Interaction between Heavy Water and Single-Strand DNA: A SERS Study

The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental D₂O. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between D₂O and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing D₂O proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and D₂O and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and D₂O. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules.

Multiplexed SERS Detection of Microcystins with Aptamer-Driven Core-Satellite Assemblies

We describe surface-enhanced Raman spectroscopy (SERS) aptasensors that can indirectly detect MC-LR and MC-RR, individually or simultaneously, in natural water and in algal culture. The sensor is constructed from nanoparticles composed of successive layers of Au core-SERS label-silver shell-gold shell (Au@label@Ag@Au NPs), functionalized on the outer Au surface by MC-LR and/or MC-RR aptamers. These NPs are immobilized on asymmetric Au nanoflowers (AuNFs) dispersed on planar silicon substrates through DNA hybridization of the aptamers and capture DNA sequences with which the AuNFs are functionalized, thereby forming core-satellite nanostructures on the substrates. This construction led to greater electromagnetic (EM) field enhancement of the Raman label-modified region, as supported by finite-difference time-domain (FDTD) simulations of the core-satellite assembly. In the presence of MC-LR and/or MC-RR, the aptamer-functionalized NPs dissociate from the AuNFs because of the stronger affinity of the aptamers with the MCs, which decreases the SERS signal, thus allowing indirect detection of the MCs. The improved SERS sensitivity significantly decreased the limit of detection (LOD) for separate MC-LR detection (0.8 pM) and for multiplex detection (1.5 pM for MC-LR and 1.3 pM for MC-RR), compared with other recently reported SERS-based methods for MC-LR detection. The aptasensors show excellent selectivity to MC-LR/MC-RR and excellent recoveries (96-105%). The use of these SERS aptasensors to monitor MC-LR production over 1 week in a culture medium of M. aeruginosa cells demonstrates the applicability of the sensors in a realistic environment.

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

Field effect transistors (FETs) based on networks of randomly oriented Si nanowires (Si nanonets or Si NNs) were biomodified using Thrombin Binding Aptamer (TBA-15) probe with the final objective to sense thrombin by electrical detection. In this work, the impact of the biomodification on the electrical properties of the Si NN-FETs was studied. First, the results that were obtained for the optimization of the (3-Glycidyloxypropyl)trimethoxysilane (GOPS)-based biofunctionalization process by using UV radiation are reported. The biofunctionalized devices were analyzed by atomic force microscopy (AFM) and scanning transmission electron microscopy (STEM), proving that TBA-15 probes were properly grafted on the surface of the devices, and by means of epifluorescence microscopy it was possible to demonstrate that the UV-assisted GOPS-based functionalization notably improves the homogeneity of the surface DNA distribution. Later, the electrical characteristics of 80 devices were analyzed before and after the biofunctionalization process, indicating that the results are highly dependent on the experimental protocol. We found that the TBA-15 hybridization capacity with its complementary strand is time dependent and that the transfer characteristics of the Si NN-FETs obtained after the TBA-15 probe grafting are also time dependent. These results help to elucidate and define the experimental precautions that must be taken into account to fabricate reproducible devices.

Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach

This study introduces a computational method to design a new aptamer with higher binding affinity to a special target in comparison with the experimentally available aptamers. The method is called step by step mutation based on MD simulation, which includes some steps. First, MD simulation is performed for the SELEX-introduced (native) aptamer in the presence of the target. Afterwards, conformational factor (P_i) is calculated for the simulated system, which obtains the affinity of the aptamer residues to the target. A nucleotide exchange is done for the residue with the least P_i parameter to the nucleotide with the highest P_i value that results in a mutant aptamer. MD simulation is performed for the target-mutant complex, and P_i values are calculated again. The nucleotide exchange is performed similarly, and the designing process is proceeded repeatedly that results in a mutant with the improved specificity to the target. The aptamer affinity to the target is also determined in each step through calculating the binding Gibbs energy (ΔG_Bind) as a reliable parameter. The introduced strategy is utilized efficiently to design a mutant aptamer with improved specificity toward sulfadimethoxine (SDM) antibiotic as a case study. The great difference in the ΔG_Bind values about 579.856 kJ mol^-1 highlights that the M5 mutant possesses the improved specificity toward SDM in comparison with the native aptamer. Besides, the selectivity of the M5 aptamer toward SDM is examined among some conventional interfering compounds by using MD simulation that confirms the applicability of the designed aptamer for further experimental studies.

Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation

This paper provides a feasible model for molecular structure analysis and interaction mechanism of aptamer and micromolecule. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin, PTX) were performed separately. Then, the complex structure between DNA and PTX was predicted, and docking results showed that PTX could combine steadily at the groove’s top of DNA model by strong hydrogen-bonds and electrostatic interaction. Thus, we truncated and optimized P-18S2 by simulating. At the same time, we also confirmed the reliability of simulation results by experiments. With the experimental and computational results, the study provided a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX, which laid the foundation for further optimization and development of aptamers in molecular diagnostics and therapeutic applications.

The Bound Structures of 17β-Estradiol-Binding Aptamers

DNA aptamers can exhibit high affinity and selectivity towards their targets, but the aptamer-target complex structures are rarely available from crystallography and often difficult to elucidate. This is particularly true of small molecule targets, including 17β-estradiol (E2), which is becoming one of the most widely encountered endocrine-disrupting chemicals in the environment. Using molecular dynamics simulations, we demonstrate that E2 binds to a thymine loop region common to all E2-specific aptamers in the literature. Analyzing these structures allows us to design new E2 binding sequences. As well as illuminating the essential sequence and structural factors for generating specificity for E2, we demonstrate the effectiveness of molecular dynamics simulations for aptamer science.

Enzyme-linked, aptamer-based, competitive biolayer interferometry biosensor for palytoxin

In this study, we coupled biolayer interferometry (BLI) with competitive binding assay through an enzyme-linked aptamer and developed a real-time, ultra-sensitive, rapid quantitative method for detection of the marine biotoxin palytoxin. Horseradish peroxidase-labeled aptamers were used as biorecognition receptors to competitively bind with palytoxin, which was immobilized on the biosensor surface. The palytoxin: horseradish peroxidase-aptamer complex was then submerged in a 3,3'-diaminobenzidine solution, which resulted in formation of a precipitated polymeric product directly on the biosensor surface and a large change in the optical thickness of the biosensor layer. This change could obviously shift the interference pattern and generate a response profile on the BLI biosensor. The biosensor showed a broad linear range for palytoxin (200-700pg/mL) with a low detection limit (0.04pg/mL). Moreover, the biosensor was applied to the detection of palytoxin in spiked extracts and showed a high degree of selectivity for palytoxin, good reproducibility, and stability. This enzyme-linked, aptamer-based, competitive BLI biosensor offers a promising method for rapid and sensitive detection of palytoxin and other analytes.