Thermodynamic basis of chiral recognition in a DNA aptamer

Detection of Glucose Based on Noble Metal Nanozymes: Mechanism, Activity Regulation, and Enantioselective Recognition

Glucose monitoring is essential to evaluate the degree of glucose metabolism disorders. The enzymatic determination has been the most widely used method in glucose detection because of its high efficiency, accuracy, and sensitivity. Noble metal nanomaterials (NMs, i.e., Au, Ag, Pt, and Pd), inheriting their excellent electronic, optical, and enzyme-like properties, are classified as noble metal nanozymes (NMNZs). As the NMNZs are often involved in two series of reactions, the oxidation of glucose and the chromogenic reaction of peroxide, here the chemical mechanism by employing NMNZs with glucose oxidase (GOx) and peroxidase (POD) mimicking activities is briefly summarized first. Subsequently, the regulation strategies of the GOx-like, POD-like and tandem enzyme-like activities of NMNZs are presented in detail, including the materials, size, morphology, composition, and the reaction condition of the representative NMs. In addition, in order to further mimic the enantioselectivity of enzyme, the design of NMNZs with enantioselective recognition of d-glucose and l-glucose by using different chiral compounds (DNA, amino acids, and cyclodextrins) and molecular imprinting is further described in this review. Finally, the feasible solutions to the existing challenges and a vision for future development possibilities are discussed.

Rapid nanomolar detection of methamphetamine in biofluids via a reagentless electrochemical aptamer-based biosensor

The availability of sensing platforms able to rapidly measure abused drugs directly in biological fluids in a single step would allow performing drugged driving screening on the site. The achievement of this goal is extremely important for preventing and controlling drug abuse and crime incidence. Motived by this, we constructed a simple, cost-effective and reagentless electrochemical aptamer-based (EAB) sensor with methamphetamine (MAMP) as the target molecule. This EAB sensor produced a nanomolar level of detection accuracy in unprocessed or minimally processed bio-samples. Specifically, circular dichroic spectrum was used to confirm that the truncated aptamer from the original sequence would undergo large binding-induced conformational changes. We then engineered the aptamer to work in the EAB platform and the resulting sensor enabled sensitive and specific detection of MAMP with the detection limit of 30 nM in undiluted serum, 50 nM in undiluted urine and 20 nM in 50% saliva. The sensor has good recovery rate, implying this method has good reliability and repeatability. The detection limit is far below the clinical detection threshold, it would be hopefully used for preliminary screening of drugged driving in real world.

Binding of l-Argininamide to a DNA Aptamer: A Volumetric Study

We use a combination of volumetric and spectroscopic techniques to characterize the binding of l-argininamide to its aptamer, the 24-base DNA hairpin 5'-d(GATCGAAACGTAGCGCCTTCGATC)-3'. The binding causes increases in volume, Δ V, and adiabatic compressibility, Δ K_S, of 12 ± 7 cm³ mol^-1 bar and (73 ± 8) × 10^-4 cm³ mol^-1 bar^-1, respectively. These volumetric results combined with structural data reveal that the binding is accompanied by release of 73 ± 27 waters from the hydration shells of the interacting molecules to the bulk. We use the estimated change in hydration to estimate the hydration, Δ S_hyd, and configurational, Δ S_conf, contributions to the binding entropy. The large and unfavorable change in configurational entropy, Δ S_conf, is nearly compensated by a favorable change in the hydration contribution, Δ S_hyd.

Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space

To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we performed a SELEX in silico study to investigate the fitness distribution of the l-Arm-binding aptamer genotype neighborhoods. Two novel functional genotype neighborhoods were isolated and experimentally verified to have comparable fitness as the wild-type. The experimental aptamer fitness landscape suggests the mutational robustness is strongly influenced by the local base environment and ligand-binding mode, whereas bases distant from the binding pocket provide potential evolutionary pathways to approach the global fitness maximum. Our work provides an example of successful application of SELEX in silico to optimize an aptamer and demonstrates the strong sensitivity of mutational robustness to the site of genetic variation.

Computational docking simulations of a DNA-aptamer for argininamide and related ligands

The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.

