Analytical applications of aptamers

Assembling Amperometric Biosensors for Clinical Diagnostics

Clinical diagnosis and disease prevention routinely require the assessment ofspecies determined by chemical analysis. Biosensor technology offers several benefits overconventional diagnostic analysis. They include simplicity of use, specificity for the targetanalyte, speed to arise to a result, capability for continuous monitoring and multiplexing,together with the potentiality of coupling to low-cost, portable instrumentation. This workfocuses on the basic lines of decisions when designing electron-transfer-based biosensorsfor clinical analysis, with emphasis on the strategies currently used to improve the deviceperformance, the present status of amperometric electrodes for biomedicine, and the trendsand challenges envisaged for the near future.

Aspects of recent development of immunosensors

This chapter focuses on the recent developments in the field of immunosensors. Immunosensors incorporate the specific immunochemical reaction with the modern transducers including electrochemical (potentiometric, conductometric, capacitative, impedance, amperometric), optical (fluorescence, luminescence, refractive index), and microgravimetric transducers. These immunosensor devices with dramatic improvements in the sensitivity and selectivity possess the abilities to investigate the reaction dynamics of antibody–antigen binding and the potential to revolutionize conventional immunoassay techniques. With the rapid development of immunological reagents and detection equipments, immunosensors have allowed an increasing range of analytes to be identified and quantified and in particular, simple-to-use, inexpensive, and reliable immunosensing systems have been developed for areas such as outpatient monitoring, large screening programs, and remote environmental surveillance. Immunosensors with lowered detection limits and increased sensitivities have been developed in various fields, particularly in clinical analysis. A noticeable development trend is also observed in the development of immunosensors combining with other techniques such as flow injection analysis (FIA) or capillary electrophoretic (CE) analysis, which complement and improve the present immunoassay methods. Belov et al. have proposed a novel immunophenotyping method for leukemias which uses a cluster of differentiation antibody microarray, and a microarray of enzyme-linked immunosorbent assay has been developed for autoimmune diagnosis of systematic rheumatic disease. Development of microfluidic immunosensor systems for proteomics and drug discovery have also been reported in recent years where the microfluidic system integrates multiple processes in a single device to improve analytical performance by reducing the reagent consumption and the analysis time, and increasing reliability and sensitivity through automation.

Characterizing the interaction between aptamers and human IgE by use of surface plasmon resonance

Human immunoglobulin E (hIgE) is such an important protein, because of its involvement in allergic disease, that it is of significance to study the interactions between it and its recognizing elements. In this report an analytical strategy based on surface plasmon resonance (SPR) was developed to probe the pattern of interaction between hIgE and its recognizing molecules, including aptamers and antibodies. The affinity constants of hIgE for the antibody and the aptamer were compared first; the aptamer has more affinity than the antibody for human IgE. To study their pattern of interaction, three different binding approaches, including adding the antibody and the streptavidin-coupled aptamer to the sensing surface, were designed. The results showed that hIgE captured on the sensing surface could form a multivalent complex with the aptamer. An ELISA-like assay using the aptamer as both capture and detection probes was then developed. This work highlights an SPR method for characterizing the interaction between the protein and aptamers that is useful for study of biomolecular interaction patterns and binding properties.

Development of an optical RNA-based aptasensor for C-reactive protein

The development of a RNA-aptamer-based optical biosensor (aptasensor) for C-reactive protein (CRP) is reported. CRP is an important clinical biomarker; it was the first acute-phase protein to be discovered (1930) and is a sensitive systemic marker of inflammation and tissue damage. It has also a prognostic value for patients with acute coronary syndrome. The average concentration of CRP in serum is 0.8 ppm and it increases in response to a variety of inflammatory stimuli, such as trauma, tissue necrosis, infection and myocardial infarction. The interaction between the 44-base RNA aptamer and the target analyte CRP is studied. In particular, the influence of the aptamer immobilization procedure (chemistry, length, concentration), as well as the binding conditions, i.e., the influence on the binding of different buffers, the presence of Ca2+ ion and the specificity (against human serum albumin) have been evaluated. Using the best working conditions, we achieved a detection limit of 0.005 ppm, with good selectivity towards human serum albumin. Some preliminary experiments in serum are reported.

