Evaluation of the binding of natural products with thrombin binding aptamer G-quadruplex using electrospray ionization mass spectrometry and spectroscopic methods

Screening Aptamers that Are Specific for Beclomethasone and the Development of Quantum Dot-Based Assay

We developed an aptamer that was specific for beclomethasone (BEC) via systematic evolution of ligands by exponential enrichment (SELEX). Development was monitored by real-time quantitative PCR (Q-PCR) and the enriched library was sequenced by high-throughput sequencing. Forty-seven aptamer candidates were obtained; of these, BEC-6 showed the highest affinity (Kd = 0.15 ± 0.02 μM) and did not cross-react with other BEC analogs. We also developed a quantum dot-based assay (QDA) for the detection of BEC that was based upon a quantum dot (QD) composite probe. Under optimized reaction conditions, the linear range of this method for BEC was 0.1 to 10 μM with a low detection limit (LOD) of 0.1 μM. Subsequently, the method was used to detect BEC in Traditional Chinese Medicine (TCM) with a mean recovery of 81.72-91.84%. This is the first report to describe the development of an aptamer against BEC; BEC-6 can also be engineered into QDA for the detection of BEC.

Quantitative characterization of human oncogene promoter G-quadruplex DNA-ligand interactions using a combination of mass spectrometry and capillary electrophoresis

Human c-KIT oncogene is known to regulate cell growth and proliferation, and thus, acts as a probable target in the treatment of gastrointestinal tumors (GIST). To identify small molecule ligands which can specifically bind with the G-quadruplex (G4) in the c-KIT promoter region as potential antitumor agents, we propose the combination of electrospray ionization-mass spectrometry (ESI-MS), capillary electrophoresis frontal analysis (CE-FA), and Taylor dispersion analysis (TDA) to accurately investigate the G4/ligands binding properties. First, ESI-MS was used for initial screening of natural products (NPs). CE-FA was then used to calculate specific binding constants and the stoichiometry of the native state binding pair in solution. Next, TDA, a micro-capillary flow technique was used to examine the effect of the ligand binding on the diffusivity and particle size of the c-KIT G4. Two of the screened NPs, scopolamine butylbromide (L1) and isorhamnetin-3-O-neohesperidoside (L3), were found to specifically bind to the c-KIT G4 with binding constants of around 10⁴ M^-1 and 1:1 stoichiometry in a free solution. TDA data showed that ligand binding (both L1 and L3) induced the c-KIT strands to fold into a tightly structured G4 with a decreased hydrodynamic radius. These ligands have the potential to be drug candidates for the regulation of c-KIT gene transcription by stabilizing the G4 structure. This methodology not only increased the speed of analysis but also improved its accuracy and specificity compared with the conventional binding approaches.

Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches

Elucidating the recognition mechanisms of the noncovalent interactions between pharmaceutical molecules and proteins is important for understanding drug delivery in vivo, and for the further rapid screening of clinical drug candidates and biomarkers. In this work, a strategy based on cold spray ionization mass spectrometry (CSI-MS), combined with fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and molecular docking methods, was developed and applied to the study of the noncovalent interactions between phenolic acid and lysozyme (Lys). Based on the real characterization of noncovalent complex, the detailed binding parameters, as well as the protein conformational changes and specific binding sites could be obtained. CSI-MS and tandem mass spectrometry (MS/MS) technique were used to investigate the phenolic acid-Lys complexes and the structure-affinity relationship, and to assess their structural composition and gas phase stability. The binding affinity was obtained by direct and indirect MS methods. The fluorescence spectra showed that the intrinsic fluorescence quenching of Lys in solution was a static quenching mechanism caused by complex formation, which supported the MS results. The CD and FTIR spectra revealed that phenolic acid changed the secondary structure of Lys and increased the α-helix content, indicating an increase in the tryptophan (W) hydrophobicity near the protein binding site resulting in a conformational alteration of the protein. In addition, molecular docking studies were performed to investigate the binding sites and binding modes of phenolic acid on Lys. This strategy can more comprehensively and truly characterize the noncovalent interactions and can guide further research on the interactions of phenolic acid with other proteins.

An ultrasensitive electrochemical sensing method for detection of microcystin-LR based on infinity-shaped DNA structure using double aptamer and terminal deoxynucleotidyl transferase

This study develops a novel electrochemical sensing platform for microcystin-LR (MC-LR) detection. This aptasensor comprises the hybridization of double aptamer to its complementary strand (CS) on the surface of electrode and generation of an Infinity-shaped DNA structure in the absence of target by terminal deoxynucleotidyl transferase (TdT). The formation of Infinity-shaped construction leads to the development of an ultrasensitive aptasensor for MC-LR detection. In the presence of MC-LR, double aptamer is dissociated from its CS because of its high affinity for MC-LR and leaves the surface of electrode. Subsequently, no Infinity-shaped structure is formed following the introduction of TdT and a strong current signal is observed. The proposed method was employed for specific detection of MC-LR in the range from 60 pM to 1000 nM with a detection limit of 15 pM. The credibility of the approach was confirmed by detection of MC-LR in real samples like serum and tap water samples. This study provides a new aptasensor for detection of MC-LR as well as other toxin analysis.