Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms.

Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.

Small molecule aptamer assays based on fluorescence anisotropy signal-enhancer oligonucleotides.

Herein, we design novel fluorescence anisotropy (FA) aptamer sensing platforms dedicated to small molecule detection. The assay strategy relied on enhanced fluctuations of segmental motion dynamics of the aptamer tracer mediated by an unlabelled, partially complementary oligonucleotide. The signal-enhancer oligonucleotide (SEO) essentially served as a free probe fraction revealer. By targeting specific regions of the signalling functional nucleic acid, the SEO binding to the unbound aptamer triggered perturbations of both the internal DNA flexibility and the localized dye environment upon the free probe to duplex structure transition. This potentiating effect determined increased FA variations between the duplex and target bound states of the aptameric probe. FA assay responses were obtained with both pre-structured (adenosine) and unstructured (tyrosinamide) aptamers and with dyes of different photochemical properties (fluorescein and texas red). The multiplexed analysis ability was further demonstrated through the simultaneous multicolour detection of the two small targets. The FA method appears to be especially simple, sensitive and widely applicable.

Fluorescence anisotropy-based structure-switching aptamer assay using a peptide nucleic acid (PNA) probe.

This study describes for the first time the feasibility of using peptide nucleic acids (PNAs) as an alternative to the DNA probes in structure-switching aptamer fluorescence polarisation assays. The effects of experimental parameters such as the length of the PNA strand, the nature of dye and the buffer conditions on the assay performances are first explored using two different methodologies based on the competition between the PNA/aptamer hydribridisation and the target/aptamer complexation. D-ATP can be detected from 1 to 25 µM in a linear range and a detection limit (LOD) of 3 µM can be reached. For this target, this lowers by a factor >5 the LOD reported with conventional DNA-based fluorescent structure switching aptamer-based assays and by a factor 3 the LOD observed with non-competitive fluorescent sensing platform indicating the usefulness of the PNA-based approach.

Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H†NMR Spectroscopy and Molecular Modeling.

Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.

Macrocyclic host-dye reporter for sensitive sandwich-type fluorescent aptamer sensor.

We describe herein a novel approach for the fluorescent detection of small molecules using a sandwich-type aptamer strategy based on a signaling macrocyclic host-dye system. One split adenosine aptamer fragment was 5'-conjugated to a ß-cylodextrin (CD) molecule while the other nucleic acid fragment was labeled at the 3'-end by a dansyl molecule prone to be included into the macrocycle. The presence of the small target analyte governed the assembly of the two fragments, bringing the dye molecule and its specific receptor in close proximity and promoting the inclusion interaction. Upon the inclusion complex formation, the microenvironment of dansyl was modified in such a way that the fluorescent intensity increased. Concomitantly, this supplementary interaction at the aptamer extremities induced stabilizing effects on the ternary complex. We next proposed a bivalent signaling design where the two extremities of one split aptamer fragment were conjugated to the ß-CD molecule while those of the other fragment were tagged by the dansyl dye. The dual reporting dye inclusion promoted an improvement of both the signal-to-background change and the assay sensitivity. Owing to the vast diversity of responsive host-macrocycle systems available, this aptasensor strategy has potential to be extended to the multiplexed analysis and to other kinds of transducers (such as electrochemical).

Capillary gel electrophoresis-coupled aptamer enzymatic cleavage protection strategy for the simultaneous detection of multiple small analytes.

This novel, multi small-analyte sensing strategy is the result of combining the target-induced aptamer enzymatic protection approach with the CGE-LIF (capillary gel electrophoresis with laser-induced fluorescence) technique. The implemented assay principle is based on an analysis of the phosphodiesterase I (PDE I)-mediated size variation of a fluorescein-labeled aptamer (FApt), the enzyme catalyzing the removal of nucleotides from DNA in the 3' to 5' direction. In the absence of the target, the unfolded aptamer was enzymatically cleaved into short DNA fragments. Upon target binding, the DNA substrate was partially protected against enzymatic hydrolysis. The amount of bound aptamer remaining after the exonuclease reaction was proportional to the concentration of the target. The CGE technique, which was used to determine the separation of FApt species from DNA digested products, permitted the quantification of adenosine (A), ochratoxin A (O), and tyrosinamide (T) under the same optimized enzymatic conditions. This assay strategy was subsequently applied to the simultaneous detection of A, O, and T in a single capillary under buffered conditions using corresponding FApt probes of different lengths (23, 36, and 49 nucleotides, respectively). Additionally, the detection of these three small molecules was successfully achieved in a complex medium (diluted, heat-treated human serum) showing a good recovery. It is worth noting that the multiplexed analysis was accomplished for targets with different charge states by using aptamers possessing various structural features. This sensing platform constitutes a rationalized and reliable approach with an expanded potential for a high-throughput determination of small analytes in a single capillary.

