Inclusion kinetics of a nucleotide into a cyclodextrin cavity by means of ultrasonic relaxation

Polynucleotide transport through lipid membrane in the presence of starburst cyclodextrin-based poly(ethylene glycol)s

Symmetrical cyclodextrin-based 14-arm star polymers with poly(ethylene glycol) PEG branches were synthesized and characterized. Interactions of the star polymers with lipid bilayers were studied by the "black lipid membrane" technique in order to demonstrate the formation of monomolecular artificial channels. The conditions for the insertion are mainly based on dimensions and amphiphilic properties of the star polymers, in particular the molar mass of the water-soluble polymer branches. Translocation of single-strand DNA (ssDNA) through those synthetic nanopores was investigated, and the close dimension between the cross-section of ssDNA and the cyclodextrin cavity led to an energy barrier that slowed down the translocation process.

Why does β-cyclodextrin prefer to bind nucleotides with an adenine base rather than other 2'-deoxyribonucleoside 5'-monophosphates?

β-Cyclodextrin (β-CD), which resides in the α-hemolysin (αHL) protein pore, can act as a molecular adapter in single-molecule exonuclease DNA sequencing approaches, where the different nucleotide binding behavior of β-CD is crucial for base discrimination. In the present contribution, the inclusion modes of β-CD towards four 2'-deoxyribonucleoside 5'-monophosphates (dNMPs) were investigated using quantum mechanics (QM) calculations. The calculated binding energy suggests that the binding affinity of dAMP to β-CD are highest among all the dNMPs in solution, in agreement with experimental results. Geometry analysis shows that β-CD in the dAMP complex undergoes a small conformational change, and weak interaction analysis indicates that there are small steric repulsion regions in β-CD. These results suggest that β-CD has lower geometric deformation energy in complexation with dAMP. Furthermore, topological analysis and weak interaction analysis suggest that the number and strength of intermolecular hydrogen bonds and van der Waals interactions are critical to dAMP binding, and they both make favorable contributions to the lower interaction energy. This work reveals the reason why β-CD prefers to bind dAMP rather than other dNMPs, while opening exciting perspectives for the design of novel β-CD-based molecular adapters in the single-molecule exonuclease method of sequencing DNA. Graphical Abstract The binding affinity of β-cyclodextrin towards four 2'-deoxyribonucleoside 5'-monophosphates was investigated using quantum mechanics calculations.

Electrochemiluminescence aptasensor for adenosine triphosphate detection using host-guest recognition between metallocyclodextrin complex and aptamer

A sensitive and label-free electrochemiluminescence (ECL) aptasensor for the detection of adenosine triphosphate (ATP) was successfully designed using host-guest recognition between a metallocyclodextrin complex, i.e., tris(bipyridine)ruthenium(II)-β-cyclodextrin [tris(bpyRu)-β-CD], and an ATP-binding aptamer. In the protocol, the NH2-terminated aptamer was immobilized on a glassy carbon electrode (GCE) by a coupling interaction. After host-guest recognition between tris(bpyRu)-β-CD and aptamer, the tris(bpyRu)-β-CD/aptamer/GCE produced a strong ECL signal as a result of the photoactive properties of tris(bpyRu)-β-CD. However, in the presence of ATP, the ATP/aptamer complex was formed preferentially, which restricted host-guest recognition, and therefore less tris(bpyRu)-β-CD was attached to the GCE surface, resulting in an obvious decrease in the ECL intensity. Under optimal determination conditions, an excellent logarithmic linear relationship between the ECL decrease and ATP concentration was obtained in the range 10.0-0.05 nM, with a detection limit of 0.01 nM at the S/N ratio of 3. The proposed ECL-based ATP aptasensor exhibited high sensitivity and selectivity, without time-consuming signal-labeling procedures, and is considered to be a promising model for detection of aptamer-specific targets.

