Streptavidin binding bifunctional aptamers and their interaction with low molecular weight ligands

This paper describes the measurement of the binding affinities of two bifunctional RNA aptamers to their respective ligands. The aptamers comprise either a theophylline or malachite green binding sequence fused to a streptavidin binding sequence. These bifunctional aptamers are shown to bind simultaneously to both the small ligand and to streptavidin whether in free solution or on gold surfaces. Binding isotherms for both interactions were measured by different physiochemical techniques: surface plasmon resonance, fluorescence spectroscopy and dynamic light scattering. Both qualitatively and quantitatively there is little difference in binding affinities between the bifunctional aptamers and their monofunctional components. The respective K_d values for streptavidin binding in the monofunctional aptamer and in the theophylline bifunctional aptamer were 12 nM and 65 nM, respectively whilst the K_d values for theophylline binding in the monofunctional aptamer and the streptavidin bifunctional aptamer were 300 nM and 120 nM. These results are consistent with treating each aptamer sequence as a module that can be combined with others without significant loss of function. This allows for the use of streptavidin based immobilization strategies without either the cost of biotinylated dNTPs or the variable yields associated with the chemical biotinylation of RNA.     

DNA binding and photocleavage properties of two mixed-ligand oxovanadium complexes

An oxovanadium complex [VO(satsc)(bipy)] (1) (satsc = salicylaldehyde thiosemicarbazone, bipy = 2,2′-bipyridine) and its dibromo derivative [VO(3,5-dibrsatsc)(bipy)] (2) (3,5-dibrsatsc = 3,5-dibromosalicylaldehyde thiosemicarbazone) have been synthesized and characterized by elemental analysis, IR, ES-MS and ¹H NMR. The interaction of these two complexes with calf-thymus DNA (CT-DNA) was studied using UV/Vis, fluorescence spectroscopic titration, viscosity measurements and thermal denaturation. The results suggest that complexes 1 and 2 interact with CT-DNA by intercalative modes. The DNA-binding affinity of complex 1 is larger than that of complex 2. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated by gel electrophoresis experiments. Both complexes exhibit significant DNA cleavage activity, and complex 1 showed greater cleaving efficiency than complex 2.     

Sensitive and simple detection of Escherichia coli strain based on time-resolved fluorescence DNA hybridization assay

A two-probe tandem DNA hybridization assay based on time-resolved fluorescence was employed to detect Escherichia coli strain. The amino modified capture probe was covalently immobilized on the common glass slide surface. The Eu(TTA)₃(5-NH₂-phen) with the characteristics of long lifetime and intense luminescence was labeled with reporter probe. The original extracted DNA samples without the purification and amplification process were directly used in the hybridization assay. The concentration of capture probe, hybridization temperature, hybridization and washing time were optimized. The detection limit is about 1.49 × 10³ CFU mL⁻¹E. coli cells, which is comparable to the value of most microbiology methods. The proposed method has the advantages of easy operation, satisfactory sensitivity and specificity, which can provide a promising technique for monitoring the microorganisms.     

The synthesis and spectral properties of new DNA binding ligands

Two new ligands based on anthracene or carbazole planar skeletons, and a phenyloxazoline moiety linked by a vinyl bridge are synthesized as potential DNA-interacting drugs. Their spectral characteristics and DNA binding affinity are assessed.     

Sensitive miniature single-particle immunoassay of prostate-specific antigen using time-resolved fluorescence

The present study describes the development of a quantitative miniaturized single microparticle immunoassay. The main objective of the study was to evaluate the performance of a miniature heterogeneous immunoassay on a single microparticle in respect to assay kinetics, volume, and sensitivity, binding capacity of microparticles and sensitivity using europium(III) nanoparticle labels. The performance of the single microparticle assay of prostate-specific antigen (PSA) was investigated using different-sized microparticles (60-920 μm in diameter) and microtiter well as a solid-phase. Equilibration time of the assay was shown to be dependent in a linear manner on surface-to-volume ratio, i.e. larger surface-to-volume translated to a faster reaction. However, no correlation between PSA binding capacity and equilibration time was observed in these kinetic studies. Only moderate improvement in assay kinetics was found when PSA binding capacity was increased on a microparticle. Using europium(III) nanoparticle labels, 107 nm in diameter, coated with streptavidin a detection sensitivity of 30 ng l⁻¹ (0.1 amol) was achieved in 1 μl total assay volume per microparticle. This was 50-fold higher compared to the same assay performed with intrinsically fluorescent europium(III) labels.     