Revisiting the streptavidin-biotin binding by using an aptamer and displacement isothermal calorimetry titration

The association constant of a well-known streptavidin-biotin binding has only been inferred from separately measured kinetic parameters. In a single experiment, we obtained Ka 1 × 10(12)  M(-1) by using a streptavidin-binding aptamer and ligand-displacement isothermal titration calorimetry. This study explores the challenges of determining thermodynamic parameters and the derived equilibrium binding affinity of tight ligand-receptor binding.

Enantioselective recognition mechanism of ofloxacin via Cu(II)-modulated DNA

The specific interactions of Cu(2+) with self-complementary DNA sequences involving d[G4C4(GC)2G4C4], d[(GC)10], and d[(AT)10], as well as the chiral recognition mechanism of ofloxacin enantiomers via the Cu(II)-modulated DNAs, were investigated using characterizations of circular dichroism, gel electrophoresis, FT-IR spectroscopy, UV melting measurement, electron paramagnetic resonance, and HPLC. The Cu(II)-coordinated GC-rich DNAs exhibit amplified enantioselectivity toward the S-enantiomer of ofloxacin. Especially in the case of d[G4C4(GC)2G4C4], ofloxacin enantiomers intercalate into the two adjacent guanine bases through the minor groove mediated by Cu(2+), which leads to a more favorable binding between S-ofloxacin and DNA. The highest ee value of ofloxacin enantiomers in the permeate after being adsorbed by the Cu(II)-DNA complex is obtained as 49.2% in the R-enantiomer at the [Cu(2+)]/[base] molar ratio of 0.25, while at the [Cu(2+)]/[base] molar ratio of 0.05 the highest ee value of ofloxacin enantiomers in the retentate reaches 26.3% in the S-enantiomer. This work illustrates a novel promising route to construct DNA-based chiral selectors toward certain drug enantiomers through the programmable enantioselective recognition on the basis of DNA chirality and the specific binding of transition metal ions.

Selection and characterization of single stranded DNA aptamers for the hormone abscisic Acid

The hormone abscisic acid (ABA) is a small molecule involved in pivotal physiological functions in higher plants. Recently, ABA has been also identified as an endogenous hormone in mammals, regulating different cell functions including inflammatory processes, stem cell expansion, insulin release, and glucose uptake. Aptamers are short, single-stranded (ss) oligonucleotidesable to recognize target molecules with high affinity. The small size of the ABA molecule represented a challenge for aptamer development and the aim of this study was to develop specific anti-ABA DNA aptamers. Biotinylated abscisic acid (bio-ABA) was immobilized on streptavidin-coated magnetic beads. DNA aptamers against bio-ABA were selected with 7 iterative rounds of the systematic evolution of ligands by exponential enrichment method (SELEX), each round comprising incubation of the ABA-binding beads with the ssDNA sequences, DNA elution, electrophoresis, and polymerase chain reaction (PCR) amplification. The PCR product was cloned and sequenced. The binding affinity of several clones was determined using bio-ABA immobilized on streptavidin-coated plates. Aptamer 2 and aptamer 9 showed the highest binding affinity, with dissociation constants values of 0.98 ± 0.14 μM and 0.80 ± 0.07 μM, respectively. Aptamers 2 and 9 were also able to bind free, unmodified ABA and to discriminate between different ABA enantiomers and isomers. Our findings indicate that ssDNA aptamers can selectively bind ABA and could be used for the development of ABA quantitation assays.

Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer--thermodynamics and spectroscopic evidences