Anti-coagulant aptamers

In the past decade development of aptamer technology is poised into several fields with various clinical applications. With this progress, aptamer based anti-coagulant agents are evolved and continuing their applications with clinical trials. At present several anti-coagulant aptamers are available against different proteins from blood coagulation cascade. In this review, the mechanism and functions of anti-coagulant aptamers, as an alternate candidate to other available anti-coagulant agents are discussed.

Electronic aptamer-based sensors

The selection of aptamers-nucleic acids that specifically bind low-molecular-weight substrates or proteins-by the SELEX (systematic evolution of ligands by exponential enrichment) procedure has attracted recent efforts directed to the development of new specific recognition units. In particular, extensive activities have been directed to the application of aptamers as versatile materials for the design of biosensors. The Minireview summarizes the recent accomplishments in developing electronic aptamer-based sensors (aptasensors), which include electrochemical, field-effect transistor, and microgravimetric quartz crystal microbalance sensors, and describes methods to develop amplified aptasensor devices and label-free aptasensors.

Exploring the sequence space of a DNA aptamer using microarrays

The relationship between sequence and binding properties of an aptamer for immunoglobulin E (IgE) was investigated using custom DNA microarrays. Single, double and some triple mutations of the aptamer sequence were created to evaluate the importance of specific base composition on aptamer binding. The majority of the positions in the aptamer sequence were found to be immutable, with changes at these positions resulting in more than a 100-fold decrease in binding affinity. Improvements in binding were observed by altering the stem region of the aptamer, suggesting that it plays a significant role in binding. Results obtained for the various mutations were used to estimate the information content and the probability of finding a functional aptamer sequence by selection from a random library. For the IgE-binding aptamer, this probability is on the order of 10⁻¹⁰ to 10⁻⁹. Results obtained for the double and triple mutations also show that there are no compensatory mutations within the space defined by those mutations. Apparently, at least for this particular aptamer, the functional sequence space can be represented as a rugged landscape with sharp peaks defined by highly constrained base compositions. This makes the rational optimization of aptamer sequences using step-wise mutagenesis approaches very challenging.

Microfluidic selection and applications of aptamers

The high affinity and specificity of aptamers make them ideal reagents for a wide range of analytical applications. It is not surprising that they are finding application in microfluidics as well. CE has proven to be an efficient technique for isolating aptamers. Aptamers have been used as affinity reagents in CE assays. Aptamer-based chromatography stationary phases have demonstrated unique selectivities. Possibly the application that holds the highest potential is aptamer microarrays for screening proteomic samples.

Characterization and application of a novel RNA aptamer against the mouse prion protein

In order to isolate RNA aptamers against the mouse prion protein (mPrP), we carried out in vitro selection from RNA pools containing a 30-nucleotide randomized region. Aptamer 60-3 was found to have a high affinity for mPrP (K(d) = 5.6 +/- 1.5 nM), and 2'-fluoro-pyrimidine modifications for RNase resistance did not abolish its binding activity (K(d) = 22 +/- 4 nM). Following 5' biotinylation, aptamer 60-3 specifically detected PrP in mouse brain homogenate in a Northwestern blotting assay. To determine the mPrP-aptamer binding region, we performed protein-deletion-mutant analysis and competition-binding analysis using heparin. The results showed that aptamer 60-3 appears to have binding sites located between amino acids 23-108.