Synthesis and binding properties of a macrocycle with two binding subcavities

A large, covalent macrocycle that can be served as an artificial allosteric model was prepared in a reasonable yield (36%) through the template-directed synthesis. The macrocycle contains two topologically discrete subcavities, each of which consists of four amide NHs of pyridine-2,6-dicarboxamide units. The macrocycle strongly binds two molecules of N,N,N′,N′-tetramethylterephthalamide in positive cooperative manner by hydrogen-bonding interactions. The association constants were calculated to be K₁ = 1480 ± 90 and K₂ = 5580 ± 150 M⁻¹ with the Hill coefficient (h) of 1.6 at 25 °C in CDCl₃.     

EPR properties of two new cyclic phosphinylhydrazyl radicals and of their inclusion complexes with cyclodextrins

Two phosphorus-containing hydrazines, namely morpholin-4-ylphosphoramidic acid diethyl ester (1a) and (2,2,6,6-tetramethylpiperidin-1-yl)phosphoramidic acid diethyl ester (2a), have been synthesized. The corresponding hydrazyl radicals (1b and 2b) have been obtained, by in situ oxidation, and their properties have been investigated by EPR spectroscopy. The 1b radical shows spectra strongly dependent on temperature due to the inversion of the morpholin ring and to rotation about the N-N bond. Since, in the investigated temperature range, both motions take place in the EPR time scale, a kinetic study of these process could be made by analyzing the spectral line-shape variations. The 2b radical is highly persistent and shows a strong temperature and solvent dependence of the phosphorus splitting. The latter property was usefully exploited to study the guest-host interaction of this radical with cyclodextrins. A method is also proposed for the determination of affinity constants for cyclodextrins of nonparamagnetic compounds.     

Characterization of troponin T binding aptamers for an innovative enzyme-linked oligonucleotide assay (ELONA)

Early diagnosis of acute myocardial infarction (AMI) is of outmost importance to reduce the mortality rate, and cardiac troponins are considered the gold standard biomarkers of myocardial necrosis. In this scenario, the characterization of two troponin T (TnT)-binding aptamers as viable alternative to antibodies employed on clinical immunoassays is here reported for the first time. Their recognition ability was first investigated through surface plasmon resonance (SPR). Subsequently, an enzyme-linked oligonucleotide assay (ELONA) was developed on common 96-well polystyrene plates, both by direct and sandwich detection strategies for comparison. In both cases, the assay exhibits a detection ability of TnT in the range of low nanomolar but a great advantage on serum interference was obtained by using both aptamers in a sandwich format, with excellent reproducibility and recovery values. Despite the sensitivity needing to be enhanced to the low picomolar range, these results are encouraging for the development of new, low-cost, and rapid antibody-free colorimetric assays for AMI studies based on aptamer–Troponin T recognition.

     

Cationic porphyrins with inverted pyridinium groups and their fluorescence properties

One of the applications of cationic porphyrins is their use in microbial photodynamic inactivation (PDI). For this purpose there is a constant quest for new cationic photoactive derivatives. In this work, we synthesized and fully characterized a new porphyrin 3a and the corresponding cationic derivative 3b. The results presented here show that meso-tetrakis(pentafluorophenyl)porphyrin (TPPF₂₀, 1) can be used as scaffold to prepare different soluble compounds with interesting photophysical properties.     