Protein-nucleic acids binding driven by electrostatic interactions typically are characterized by the release of counter ions, and the salt-inhibited binding association constant (K(a)) and the magnitude of exothermic binding enthalpy (ΔH). Here, we report a non-classical thermodynamics of streptavidin (SA)-aptamer binding in NaCl (140-350 mM) solutions near room temperatures (23-27 °C). By using isothermal titration calorimetry (ITC) and circular dichroism (CD)/fluorescence spectroscopy, we found that the binding was enthalpy driven with a large entropy cost (ΔH -20.58 kcal mol(-1), TΔS -10.99 kcal mol(-1), and K(a) 1.08 × 10(7)  M(-1) at 140 mM NaCl 25 °C). With the raise of salt concentrations, the ΔH became more exothermic, yet the K(a) was almost unchanged (ΔH -26.29 kcal mol(-1) and K(a) 1.50 × 10(7)  M(-1) at 350 mM NaCl 25 °C). The data suggest that no counter Na(+) was released in the binding. Spectroscopy data suggest that the binding, with a stoichiometry of 2, was accompanied with substantial conformational changes on SA, and the changes were insensitive to the variation of salt concentrations. To account for the non-classical results, we propose a salt bridge exchange model. The intramolecular binding-site salt bridge(s) of the free SA and the charged phosphate group of aptamers re-organize to form the binding complex by forming a new intermolecular salt bridge(s). The salt bridge exchange binding process requires minimum amount of counter ions releasing but dehydration of the contacting surface of SA and the aptamer. The energy required for dehydration is reduced in the case of binding solution with higher salt concentration and account for the higher binding exothermic mainly.

Selective detection of endotoxin using an impedance aptasensor with electrochemically deposited gold nanoparticles

Using a single-stranded DNA (ssDNA) aptamer exhibiting high binding affinity (Kd = 12 nM) to endotoxin as a probe, an impedance sensor where aptamer-conjugated gold nanoparticles (AuNPs) were electrochemically deposited on a gold electrode was fabricated and its performance in regard to endotoxin detection assessed. AuNPs have been employed widely as biosensors because of their unique physical and chemical properties. In order to maximize the performance of the impedance aptasensor on endotoxin detection, some critical factors affecting aptamer conjugation to AuNPs and target recognition ability (i.e. concentrations of aptamer coupled with AuNPs, pH, ion strength and cation effect at the time of aptamer-endotoxin interaction) were optimized. Electrochemical impendence spectroscopy, cyclic voltametry, atomic force microscope, scanning electron microscope and quartz crystal microbalance were employed to characterize all the modification/detection procedures during the sensor fabrication. The developed aptasensor showed a broad linear dynamic detection range (0.01-10.24 ng/ml) with a very low detection limit for endotoxin (0.005 ng/ml), despite the presence of several biomolecules (e.g. plasmid DNA, RNA, serum albumin, Glc and sucrose) known to interfere with other endotoxin assays. The demonstrated aptasensor required a detection time of only 10 min, providing a simple and fast analytical method to specifically detect endotoxin from complex biological liqors.

Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide

Aptamers are rare functional nucleic acids with binding affinity to and specificity for target ligands. Recent experiments have lead to the proposal of an induced-fit binding mechanism for L-argininamide (Arm) and its binding aptamer. However, at the molecular level, this mechanism between the aptamer and its coupled ligand is still poorly understood. The present study used explicit solvent molecular dynamics (MD) simulations to examine the critical bases involved in aptamer-Arm binding and the induced-fit binding process at atomic resolution. The simulation results revealed that the Watson-Crick pair (G10-C16), C9, A12, and C17 bases play important roles in aptamer-Arm binding, and that binding of Arm results in an aptamer conformation optimized through a general induced-fit process. In an aqueous solution, the mechanism has the following characteristic stages: (a) adsorption stage, the Arm anchors to the binding site of aptamer with strong electrostatic interaction; (b) binding stage, the Arm fits into the binding site of aptamer by hydrogen-bond formation; and (c) complex stabilization stage, the hydrogen bonding and electrostatic interactions cooperatively stabilize the complex structure. This study provides dynamics information on the aptamer-ligand induced-fit binding mechanism. The critical bases in aptamer-ligand binding may provide a guideline in aptamer design for molecular recognition engineering.

Biosensors - classification, characterization and new trends

Biosensors represent promising analytical tools applicable in areas such as clinical diagnosis, food industry, environment monitoring and in other fields, where rapid and reliable analyses are needed. Some biosensors were successfully implemented in the commercial sphere, but majority needs to be improved in order to overcome some imperfections. This review covers the basic types, principles, constructions and use of biosensors as well as new trends used for their fabrication.

Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach

Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-à-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK(pred), of the electrostatic binding free energy, DeltaG(el), with respect to the logarithm of the 1:1 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK(pred) is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK(pred), whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK(pred) were not correlated with DeltaG(el) in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of DeltaG(el) against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK(pred), at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of DeltaG(el) will require further development in theoretical and experimental approaches.