Surface immobilization methods for aptamer diagnostic applications

In this review we examine various methods for the immobilization of aptamers onto different substrates that can be utilized in a diverse array of analytical formats. In most cases, covalent linking to surfaces is preferred over physisorption, which is reflected in the bulk of the reports covered within this review. Conjugation of aptamers with appropriate linkers directly to gold films or particles is discussed first, followed by methods for conjugating aptamers to functionally modified surfaces. In many aptamer-based applications, silicates and silicon oxide surfaces provide an advantage over metallic substrates, and generally require surface modification prior to covalent attachment of the aptamers. Chemical protocols for covalent attachment of aptamers to functionalized surfaces are summarized in the review, showing common pathways employed for aptamer immobilization on different surfaces. Biocoatings, such as avidin or one of its derivatives, have been shown to be highly successful for immobilizing biotin-tethered aptamers on various surfaces (e.g., gold, silicates, polymers). There are also a few examples reported of aptamer immobilization on other novel substrates, such as quantum dots, carbon nanotubes, and carbohydrates. This review covers the literature on aptamer immobilization up to March 2007, including comparison of different linkers of varying size and chemical structure, 3' versus 5' attachment, and regeneration methods of aptamers on surfaces.

Ultrasensitive electrochemical detection of proteins by amplification of aptamer-nanoparticle bio bar codes

An ultrasensitive label-free bioelectrochemical method for rapid determination of thrombin has been developed by directly detecting the redox activity of adenine (A) nucleobases of anti-thrombin aptamer using a pyrolytic graphite electrode. The bioelectrochemical protocol involves a sandwich format. Thrombin, captured by immobilzed anti-thrombin antibody on microtiter plates, is detected by anti-thrombin aptamer-Au nanoparticle bio bar codes. A systematic optimization of the parameters has been carried out via ELAA (enzyme linked aptamer assay) performance. The adenine nucleobases were released by acid or nuclease from Au nanoparticles bound on microtiter plates. Differential pulse voltammetry was employed to investigate the electrochemical behaviors of the purine nucleobases. Well-defined adenine signal was observed at about 0.85 V in pH 5.9 acetate buffer. Because the nanoparticle carries a large number of aptamers per thrombin binding event, there is substantial amplification and thrombin can be detected at a very low level of detection (0.1 ng/mL). This method has been used to detect thrombin in complex matrix such as fetal calf serum with minimum background interference.

Antiviral aptamers

Aptamers are rare nucleic acid ligands, which can be concocted in the laboratory from the randomized pool of molecules by affinity and amplification processes. Aptamers have several properties as they can be applied complementarily to antibodies and have several advantages over antibodies. In the past, several aptamers have been selected with a view to develop antiviral agents for therapeutic applications. This review summarizes potent antiviral aptamers and their strategies to prevent the viral replication.

Complex SELEX against target mixture: stochastic computer model, simulation, and analysis

Systematic evolution of ligands by exponential enrichment (SELEX) is an important technology in combinatorial chemistry and molecular biology of developing high affinity target-binding molecules (aptamers) from highly complex nucleic acid ligand libraries. Schematically, the SELEX is a series of iterative rounds of operations where in each operational round ligands are incubated with the target (e.g., a purified protein), and target-binding ligands are extracted and amplified. In the recent development of biological study and drug discovery, by incubating ligand libraries with complex target mixtures (e.g., cell fragments), the SELEX experiments have been explored to simultaneously develop aptamers for targets embedded in target mixtures: the complex SELEX. While holding the considerable advantages of saving experimental resources, practicing the complex SELEX has often accompanied with unstable experimental performances. It is therefore important to understand the behaviors of the new application. In this paper, we develop stochastic computer model, and customized computational algorithm to numerically mimic the complex SELEX. We model the ligand selection through the probability of ligand binding to complex targets at the binding equilibrium, and efficiency of separating target-binders for amplification. The customized computational algorithm allows us to simulate real experiments that operate on huge ligand libraries. We evaluate the ligand evolution, and aptamer enrichment of complex SELEX under various experimental conditions by stochastic simulations, and theorize the simulated results. We argue that the stochastic effects, which were not previously captured in the studies of complex SELEX, may significantly affect the results of experiments.

