Spotlighting of cocaine by an autonomous aptamer-based machine

Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç

The cocaine aptamer is a DNA molecule that binds cocaine at the junction of three helices. The bifunctional spectroscopic probe Ç was incorporated independently into three different positions of the aptamer and changes in structure and dynamics upon addition of the cocaine ligand were studied. Nucleoside Ç contains a rigid nitroxide spin label and can be studied directly by electron paramagnetic resonance (EPR) spectroscopy and fluorescence spectroscopy after reduction of the nitroxide to yield the fluoroside Ç(f). Both the EPR and the fluorescence data for aptamer 2 indicate that helix III is formed before cocaine binding. Upon addition of cocaine, increased fluorescence of a fully base-paired Ç(f), placed at the three-way junction in helix III, was observed and is consistent with a helical tilt from a coaxial stack of helices II and III. EPR and fluorescence data clearly show that helix I is formed upon addition of cocaine, concomitant with the formation of the Y-shaped three-way helical junction. The EPR data indicate that nucleotides in helix I are more mobile than nucleotides in regular duplex regions and may reflect increased dynamics due to the short length of helix I.

Single quantum-dot-based aptameric nanosensor for cocaine

Recent advances in single-molecule detection, nanotechnology, and aptameric sensors hold exciting promise for many potential applications. By functionalizing the surface of a quantum dot (QD) with aptamers which can recognize cocaine, and taking advantage of single-molecule detection and fluorescence resonance energy transfer (FRET) between 605QD and Cy5 and Iowa Black RQ, we develop a single-QD-based aptameric sensor that is capable of sensing the presence of cocaine through both signal-off and signal-on modes. In comparison with the established aptameric sensors, this single-QD-based aptameric sensor has the significant advantages of simple sample preparation, high sensitivity, and extremely low sample consumption. With the advances in the development of varieties of aptamers for small molecules, nucleic acids, metal ions, and proteins, this single-QD-based aptameric sensor might find wide application in forensic analysis, environmental monitoring, and clinic diagnostics.

Impedimetric aptasensor with femtomolar sensitivity based on the enlargement of surface-charged gold nanoparticles

A simple and ultrasensitive label-free electrochemical impedimetric aptasensor for thrombin based on the cascaded signal amplification was reported. The sandwich system of aptamer/thrombin/aptamer-functionalized Au nanoparticles (Apt-AuNPs) was fabricated as the sensing platform. The change of the interfacial feature of the electrode was characterized by electrochemical impedance analysis with the redox probe [Fe(CN)(6)](3-/4-). For improving detection sensitivity, the three-level cascaded impedimetric signal amplification was developed: (1) Apt-AuNPs as the first-level signal enhancer; (2) the steric-hindrance between the enlarged Apt-AuNPs as the second-level signal amplification; (3) the electrostatic-repulsion between sodium dodecylsulfate (SDS) stabilized Apt-AuNPs and the redox probe [Fe(CN)(6)](3-/4-) as the third-level signal amplification. Enlargement of Apt-AuNPs integrated with negatively charged surfactant (SDS) capping could not only improve the detection sensitivity of the impedimetric aptasensor for thrombin but also present a simple and general signal-amplification model for impedimetric sensor. The aptasensor based on the enlargement of negatively charged Apt-AuNPs showed an increased response of the electron-transfer resistance to the increase of thrombin concentration through a wide detection range from 100 fM to 100 nM. The linear detection range was 0.05-35 nM, and thrombin was easily detectable to a concentration of 100 fM. The aptasensor also has good selectivity and reproducibility.

Sensitive fluorescence detection of nucleic acids based on isothermal circular strand-displacement polymerization reaction

Here we have developed a sensitive DNA amplified detection method based on isothermal strand-displacement polymerization reaction. This method takes advantage of both the hybridization property of DNA and the strand-displacement property of polymerase. Importantly, we demonstrate that our method produces a circular polymerization reaction activated by the target, which essentially allows it to self-detect. Functionally, this DNA system consists of a hairpin fluorescence probe, a short primer and polymerase. Upon recognition and hybridization with the target ssDNA, the stem of the hairpin probe is opened, after which the opened probe anneals with the primer and triggers the polymerization reaction. During this process of the polymerization reaction, a complementary DNA is synthesized and the hybridized target is displaced. Finally, the displaced target recognizes and hybridizes with another probe, triggering the next round of polymerization reaction, reaching a target detection limit of 6.4 × 10⁻¹⁵ M.

Aptamer-based SERRS sensor for thrombin detection

We describe an aptamer-based surface enhanced resonance Raman scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human alpha-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single-step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes. The specific recognition and binding of thrombin by the thrombin binding aptamer is essential to the mechanism of the aptamer-based sensor, as shown through measurements using negative control oligonucleotides. In addition, the sensor can detect 1 nM thrombin in the presence of complex biofluids, such as 10% fetal calf serum, demonstrating that the immobilized, 5'-capped, 3'-capped aptamer is sufficiently robust for clinical diagnostic applications. Furthermore, the proposed sensor may be implemented for multiplexed detection using different aptamer-Raman probe complexes.