Catalytic DNA-based fluorescence polarization chiral sensing platform for L-histidine detection at trace level.

This paper reports a novel fluorescence polarization (FP) chiral sensor approach based on a catalytic DNA. This platform involves an enzyme module (E), which was able to trigger the L-histidine-dependent cleavage of an RNA phosphoester bond of a substrate domain (S), whereas it did not accept the D-enantiomer as cofactor. Two assay formats were proposed, based on bi- and unimolecular strategies. The bimolecular design was related to the use of separate E and fluorescently labelled S* sequences. The two oligonucleotide strands were pre-assembled via complementary regions at their extremities. As the result of the large molecular volume of the formed assembly, the S* probe displayed a high fluorescence anisotropy signal. Upon addition of the L-histidine, the DNAzyme cleaved the phosphoester bond of the S* component, leading to the loss of stem stability and the release of single-stranded products of lower size. This was accompanied by a significant decrease in the fluorescence anisotropy response. As a simpler alternative, the unimolecular design, where E and S sequences are linked together through a loop to form a single fluorescent probe E-S*, was also investigated. It was found that the unimolecular approach provided an improved FP response relative to the bimolecular one. Under optimized operating conditions, such a chiral sensing platform allowed the detection of as low as 0.05% of the L-histidine enantiomer in a non-racemic mixture.

Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules.

Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.

Optimization of the structure-switching aptamer-based fluorescence polarization assay for the sensitive tyrosinamide sensing.

In this paper, a structure-switching aptamer assay based on a fluorescence polarization (FP) signal transduction approach and dedicated to the L-tyrosinamide sensing was described and optimized. A fluorescently labelled complementary strand (CS) of the aptamer central region was used as a probe. The effects of critical parameters such as buffer composition and pH, temperature, aptamer:CS stoichiometry, nature of the dye (Fluorescein (F) or Texas Red (TR)) and length of the CS (15-, 12-, 9- and 6-mer) on the assay analytical performances were evaluated. Under optimized experimental conditions (10 mM Tris-HCl, 5 mM MgCl(2) and 25 mM NaCl, pH 7.5 temperature of 22°C and stoichiometry 1:1), the results showed that, for a 12-mer CS, the F dye moderately increased the method sensitivity in comparison to the TR label. The F labelled 9-mer CS, however, did not allow the hybrid formation with the functional nucleic acid, thus emphasizing the importance of the nature of the fluorophore. In contrast, the same 9-mer CS labelled with the TR dye was able to effectively associate with the aptamer and was easily displaced upon target binding as demonstrated by a significant improvement of the sensitivity and a detection limit of 250 nM, comparable to those reported with direct aptasensing methods. The present study demonstrates that not only the CS length but also the nature of the dye played a preponderant role in the performance of the structure-switching aptamer assay, highlighting the importance of interdependently controlling these two factors for an optimal FP-based sensing platform.

Aptamer enzymatic cleavage protection assay for the gold nanoparticle-based colorimetric sensing of small molecules.

