Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor

Design single-stranded DNA aptamer of cluster of differentiation 47 protein by stochastic tunnelling-basin hopping-discrete molecular dynamics method

The formation of the Cluster of Differentiation 47 (CD47, PDB code: 2JJT)/signal regulatory protein α (SIRPα) complex is very important as it protects healthy cells from immune clearance while promoting macrophage phagocytosis for tumour elimination. Although several antibodies have been developed for cancer therapy, new function-blocking aptamers are still under development. This study aims to design the aptamer AptCD47, which can block the formation of the CD47/SIRPα complex. This study employs the MARTINI coarse-grained (CG) force field and the stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method to identify the most stable AptCD47/CD47 complexes. Coarse-grained molecular dynamics (CGMD) simulations were used to obtain root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses. The results demonstrate that the formation of AptCD47/CD47 complexes renders the CD47 structure more stable than the single CD47 molecule in a water environment. The minimum energy pathway (MEP) obtained by the nudged elastic band (NEB) method indicates that the binding processes of 5'-ATTCAATTCC-3' and 5'-AGTGCAATCT-3' to CD47 are barrierless, which is much lower than the binding barrier of SIRPα to CD47 of about 14.23 kcal/mol. Therefore, these two AptCD47/CD47 complexes can create a high spatial binding barrier for SIRPα, preventing the formation of a stable CD47/SIRPα complex. The proposed numerical process with the MARTINI CG force field can be used to design CD47 aptamers that efficiently block SIRPα from binding to CD47.Communicated by Ramaswamy H. Sarma.

Design the RNA aptamer of PCA3 long non-coding ribonucleic acid by the coarse-grained molecular mechanics

The stochastic tunneling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to predict the tertiary structure of the prostate cancer marker PCA3 using two respective secondary structures predicted by the Vienna RNA package and Mathews lab package. The RNA CG force field with the geometrical restraints for maintaining PCA3 secondary structures is used. For each secondary structure, 5000 PCA3 structures were predicted by using 5000 independent initial structures. These structures were then evaluated by a scoring function, considering the contributions from the radius of gyration, contact energy, and surface fraction of complementary nucleotides to ASO683 and ASO735 used in the related experiment. For each secondary structure, the PCA3 structures with the highest three scores were selected for aptamer design and further adsorption simulation. The ASOs complementary to PCA3 surface segments possessing relatively higher RMSF values are selected to be the potential PCA3 aptamers. After the adsorption simulation, the adsorption energies of ASO961, ASO3181, ASO3533, and ASO3595 are higher than or comparable to those of ASO683 and ASO735 used in the experiment. The NEB method was used to obtain MEPs for the adsorption process of all predicted ASOs onto PCA3. The adsorption barriers range between 29 ∼ 39 kcal/mol, while the desorption barriers range between 112 ∼ 352 kcal/mol, indicating these aptamer/PCA3 complexes are very stable. Using PCA3 surface segments with relatively higher RMSF values, longer ASOs can be also obtained and most longer ASOs possess lower binding energy, ranging between -486.1 and -618.2 kcal/mol.Communicated by Ramaswamy H. Sarma.

Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (Apt_EpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the Apt_EpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the Apt_EpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For Apt_EpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each Apt_EpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable Apt_EpA/EpCAM complex in water.

A review: Recent advances in ultrasensitive and highly specific recognition aptasensors with various detection strategies

One of the most studied topics in analytical chemistry and physics is to develop bio-sensors. Aptamers are small single-stranded RNA or DNA oligonucleotides (5-25 kDa), which have advantages in comparison to their antibodies such as physicochemical stability and high binding specificity. They are able to integrate with proteins or small molecules, including intact viral particles, plant lectins, gene-regulation factor, growth factors, antibodies and enzymes. The aptamers have reportedly shown some unique characteristics, including long shelf-life, simple modification to provide covalent bonds to material surfaces, minor batch variation, cost-effectiveness and slight denaturation susceptibility. These features led important efforts toward the development of aptamer-based sensors, known as apta-sensors classified into optical, electrical and mass-sensitive based on the signal transduction mode. This review provided a number of current advancements in selecting, development criteria, and aptamers application with the focus on the effect of apta-sensors, specifically for disease-associated analyses. The review concentrated on the current reports of apta-sensors that are used for evaluating different food and environmental pollutants.

Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications-The Role of Molecular Dynamics Simulation

Theranostics cover emerging technologies for cell biomarking for disease diagnosis and targeted introduction of drug ingredients to specific malignant sites. Theranostics development has become a significant biomedical research endeavor for effective diagnosis and treatment of diseases, especially cancer. An efficient biomarking and targeted delivery strategy for theranostic applications requires effective molecular coupling of binding ligands with high affinities to specific receptors on the cancer cell surface. Bioaffinity offers a unique mechanism to bind specific target and receptor molecules from a range of non-targets. The binding efficacy depends on the specificity of the affinity ligand toward the target molecule even at low concentrations. Aptamers are fragments of genetic materials, peptides, or oligonucleotides which possess enhanced specificity in targeting desired cell surface receptor molecules. Aptamer-target binding results from several inter-molecular interactions including hydrogen bond formation, aromatic stacking of flat moieties, hydrophobic interaction, electrostatic, and van der Waals interactions. Advancements in Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has created the opportunity to artificially generate aptamers that specifically bind to desired cancer and tumor surface receptors with high affinities. This article discusses the potential application of molecular dynamics (MD) simulation to advance aptamer-mediated receptor targeting in targeted cancer therapy. MD simulation offers real-time analysis of the molecular drivers of the aptamer-receptor binding and generate optimal receptor binding conditions for theranostic applications. The article also provides an overview of different cancer types with focus on receptor biomarking and targeted treatment approaches, conventional molecular probes, and aptamers that have been explored for cancer cells targeting.

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods

The terephthalic acid (TPA) supramolecular growth mechanisms on the stearic acid (STA) buffer layer, such as the phase separation and layer-by-layer (LBL) mechanisms, were considered by molecular simulations.

Investigation of the interaction between split aptamer and vascular endothelial growth factor 165 using single molecule force spectroscopy

Understanding the binding of split aptamer/its target could become a breakthrough in the application of split aptamer. Herein, vascular endothelial growth factor (VEGF), a major biomarker of human diseases, was used as a model, and its interaction with split aptamer was explored with single molecule force spectroscopy (SMFS). SMFS demonstrated that the interaction force of split aptamer/VEGF₁₆₅ was 169.44 ± 6.59 pN at the loading rate of 35.2 nN/s, and the binding probability of split aptamer/VEGF₁₆₅ was dependent on the concentration of VEGF₁₆₅ . On the basis of dynamic force spectroscopy results, one activation barrier in the dissociation process of split aptamer/VEGF₁₆₅ complexes was revealed, which was similar to that of the intact aptamer/VEGF₁₆₅ . Besides, the dissociation rate constant (k_off ) of split aptamer/VEGF₁₆₅ was close to that of intact aptamer/VEGF₁₆₅ , and the interaction force of split aptamer/VEGF₁₆₅ was higher than the force of intact aptamer/VEGF₁₆₅ . It indicated that split aptamer also possessed high affinity with VEGF₁₆₅ . The work can provide a new method for exploring the interaction of split aptamer/its targets at single-molecule level.

Predicting the Most Stable Aptamer/Target Molecule Complex Configuration Using a Stochastic-Tunnelling Basin-Hopping Discrete Molecular Dynamics Method: A Novel Global Minimum Search Method for a Biomolecule Complex

This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling-basin hopping (STUN-BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (Apt_EpA). For the most stable Apt_EpA/EpCAM complex predicted by our new method, the Apt_EpA was attached to the entangling loop fragments of the two EpCAM molecules with the most Apt_EpA residues. After the Apt_EpA/EpCAM complex had equilibrated with the water environment through a molecular dynamics simulation at 300 K for 10 ns, stable hydrogen bonds formed between the bases of Apt_EpA and EpCAM residues of the secondary structures, which included the alpha helix and beta sheet becoming less stable in the water environment. Those hydrogen bonds formed between the bases of Apt_EpA and EpCAM loop fragment residues remained stable in the water environment.

A signal-on nanobiosensor for VEGF165 detection based on supraparticle copper nanoclusters formed on bivalent aptamer

In this study, a signal-on nanobiosensor based on bivalent aptamer-Cu nanocluster was designed and optimized for specific and sensitive detection of VEGF₁₆₅. The VEGF₁₆₅ is known as a promising biomarker in different diseases such as cancer in the angiogenic stage. Detection and quantification of VEGF₁₆₅ is a crucial step in diagnosis and monitoring the treatment plan. The represented nanostructure consists of multimerized VEGF₁₆₅ aptamer joint with ssDNA based linker in the middle and poly thymine sequences on both 3' and 5' ends as a template for Cu-nanocluster supraparticle formation. This self-assembled structure leads to accurate controlling of aggregation in the presence of VEGF₁₆₅. This study is the first report for Cu nanocluster nucleation on ploy thymine tails of ssDNA which performed in two reduction steps to form stable CuNC supraparticle. The sensing strategy was designed based on the target-induced structure switching mode of the aptamer. In the presence of VEGF₁₆₅, due to self-assembly induced emission and aggregation-induced emission phenomena this nanostructure depicted the visible wavelength shift and enhancement in the fluorescence emission intensity. Also, the results of the analytical performance of this nanobiosensor indicated the LOD of 12 pM which revealed high rate sensitivity. This aptasensor exhibited stability and decent response linearity range (10-800 pM, R² = 0.9943). The selectivity and specificity assessment showed high discriminant capability in the real serum sample. In conclusion, this signal-on nanobiosensor provides a facile, sensitive and reliable assay for clinical monitoring of the VEGF₁₆₅ concentration in serum without further sample preparation.