0c00064. View

19.

Kobayashi H, Ogawa M, Alford R, Choyke P, Urano Y . New strategies for fluorescent probe design in medical diagnostic imaging. Chem Rev. 2009; 110(5):2620-40. PMC: 3241938. DOI: 10.1021/cr900263j. View

20.

Brahimi-Horn M, Pouyssegur J . Oxygen, a source of life and stress. FEBS Lett. 2007; 581(19):3582-91. DOI: 10.1016/j.febslet.2007.06.018. View