Aptamer switch probe based on intramolecular displacement

A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design utilizes both a fluorophore and a quencher which are respectively modified at the two termini of the ASP. In the absence of the target molecule, the short DNA will hybridize with the aptamer, keeping the fluorophore and quencher in close proximity, thus switching off the fluorescence. However, when the ASP meets its target, the binding between the aptamer and the target molecule will disturb the intramolecular DNA hybridization, move the quencher away from the fluorophore, and, in effect, switch on the fluorescence. Both ATP and human alpha-thrombin aptamers were engineered to demonstrate this design, and both showed that fluorescence enhancement could be quantitatively mediated by the addition of various amounts of target molecules. Both of these ASPs presented excellent selectivity and prompt response toward their targets. With intrinsic advantages resulting from its intramolecular signal transduction architecture, the ASP design holds promising potential for future applications, such as biochip and in situ imaging, which require reusability, excellent stability, prompt response, and high sensitivity.

Visual cocaine detection with gold nanoparticles and rationally engineered aptamer structures

A novel bioassay strategy is designed to detect small-molecule targets such as cocaine, potassium, and adenosine, based on gold nanoparticles (AuNPs) and engineered DNA aptamers. In this design, an aptamer is engineered to be two pieces of random, coil-like single-stranded DNA, which reassembles into the intact aptamer tertiary structure in the presence of the specific target. AuNPs can effectively differentiate between these two states via their characteristic surface-plasmon resonance-based color change. Using this method, cocaine in the low-micromolar range is selectively detected within minutes. This strategy is also shown to be generic and applicable to the detection of several other small-molecule targets.

Preparation of a DNA aptamer-Pt complex and its use in the colorimetric sensing of thrombin and anti-thrombin antibodies

DNA aptamers carrying Pt nanoparticles were prepared by the reaction of DNA aptamers (without functionalization with biotin, thiol, or other reactive groups) with K 2[PtCl 4] in solution at 60-90 degrees C. The DNA-Pt complexes possessed peroxidase enzymatic activity while retaining the specific binding ability of the aptamers. The enzymatic reaction of these complexes obeyed Michaelis-Menten kinetics. K M for the DNA-Pt complex was found to be on the same order as K M for hemin and hemin-DNA complex but 1 or 2 orders of magnitude higher than that of horseradish peroxidase. The rate of the reaction catalyzed by the DNA-Pt complex, k cat, was found to be on the same order as that of hemin and hemin-DNA complex but 2 or 3 orders of magnitude lower than that of horseradish peroxidase. Two types of DNAzyme-linked aptamer assays (DLAAs) were developed using these complexes, which successfully detected target proteins, with the sandwich type of DLAA targeting thrombin and the competitive type of DLAA targeting anti-thrombin IgA/G/M in serum. The DNA-Pt complexes retained their peroxidase enzymatic activity even after heat treatment. DLAAs having high thermal stability were developed using these complexes, which were free of animal and plant matter because neither antibodies nor horseradish peroxidase were used in their synthesis.

Parallel analysis of two analytes in solutions or on surfaces by using a bifunctional aptamer: applications for biosensing and logic gate operations

A bifunctional aptamer that includes two aptamer units for cocaine and adenosine 5'-monophosphate (AMP) is blocked by a nucleic acid to form a hybrid structure with two duplex regions. The blocked bifunctional aptamer assembly is used as a functional structure for the simultaneous sensing of cocaine or AMP. The blocked bifunctional aptamer is dissociated by either of the two analytes, and the readout of the separation of the sensing structure is accomplished by a colorimetric detection, by a released DNAzyme, or by electronic means that use Faradaic impedance spectroscopy or field-effect transistors. In one configuration, the blocked bifunctional aptamer structure is separated by the substrates cocaine or AMP, and the displaced blocker units act as a horseradish peroxidase-mimicking DNAzyme that permits the colorimetric detection of the analytes. In the second system, the blocked bifunctional aptamer hybrid is associated with a Au electrode. The displacement of the aptamer by any of the substrates alters the interfacial electron transfer resistance at the electrode surface, thus providing an electronic signal for the sensing process. In the third configuration, the blocked aptamer hybrid is linked to the gate of a field-effect transistor device. The separation of the complex by means of any of the analytes, cocaine, or AMP alters the gate potential, and this allows the electronic transduction of the sensing process by following the changes in the gate-to-source potentials. The different systems enable not only the simultaneous detection of the two analytes, but they provide a functional assembly that performs a logic gate "OR" operation.

Towards biomedical applications for nucleic acid nanodevices

DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.

Homogeneous DNA-detection based on the non-enzymatic reactions promoted by target DNA

Much effort has focused on methods for detecting various genetic differences in individuals, including single nucleotide polymorphisms (SNPs). SNP can be characterized as a substitution, insertion, or deletion at a single base position on a DNA strand. There is expected to be on average one SNP for every 1000 bases of the human genome, and some variations located in genes are suspected to alter both the protein structure and the expression level. Therefore, highly sensitive techniques with a simple procedure would be desirable for a high-throughput screening of millions of SNPs widely dispersed throughout the human genome. In this short review, we consider recently reported unique techniques for genotyping in a homogeneous solution, and organize them in terms of the chemical and physical processes accelerated on DNA.