Detection of proteins and bacteria using an array of feedback capacitance sensors

An integrated array of micron-dimension capacitors, originally developed for biometric applications (fingerprint identification), was engineered for detection of biological agents such as proteins and bacteria. This device consists of an array of 93,184 (256 x 364) individual capacitor-based sensing elements located underneath a thin (0.8 microm) layer of glass. This glass layer can be functionalized with organosilane-based monolayers to provide groups amenable for the immobilization of bioreceptors such as antibodies, enzymes, peptides, aptamers, and nucleotides. Upon functionalization with antibodies and in conjunction with signal amplification schemes that result in perturbation of the dielectric constant around the captured antigens, this system can be used as a detector of biological agents. Two signal amplification schemes were tested in this work: one consisted of 4 microm diameter latex immunobeads and a second one was based on colloidal gold catalyzed reduction of silver. These signal amplification approaches were demonstrated and show that this system is capable of specific detection of bacteria (Escherichia coli) and proteins (ovalbumin). The present work shows proof-of-principle demonstration that a simple fingerprint detector based on feedback capacitance measurements can be implemented as a biosensor. The approach presented could be easily expanded to simultaneously test for a large number of analytes and multiple samples given that this device has a large number of detectors. The device and required instrumentation is highly portable and does not require expensive and bulky instrumentation because it relies purely on electronic detection.

Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips

We report on the use of PDMS multichannels for affinity studies of DNA aptamer-human Immunoglobulin E (IgE) interactions by surface plasmon resonance imaging (SPRi). The sensing surface was prepared with thiol-terminated aptamers through a self-assembling process in the PDMS channels defined on a gold substrate. Cysteamine was codeposited with the thiol aptamers to promote proper spatial arrangement of the aptamers and thus maintain their optimal binding efficiencies. Four aptamers with different nucleic acid sequences were studied to test their interaction affinity toward IgE, and the results confirmed that aptamer I (5'-SH-GGG GCA CGT TTA TCC GTC CCT CCT AGT GGC GTG CCC C-3') has the strongest binding affinity. Control experiments were conducted with a PEG-functionalized surface and IgG was used to replace IgE in order to verify the selective binding of aptamer I to the IgE molecules. A linear concentration-dependent relationship between IgE and aptamer I was obtained, and a 2-nM detection limit was achieved. SPRi data were further analyzed by global fitting, and the dissociation constant of aptamer I-IgE complex was found to be 2.7 x 10(-7) M, which agrees relatively well with the values reported in the literature. Aptamer affinity screening by SPR imaging demonstrates marked advantages over competing methods because it does not require labeling, can be used in real-time, and is potentially high-throughput. The ability to provide both qualitative and quantitative results on a multichannel chip further establishes SPRi as a powerful tool for the study of biological interactions in a multiplexed format.

A nucleic acid biosensor for the detection of a short sequence related to the hepatitis B virus using bis(benzimidazole)cadmium(II) dinitrate as an electrochemical indicator

A novel hybridization indicator, bis(benzimidazole)cadmium(II) dinitrate (Cd(bzim)(2)(NO(3))(2)), was utilized to develop an electrochemical DNA biosensor for the detection of a short DNA sequence related to the hepatitis B virus (HBV). The sensor relies on the immobilization and hybridization of the 21-mer single-stranded oligonucleotide from the HBV long repeat at the glassy carbon electrode (GCE). The hybridization between the probe and its complementary sequence as the target was studied by enhancement of the peak of the Cd(bzim)(2)(2+) indicator using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Numerous factors affecting the probe immobilization, target hybridization, and indicator binding reactions were optimized to maximize the sensitivity and speed of the assay time. With this approach, a sequence of the HBV could be quantified over the range from 1.49x10(-7)M to 1.06x10(-6)M, with a linear correlation of r=0.9973 and a detection limit of 8.4x10(-8)M. The Cd(bzim)(2)(2+) signal observed from the probe sequence before and after hybridization with a four-base mismatch containing sequence was lower than that observed after hybridization with a complementary sequence, showing good selectivity. These results demonstrate that the Cd(bzim)(2)(2+) indicator provides great promise for the rapid and specific measurement of the target DNA.