Surface plasmon resonance spectroscopy study of interfacial binding of thrombin to antithrombin DNA aptamers

We have applied surface plasmon resonance (SPR) spectroscopy, in combination with one-step direct binding, competition, and sandwiched assay schemes, to study thrombin binding to its DNA aptamers, with the aim to further the understanding of their interfacial binding characteristics. Using a 15-mer aptamer that binds thrombin primarily at the fibrinogen-recognition exosite as a model, we have demonstrated that introducing a DNA spacer in the aptamer enhances thrombin-binding capacity and stability, as similarly reported for hydrocarbon linkers. The bindings are aptamer surface coverage and salt concentration dependent. When free aptamers or DNA sequences complementary to the immobilized aptamer are applied after the formation of thrombin/aptamer complexes, bound thrombin is displaced to a certain extent, depending on the stability of the complexes formed under different conditions. When the 29-mer aptamer (specific to thrombin's heparin-binding exosite) is immobilized on the surface, its affinity to thrombin appears to be lower than the immobilized 15-mer aptamer, although the 29-mer aptamer is known to have a higher affinity in the solution phase. These findings underline the importance of aptamers' ability to fold into intermolecular structures and their accessibility for target capture. Using a sandwiched assay scheme followed by an additional signaling step involving biotin-streptavidin chemistry, we have observed the simultaneous binding of the 15- and 29-mer aptamers to thrombin protein at different exosites and have found that one aptamer depletes thrombin's affinity to the other when they bind together. We believe that these findings are invaluable for developing DNA aptamer-based biochips and biosensors.     

Sensitive assay for serum angiotensin-converting enzyme and separation of angiotensin analogues by high-performance liquid chromatography with fluorescence detection

A high-performance liquid chromatographic method is described for the assay of angiotensin-converting enzyme in human serum and for the separation of angiotensins and their analogues after pre-column fluorescence derivatization with benzoin. Angiotensin II, formed enzymatically from angiotensin I, is converted into a fluorescent derivative which is then separated isocratically from the substrate and biological substances in the enzyme reaction mixture on a reversed-phase column (TSK gel ODS-120T). The lower limit of detection for angiotensin II is 0.66 pmol per enzyme assay tube. The method is simple and sensitive, and requires as little as 5 microliter of human serum. Angiotensin analogues can also be separated and quantified by the chromatographic technique, and thus this method permits the use of the analogues of angiotensin I as substrates.     

A new method to assay hypoxia-inducible factor-1 based on small molecule binding DNA

Hypoxia-inducible factor-1 (HIF-1) is among the most important indicators of hypoxia in evaluating severity of many diseases. In this work, a novel method for HIF-1 detection is proposed by using electrochemical techniques based on small molecule binding DNA. In this method, since the designed DNA sequence can specifically bind with either an electroactive small molecule or HIF-1, the signal readout is inversely proportional to HIF-1 concentration, thus a simple and easily-operated method for HIF-1 detection can be developed. With the proposed method, HIF-1 can be determined in a linear range from 5 to 25 nM with a detection limit of 2.8 nM. Furthermore, the proposed method can be directly used to assay HIF-1 in placenta tissue, and the assay results can reliably reflect the severity of preeclampsia, a very dangerous condition during pregnancy. The proposed method also shows desirable sensitivity, high selectivity and excellent reproducibility, so this method can have potential applications in clinical practice.     

Preparation of silybin 23-esters and evaluation of their inhibitory ability against LPO and DNA protective properties

Twelve 23-esterified silybin derivatives with different patterns of substituents such as aromatic and aliphatic groups(1-12) were designed and synthesized.The antioxidative properties of these compounds were evaluated.The modified silybin analogues exhibited improved inhibitory effects against rat liver homogenate lipid peroxidation compared to silybin,with exception of the trimethoxylated ester(5) and the aliphatic one(9).Compounds 3,5,7,8 and 11 displayed their protective properties on DNA cleavage in ...     

