研究目的
To develop a new sensing platform for monitoring protein-ligand interaction and detecting protein activity based on binding-mediated DNA protection and the dsDNA-lighted fluorophore EBCB.
研究成果
The proposed strategy effectively monitors protein-ligand interaction and protein activity with high selectivity and sensitivity. It can be applied to detect protein denaturation and has potential for use in complex samples. EBCB shows promise for broader applications in biochemical sensing and imaging.
研究不足
The method may be limited by the specificity of the protein-ligand pair used (e.g., streptavidin-biotin) and potential interference in complex samples. Optimization of conditions is required for different systems, and the approach relies on enzymatic activity, which could be affected by environmental factors.
1:Experimental Design and Method Selection:
The study uses a fluorescence-based sensing platform where a hairpin DNA probe labeled with a ligand (e.g., biotin) binds to a target protein (e.g., streptavidin), protecting the DNA from exonuclease III digestion. The dsDNA-lighted fluorophore EBCB is used to detect conformational changes in DNA via fluorescence changes.
2:Sample Selection and Data Sources:
DNA sequences were purchased from Sangon Biotech Co., Ltd. Proteins such as streptavidin, bovine serum albumin, prostate-specific antigen, and human serum albumin were used. EBCB was synthesized as previously reported.
3:List of Experimental Equipment and Materials:
Equipment includes a PTI ASOC-10 fluorospectrophotometer for fluorescence measurements, a Millipore purification system for ultrapure water, and a ChemiDoc XRS+ imaging system for gel electrophoresis. Materials include DNA probes, EBCB, exonuclease III, proteins, and buffers.
4:Experimental Procedures and Operational Workflow:
Steps involve incubating DNA with proteins and Exo III, adding EBCB, and measuring fluorescence. Gel electrophoresis was used to confirm DNA protection. Conditions like EBCB concentration, temperature, Exo III amount, and digestion time were optimized.
5:Data Analysis Methods:
Fluorescence spectra were analyzed using the fluorospectrophotometer. Data were plotted to establish linear ranges and detection limits. Statistical analysis included calculating recovery rates for spiked samples.
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PTI ASOC-10 fluorospectrophotometer
ASOC-10
Photo Technology International
Used for performing fluorescence spectra measurements.
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Millipore purification system
Millipore
Used to produce ultrapure water with 18.2 MΩ resistivity.
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ChemiDoc XRS+ imaging system
XRS+
Bio-RAD
Used for visualizing gel electrophoresis results.
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Exonuclease III
Fermentas
Used to hydrolyze nucleotides from the 3?-terminus of dsDNA.
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DNA sequences
Sangon Biotech
Used as probes in the experiments.
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EBCB
Used as a dsDNA-lighted fluorophore for fluorescence detection.
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Proteins (SA, BSA, PSA, HSA)
Dingguo Biotech
Used as target and control proteins in interaction studies.
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DMEM
Sigma-Aldrich
Used as a complex fluid sample for spiking and recovery tests.
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