A label-free electrochemiluminescence aptasensor for thrombin detection based on host-guest recognition between tris(bipyridine)ruthenium(II)-β-cyclodextrin and aptamer

An ultrasensitive label-free electrochemiluminescence (ECL) aptasensor for the detection of thrombin was developed based on the specific recognition between tris(bipyridine)ruthenium(II)-β-cyclodextrin (tris(bpyRu)-β-CD) and the anti-thrombin aptamer (aptamer). The NH2-aptamer was first immobilized on the activated glassy carbon electrode (GCE) by coupling interaction. By use of the specific recognition between tris(bpyRu)-β-CD and aptamer, tris(bpyRu)-β-CD was then attached on the surface of GCE. Resulting from the outstanding photoactive properties of tris(bpyRu)-β-CD, the fabricated GCE performed strong ECL signal with the coreactant of 2-(dibutylamino)ethanol (DBAE). However, in the presence of thrombin, aptamer-thrombin bioaffinity complexes were formed, which restricted the recognition activities between aptamer and tris(bpyRu)-β-CD. Thus, fewer tris(bpyRu)-β-CD could be attached on the surface of GCE and led to an obvious decrease of ECL signal. Fortunately, the difference of ECL intensity before and after combination with thrombin was logarithmically linear with the concentration of thrombin in a wide range of 10 nM-1 pM. Meantime, a detection limit of 0.1 pM without any other signal labeling or amplifying procedures indicated that the biosensor performed excellent sensitivity, operability and simplicity.

Selective recognition and separation of nucleosides using carboxymethyl-β-cyclodextrin functionalized hybrid magnetic nanoparticles

A novel magnetic nanoadsorbent (CMCD-APTS-MNPs) containing the superparamagnetic and molecular recognition properties was synthesized by grafting carboxymethyl-β-cyclodextrin (CM-β-CD) on 3-aminopropyltriethoxysile (APTS) modified Fe(3)O(4) nanoparticles. The feasibility of using CMCD-APTS-MNPs as magnetic nanoadsorbent for selective adsorption of adenosine (A) and guanosine (G) based on inclusion and molecular recognition was demonstrated. The as-synthesized magnetic nanoparticles were characterized by TEM, FTIR and TGA analyses. The effects of pH and initial nucleoside concentrations on the adsorption behavior were studied. The complexation of CMCD-APTS-MNPs with both nucleosides was found to follow the Langmuir adsorption isotherm. The CMCD-APTS-MNPs showed a higher adsorption ability and selectivity for G than A under identical experimental conditions, which results from the ability of selective binding and recognition of the immobilized CM-β-CD towards G. The driving force of the separation between G and A is through the different weak interaction with grafted CM-β-CD, i.e., hydrogen bond interaction, which is evidenced by different inclusion equilibrium constants and FTIR analyses of inclusion complexes between grafted cyclodextrin and the guest molecules. Our results indicated that this nanoadsorbent would be a promising tool for easy, fast and selective separation, analysis of nucleosides and nucleotides in biological samples.

Dynamic characteristic of amitriptyline in water by ultrasonic relaxation method and molecular orbital calculation

Ultrasonic absorption coefficients in the frequency range of 0.8-220 MHz have been measured in aqueous solution of amitriptyline (3-(10,11-dihydro-5H-dibenzo[a,d]cycloheptene-5-ylidene)-N,N-dimethyl-1-propanamine) in the concentration range from 0.20 to 0.60 mol dm(-3) at 25 °C. A single relaxational phenomenon has been observed, and the relaxation frequency is independent of the concentration. It has been also observed that the amplitude of the relaxational absorption increases linearly with the analytical concentration. From these ultrasonic relaxation data, it has been concluded that the relaxation is associated with a unimolecular reaction due to a conformational change of the solute molecule, such as a structural change due to a rotational motion of a group in the solute molecule. Molecular orbital semiempirical methods using AM1 (Austin model 1) and PM3 (modified neglect of diatomic overlap parametric method 3) have been applied to obtain the standard enthalpy of formation for amitriptyline molecule at various dihedral angles around one of the bonds in alkylamine side chain. The results have shown the two clear minimum standard enthalpies of formation for amitriptyline. From the difference of the two values, the standard enthalpy change between the two stable conformers has been calculated be 2.9 kJ mol(-1). On a rough assumption that the standard enthalpy change reflects the standard free energy change, the equilibrium constant for the rotational isomers has been estimated to be 0.31. Combining this value with the experimental ultrasonic relaxation frequency, the backward and forward rate constants have been evaluated. The standard enthalpy change of the reaction has been also estimated from the concentration dependence of the maximum absorption per wavelength, and it has been close to that calculated by the semiempirical methods. The ultrasonic absorption measurements have been also carried out in amitriptyline solution in the presence of β-cyclodextrin. However, the ultrasonic relaxation has not been found in the above frequency range. The result has been discussed in relation to the host-guest complex formation between β-cyclodextrin and amitriptyline.