Preparation of silybin 23-esters ability against LPO and and evaluation of their inhibitory DNA protective properties

Twelve 23-esterified silybin derivatives with different patterns of substituents such as aromatic and aliphatic groups (1-12) were designed and synthesized. The antioxidative properties of these compounds were evaluated. The modified silybin analogues exhibited improved inhibitory effects against rat liver homogenate lipid peroxidation compared to silybin, with exception of the trimethoxylated ester (5) and the aliphatic one (9). Compounds 3, 5, 7, 8 and 11 displayed their protective properties on DNA cleavage in a dose-dependent manner.     

Modified capillary electrophoresis based measurement of the binding between DNA aptamers and an unknown concentration target

The recognition of targets such as biomacromolecules, viruses and cells by their aptamers is crucial in aptamer-based biosensor platforms and research into protein function. However, it is difficult to evaluate the binding constant of aptamers and their targets that are hard to purify and quantify, especially when the targets are undefined. Therefore, we aimed to develop a modified capillary electrophoresis based method to determine the dissociation constant of aptamers whose targets are hard to quantify. A protein target, human thrombin, and one of its aptamers were used to validate our modified method. We demonstrated that the result calculated by our method, only depending on the aptamer’s concentrations, was consistent with the classical method, which depended on the concentrations of both the aptamers and the targets. Furthermore, a series of DNA aptamers binding with avian influenza virus H9N2 were confirmed by a four-round selection of capillary electrophoresis–systematic evolution of ligands by exponential enrichment, and we identified the binding constant of these aptamers by directly using the whole virus as the target with the modified method. In conclusion, our modified method was validated to study the interaction between the aptamer and its target, and it may also advance the evaluation of other receptor–ligand interactions.     

Sensitive, label-free protein assay using 1-ethyl-3-methylimidazolium tetrafluoroborate-supported microchip electrophoresis with laser-induced fluorescence detection

Based on the dimer-monomer equilibrium movement of the fluorescent dye Pyronin Y (PY), a rapid, simple, highly sensitive, label-free method for protein detection was developed by microchip electrophoresis with LIF detection. PY formed a nonfluorescent dimer induced by the premicellar aggregation of an anionic surfactant, SDS, however, the fluorescence intensity of the system increased dramatically when proteins such as BSA, bovine hemoglobin, cytochrome c, and trypsin were added to the solution due to the transition of dimer to fluorescent monomer. Furthermore, 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) instead of PBS was applied as running buffers in microchip electrophoresis. Due to the excellent properties of EMImBF4, not only nonspecific protein adsorption was more efficiently suppressed, but also approximately ten-fold higher fluorescence intensity enhancement was obtained than that using PBS. Under the optimal conditions, detection limits for BSA, bovine hemoglobin, cytochrome c, and trypsin were 1.00x10(-6), 2x10(-6), 7x10(-7), and 5x10(-7) mg/mL, respectively. Thus, without covalent modification of the protein, a protein assay method with high sensitivity was achieved on microchips.     

A new total antioxidant potential measurements using RP-HPLC assay with fluorescence detection

In this paper, an improved total antioxidant potential (TAP) estimation using high-performance liquid chromatographic (HPLC) assay with fluorometric detection has been described. The principle of this method is based on the hydroxyl radicals generated in the Fenton-like reaction and subsequently detected using hydroxyterephthalic acid (HTPA), which is a reaction product of hydroxyl radicals and terephthalic acid (TPA), working as a sensing compound. HTPA quantity in the samples was measured by fluorescence detector working at excitation and emission wavelengths equal to 312 and 428 nm, respectively. A number of key experimental conditions including the influence of the reaction (incubation) time on the surface areas of HTPA peaks, concentration of Fe(II) ions as well as the influence of concentration of TPA on the surface area of the chromatographic peak of HTPA were optimized to the characteristic feature of TAP measurements. The elaborated assay has been used to evaluate TAP values of selected low-molecular mass compounds like pyrogallol, tryptamine, and n-alcohols (methanol, ethanol, and n-propanol) as well as chlorogenic and ascorbic acids and benzoic acid derivatives, which are commonly present in the food samples.     

Interaction of zinc and cobalt with dipeptides and their DNA binding studies

Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt complexes