A label-free, homogeneous aptamer-based sensor strategy was designed for the facile colorimetric detection of small target molecules. The format relied on the target-induced protection of DNA aptamer from the enzymatic digestion and its transduction into a detectable signal through the length-dependent adsorption of single-stranded DNA onto unmodified gold nanoparticles (AuNPs). The proof-of-principle of the approach was established by employing the anti-tyrosinamide aptamer as a model functional nucleic acid. In the absence of target, the aptamer was cleaved by the phosphodiesterase I enzymatic probe, leading to the release of mononucleotides and short DNA fragments. These governed effective electrostatic stabilization of AuNPs so that the nanoparticles remained dispersed and red-colored upon salt addition. Upon tyrosinamide binding, the enzymatic cleavage was impeded, resulting in the protection of the aptamer structure. As this long DNA molecule was unable to electrostatically stabilize AuNPs, the resulting colloidal solution turned blue after salt addition due to the formation of nanoparticle aggregates. The quantitative determination of the target can be achieved by monitoring the ratio of absorbance at 650 and 520 nm of the gold colloidal solution. A limit of detection of ~5 µM and a linear range up to 100 µM were obtained. The sensing platform was further applied, through the same experimental protocol, to the adenosine detection by using its DNA aptamer as recognition tool. This strategy could extend the potentialities, in terms of both simplicity and general applicability, of the aptamer-based sensing approaches.

Fluorescence polarization biosensor based on an aptamer enzymatic cleavage protection strategy.

A novel fluorescence polarization (FP) aptasensing platform based on target-induced aptamer enzymatic cleavage protection is reported. The method relies on the FP analysis of the phosphodiesterase I mediated size variation of a dye-labeled aptamer. The tyrosinamide/antityrosinamide DNA aptamer couple was firstly tested as a model system to establish the proof-of-concept. In the absence of the target, the labeled aptamer was enzymatically cleaved into small DNA fragments, leading to a low FP signal. Upon tyrosinamide binding, the DNA substrate was partially protected against the enzymatic attack, leading to an increase in the fluorescence anisotropy response as a result of the higher average molecular volume of the weakly digested probe. The method was subsequently applied to two other systems, i.e., for the detection of ochratoxin A and adenosine. Such an approach was found to combine simplicity and general applicability features.

Multiplexed detection of small analytes by structure-switching aptamer-based capillary electrophoresis.

Affinity probe capillary electrophoresis (APCE) assays, combining the separation power of CE with the specificity of interactions occurring between a target and a molecular recognition element (MRE), have become important analytical tools in many application fields. In this report, a rationalized strategy, derived from the structure-switching aptamer concept, is described for the design of a novel APCE mode dedicated to small molecule detection. Two assay configurations were reported. The first one, developed for the single-analyte determination, was based on the use of a cholesteryl-tagged aptamer (Chol-Apt) as the MRE and its fluorescein-labeled complementary strand (CS*) as the tracer (laser-induced fluorescence detection). Under micellar electrokinetic chromatography (MEKC) conditions, free CS* and the hybrid formed with Chol-Apt (duplex*) were efficiently separated (and then quantified) through the specific shift of the electrophoretic mobility of the cholesteryl-tagged species in the presence of a neutral micellar phase. When the target was introduced into the preincubated sample, the hybridized form was destabilized, resulting in a decrease in the duplex* peak area and a concomitant increase in the free CS* peak area. The second format, especially designed for multianalyte sensing, employed dually cholesteryl- and fluorescein-labeled complementary strands (Chol-CS*) of different lengths and unmodified aptamers (Apt). The size-dependent electrophoretic separation of different Chol-CS* forms from each other and from their corresponding duplexes* was also accomplished under MEKC conditions. The simultaneous detection of multiple analytes in a single capillary was performed by monitoring accurately each target-induced duplex-to-complex change. This method could expand significantly the potential of small solute APCE analysis in terms of simplicity, adaptability, generalizability, and high-throughput analysis capability.

Rationally designed aptamer-based fluorescence polarization sensor dedicated to the small target analysis.

A direct fluorescence polarization (FP) assay strategy, dedicated to the small molecule sensing and based on the unique induced-fit binding mechanism of end-labelled nucleic acid aptamers, has been recently developed by our group. Small target binding has been successfully converted into a significant increase of the fluorescence anisotropy signal presumably produced by the reduction of the local motional freedom of the dye. In order to generalize the approach, a rational FP sensor methodology was established herein, by engineering instability in the secondary structure of an aptameric recognition element. The anti-adenosine DNA aptamer, labelled by a single fluorescein dye at its 3' extremity, was employed as a model functional nucleic acid probe. The terminal stem of the stem-loop structure was shortened to induce a destabilized/denatured conformation which promoted the local segmental mobility of the dye and then a significant depolarization process. Upon target binding, the structural change of the aptamer induced the formation of a stable stem-loop structure, leading to the reduction of the dye mobility and the increase in the fluorescence anisotropy signal. This reasoned approach was applied to the sensing of adenosine and adenosine monophosphate and their chiral analysis.

