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Simulation and experimental study of fluorescence labeled polyphosphate in microthrix parvicella
Xuening Fei1, Weigang Li2, Cuihong Wang2
1School of Science, TianJin ChengJian University, Tianjin, China; Tianjian Engineering Technology Center of Chemical Waste-water Source Reduction and Recycling, Tianjin, China.
Journal of Molecular Graphics & Modelling
|February 2, 2021
Summary
Researchers investigated how fluorescent dyes bind to polyphosphate (Poly-P). Cy3 demonstrated superior binding and dyeing capabilities for Poly-P compared to other dyes like DAPI and Fluorescein, validated by computational and experimental methods.
Area of Science:
- Biochemistry
- Materials Science
- Analytical Chemistry
Background:
- Polyphosphate (Poly-P) is a crucial biopolymer involved in various cellular processes.
- Accurate detection and visualization of Poly-P are essential for biological and environmental studies.
- Existing fluorescent dyes may have limitations in specificity and sensitivity for Poly-P detection.
Purpose of the Study:
- To elucidate the binding mechanism between 4',6-diamidino-2-phenylindole (DAPI) and Poly-P.
- To identify superior fluorescent dyes for Poly-P detection and visualization.
- To explore structure-activity relationships for fluorescent dye-Poly-P interactions.
Main Methods:
- Computational modeling using the self-consistent-charge, density functional tight-binding (SCC-DFTB-D) method to analyze DAPI-Poly-P interactions.
- Analysis of binding energies and frontier orbital properties for DAPI, Cy3, Rhodamine 6G, and Fluorescein with Poly-P.
- Experimental validation using activated sludge smears to assess the dyeing performance of the selected fluorescent dyes.
Main Results:
- The N-containing indole ring in DAPI is critical for its interaction with Poly-P.
- Binding energies indicate stronger interactions for Cy3 (-165.4 kcal/mol) and Rhodamine 6G (-34.7 kcal/mol) with Poly-P compared to DAPI (-42.6 kcal/mol) and Fluorescein (-28.9 kcal/mol).
- Experimental results confirmed Cy3 as an effective dye for Poly-P, showing excellent dyeing and recognition capabilities, while Fluorescein showed no such effect.
Conclusions:
- Computational simulations accurately predict the experimental performance of fluorescent dyes for Poly-P.
- Cy3 is identified as a highly effective fluorescent dye for Poly-P detection.
- This study offers a validated strategy for developing more sensitive and economical fluorescent dyes for Poly-P analysis.