Detection of thrombin using electrogenerated chemiluminescence based on Ru(bpy)3(2+)-doped silica nanoparticle aptasensor via target protein-induced strand displacement

A sensitive and selective aptasensor using tri(2,2'-bipyridyl)ruthenium(II)-doped silica nanoparticles (Ru(bpy)3(2+)-doped SNPs) as DNA tags for detection of thrombin is developed based on the target protein-induced strand displacement of the DNA probe. For the proposed aptasensor, the aptamer was assembled on the surface of the Au electrode through Au-S binding. The hybridization event between the DNA probe labeled by the Ru(bpy)3(2+)-doped SNPs and the aptamer was evaluated by electrogenerated chemiluminescence (ECL) measurements. Then, the DNA probe was displaced by thrombin and the binding event between the thrombin and the aptamer was monitored by ECL measurements again. The difference of ECL intensity (deltaI(ECL)) of the two events could be used to quantify the thrombin. Other proteins, such as bovine serum albumin and bovine hemoglobin, had almost negligible deltaI(ECL). Under the optimal conditions, the deltaI(ECL) was linearly related to the concentration of the thrombin in the range of 10 fM to 10 pM and the detection limit was down to 1.0 fM since SNPs containing a large number of Ru(bpy)3(2+) molecules were labeled on the DNA probe.

SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands

SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.

Advantages and limitations of on-line solid phase extraction coupled to liquid chromatography–mass spectrometry technologies versus biosensors for monitoring of emerging contaminants in water

On-line solid phase extraction (SPE) coupled to liquid chromatography-mass spectrometry (LC-MS) and biosensors are advanced technologies that have found increasing application in the analysis of environmental contaminants although their application to the determination of emerging contaminants (previously unknown or unrecognized pollutants) has been still limited. This review covers the most recent advances occurred in the areas of on-line SPE-LC-MS and biosensors, discusses and compares the main strengths and limitations of the two approaches, and examines their most relevant applications to the analysis of emerging contaminants in environmental waters. So far, the on-line configuration most frequently used has been SPE coupled to liquid chromatography-(tandem) mass spectrometry. Sorbents used for on-line SPE have included both traditional (alkyl-bonded silicas and polymers) and novel (restricted access materials (RAMs), molecularly imprinted synthetic polymers (MIPs), and immobilized receptors or antibodies (immunosorbents) materials. The biosensor technologies most frequently applied have been based on the use of antibodies and, to a lesser extent, enzymes, bacteria, receptors and DNA as recognition elements, and the use of optical and electrochemical transducing elements. Emerging contaminants investigated by means of these two techniques have included pharmaceuticals, endocrine disrupting compounds such as estrogens, alkylphenols and bisphenol A, pesticides transformation products, disinfection by-products, and bacterial toxins and mycotoxins, among others. Both techniques offer advantageous, and frequently comparable, features such as high sensitivity and selectivity, minimum sample manipulation, and automation. Biosensors are, in addition, relatively cheap and fast, which make them ideally suited for routine testing and screening of samples; however, in most cases, they can not compete yet with on-line SPE procedures in terms of accuracy, reproducibility, reliability (confirmation) of results, and capacity for multi-analyte determination.

Aptamer-functionalized gold nanoparticles for turn-on light switch detection of platelet-derived growth factor

An aptamer modified gold nanoparticles (Apt-AuNPs) based molecular light switching sensor has been demonstrated for the analysis of breast cancer markers (platelet-derived growth factors (PDGFs) and their receptors) in homogeneous solutions. The PDGF binding aptamer has a unique structure with triple-helix conformation that allows N,N-dimethyl-2,7-diazapyrenium dication (DMDAP) and PDGF bindings. The fluorescence of DMDAP is almost completely quenched by Apt-AuNPs when it intercalates with the aptamers. Owing to high magnitudes of increases (up to 40-fold) in the turn-on fluorescence signals of DMDAP/Apt-AuNP upon PDGFs binding, the approach is highly sensitive for the detection of PDGFs. The DMDAP/Apt-AuNP probe specifically and sensitively detected PDGFs under optimal concentrations of salts and DMDAP. We also demonstrated that the Apt-AuNPs are effective selectors for enrichment of PDGF-AA from large-volume samples. The approach allows detection of PDGF-AA at a concentration down to 8 pM, showing better sensitivity than other signal aptamers. By conducting a competitive assay, we demonstrated the determination of PDGF receptor-alpha with LOD of 0.25 nM when using the DMDAP/Apt-AuNP as a probe.