Exploring photoreactions between polyazaaromatic Ru(II) complexes and biomolecules by chemically induced dynamic nuclear polarization measurements.

Steady-state (1)H photo-chemically induced dynamic nuclear polarization (CIDNP) experiments were conducted at 14.1 T on deoxygenated (buffered pH 7) aqueous solutions of [Ru(phen)(3)](2+), [Ru(tap)(2)(phen)](2+), and [Ru(tap)(3)](2+) (tap = 1,4,5,8-tetraazaphenanthrene; phen = 1,10-phenanthroline) in the presence of guanosine-5'-monophosphate or N-acetyltyrosine. For the first time, CIDNP arising from photo-oxidation by polyazaaromatic Ru(II) complexes is reported. In agreement with the occurrence of a photo-electron-transfer process, photo-CIDNP effects are observed with [Ru(tap)(3)](2+) and [Ru(tap)(2)(phen)](2+) but not with [Ru(phen)(3)](2+). With [Ru(tap)(2)(phen)](2+), no significant photo-CIDNP is observed for the (1)H nuclei of the phen ligand, consistent with the fact that the metal-to-ligand charge-transfer triplet excited states responsible for the photo-oxidation involve a tap ligand. Successive experiments with [Ru(tap)(3)](2+) highlight the accumulation of long-lived radical species in solution that cause (1)H NMR signal broadening and photo-CIDNP extinction. The (1)H photo-CIDNP observed for the biomolecules is rather weak, less than about 30% of the equilibrium magnetization. However, up to 60% polarization enhancement is observed for H-2 and H-7 of the tap ligands, which indicates high unpaired electron density in the vicinity of these atoms in the transient radical pair. This is consistent with the structure of known photoadducts formed, for instance, between the metallic compounds and the guanine base of mono- and polynucleotides. Indeed, in these adducts the covalent bond involves carbon C-2 or C-7 of a tap ligand. The occurrence of photo-CIDNP with polyazaaromatic Ru(II) complexes opens new perspectives for the study of this type of compound.

Noncompetitive fluorescence polarization aptamer-based assay for small molecule detection.

In this paper, a new fluorescence polarization (FP) assay strategy is described reporting the first demonstration of a noncompetitive FP technique dedicated to the small molecule sensing. This approach was based on the unique induced-fit binding mechanism of nucleic acid aptamers which was exploited to convert the small target binding event into a detectable fluorescence anisotropy signal. An anti-L-tyrosinamide DNA aptamer, labeled by a single fluorescent dye at its extremity, was employed as a model functional nucleic acid probe. The DNA conformational change generated by the L-tyrosinamide binding was able to induce a significant increase in the fluorescence anisotropy signal. The method allowed enantioselective sensing of tyrosinamide and analysis in practical samples. The methodology was also applied to the L-argininamide detection, suggesting the potential generalizability of the direct FP-based strategy. Such aptamer-based assay appeared to be a sensitive analytical system of remarkable simplicity and ease of use.

Enantioseparation by MEKC using a ligand exchange-based chiral pseudostationary phase.

In this paper, a new ligand-exchange -MEKC mode, based on the design of a unique lipohilic species (4'-octadecylneamine derivative), which served both as micelle-forming surfactant (by its hydrophobic part) and central ion-complexing ligand (by its hydrophilic part) is described. The CMC of the used lipophilic neamine derivative was first determined by surface tension measurements. Subsequent NMR experiments were performed in order to investigate the Cu(II) binding properties of the neamine micellar phase. The enantioseparation properties of both the octadecylneamine derivative-Cu(II) MEKC and the native neamine-Cu(II) CE systems were evaluated and compared using the tryptophan racemate as a probe analyte. The effects of several different electrophoretic conditions on the enantiomer migration behavior in the ligand-exchange-MEKC mode were examined. The developed methodology was also applied to the enantioseparation of other analytes such as 1-methyl-tryptophan, 3,5-diiodo-tyrosine and 1-naphtyl-alanine.

Aptamer-modified micellar electrokinetic chromatography for the enantioseparation of nucleotides.

In this paper, a new aptamer-based capillary electrophoresis (CE) method, which was able to separate the enantiomers of an anionic target (adenosine monophosphate, AMP) displaying the same electrophoretic mobility as that of the oligonucleotidic chiral selector, is reported. The design of the aptamer-modified micellar electrokinetic chromatography (MEKC) mode consisted of nonionic micelles which acted as a pseudostationary phase and a hydrophobic cholesteryl group-tagged aptamer (Chol-Apt) which partitioned into the uncharged micellar phase. Under partial-filling format and suppressed electroosmotic flow conditions, the strong mobility alteration of Chol-Apt permitted AMP enantiomers to pass through the micelle-anchored aptamer zone and promoted the target enantioseparation. The influence of several electrophoretic parameters (such as concentration and nature of the nonionic surfactant, preincubation of the Chol-Apt and surfactant, capillary temperature, and applied voltage) on the AMP enantiomer migration was investigated in order to define the utilization conditions of the aptamer-modified MEKC mode. The chiral resolution, in a single run, of three adenine nucleotides, i.e., AMP, ADP (adenosine diphosphate), and ATP (adenosine triphosphate), was further accomplished using such methodology. This approach demonstrates the possibility to extend the CE applicability of aptamer chiral selectors to potentially any target, without restriction on its charge-to-mass ratio.

Characterization of lysine-guanine cross-links upon one-electron oxidation of a guanine-containing oligonucleotide in the presence of a trilysine peptide.

Formation of DNA-protein cross-links involving the initial formation of a guanine radical cation was investigated. For this purpose, riboflavin-mediated photosensitization of a TGT oligonucleotide in aerated aqueous solution in the presence of the KKK tripeptide was performed. We have shown that the nucleophilic addition of the epsilon-amino group of the central lysine residue of KKK to the C8 atom of either the guanine radical cation or its deprotonated form gives rise to the efficient formation of a Nepsilon-(guanin-8-yl)-lysine cross-link. Interestingly, the time course of formation of the above-mentioned cross-link was found to be not linear with the time of irradiation, and its formation rapidly reached a plateau. This is explained by secondary decomposition of the initially generated cross-link which could be further oxidized more efficiently than starting TGT oligonucleotide. One-electron oxidation of the initially generated cross-link was found to produce mainly two diastereomeric cross-links exhibiting a spiroimino-trilysine-dihydantoin structure as inferred from enzymatic digestion, CD, UV, NMR and mass spectrometry measurements. In addition, other minor cross-links, for which formation was favored at acidic pH, were assigned as lysine-guanine adducts in which the modified guanine base exhibits a guanidino-trilysine-iminohydantoin structure. A proposed mechanism for the formation of the different detected oligonucleotide-peptide cross-links is given. The high yield of formation of the detected cross-links strongly suggests that a DNA-protein cross-link involving a lysine residue linked to the C8 position of guanine could be generated in cellular systems if a lysine is located in the close vicinity of a guanine radical cation.

Kinetic study of azole-bridged dinuclear platinum(II) complexes reacting with a hairpin-stabilized double-stranded oligonucleotide.

The cytotoxic dinuclear platinum(II) complexes [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-pz)](NO(3))(2) (pz=pyrazolate) (1) and [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-1,2,3-ta-N1,N2)](NO(3))(2) (1,2,3-ta=1,2,3-triazolate) (2), were allowed to react with the hairpin-stabilized double-stranded oligonucleotide d(TATGGCATT(4)ATGCCATA), to determine the amounts of intrastrand and interstrand DNA adducts. The reaction kinetics was investigated by reversed-phase HPLC, and the resulting products were analyzed using mass spectroscopy combined with enzymatic digestion, and Maxam-Gilbert sequencing. The reaction of 1 results in the formation of the 1,2-intrastrand d(GG) adduct as the major final product. The two most abundant products of 2 were identified as isomeric 1,2-intrastrand d(GG) adducts differing probably in platinum coordination to the triazole ring. No GG-interstrand crosslinks were detected with either compound. d(GGC)-d(GCC) sequences of DNA do thus not appear to represent significant targets for forming interstrand crosslinks with either 1 or 2.