Direct selection of RNA beacon aptamers

A method for the direct selection of RNA molecules that can be easily converted into beacon aptamers is presented. Beacon aptamers are fluorescently labeled nucleic acids that signal the presence of a specific ligand through changes in fluorescence intensity. Typically, ligand binding causes an increase in fluorescence intensity by inducing a conformational change that separates a fluorophore/quencher pair. The method presented here simultaneously selects for ligand binding and induction of an appropriate conformational change. The method was tested by selecting RNA molecules that can detect the aminoglycoside antibiotic tobramycin. After 14 rounds of selection, two sequence families emerged. Upon conversion into beacon aptamers, representatives of the two selected sequence families specifically detected tobramycin, while a negative control RNA that did not survive the selection protocol did not function as a tobramycin beacon aptamer.

Aptamer-based enantioselective competitive binding assay for the trace enantiomer detection

The development of highly enantioselective assays and sensors has received much attention for the determination of enantiomeric impurities at a low level. For chiral compounds, the efficient monitoring of the in selection procedure has allowed the isolation of nucleic acid aptamers which are able to strongly discriminate the target enantiomers. In this paper, we demonstrated for the first time that an aptamer can be successfully used to design a highly enantioselective tool for the trace enantiomer detection. The aptamer-based stereoselective assay was developed using an affinity capillary electrophoresis-based competitive, homogeneous format and an on-capillary mixing approach. Detection of as low as 0.01% of the minor enantiomer in a nonracemic mixture can be achieved, in a short analysis time (<5 min).

Label-Free Impedance Biosensors: Opportunities and Challenges

Impedance biosensors are a class of electrical biosensors that show promise for point-of-care and other applications due to low cost, ease of miniaturization, and label-free operation. Unlabeled DNA and protein targets can be detected by monitoring changes in surface impedance when a target molecule binds to an immobilized probe. The affinity capture step leads to challenges shared by all label-free affinity biosensors; these challenges are discussed along with others unique to impedance readout. Various possible mechanisms for impedance change upon target binding are discussed. We critically summarize accomplishments of past label-free impedance biosensors and identify areas for future research.

Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells

We have developed a method for the rapid collection and detection of leukemia cells using a novel two-nanoparticle assay with aptamers as the molecular recognition element. An aptamer sequence was selected using a cell-based SELEX strategy in our laboratory for CCRF-CEM acute leukemia cells that, when applied in this method, allows for specific recognition of the cells from complex mixtures including whole blood samples. Aptamer-modified magnetic nanoparticles were used for target cell extraction, while aptamer-modified fluorescent nanoparticles were simultaneously added for sensitive cell detection. Combining two types of nanoparticles allows for rapid, selective, and sensitive detection not possible by using either particle alone. Fluorescent nanoparticles amplify the signal intensity corresponding to a single aptamer binding event, resulting in improved sensitivity over methods using individual dye-labeled probes. In addition, aptamer-modified magnetic nanoparticles allow for rapid extraction of target cells not possible with other separation methods. Fluorescent imaging and flow cytometry were used for cellular detection to demonstrate the potential application of this method for medical diagnostics.

Selection of smart aptamers by methods of kinetic capillary electrophoresis

We coin the term "smart aptamers" -- aptamers with predefined binding parameters (k(on), k(off), Kd) of aptamer-target interaction. Aptamers, in general, are oligonucleotides, which are capable of binding target molecules with high affinity and selectivity. They are considered as potential therapeutic targets and also thought to rival antibodies in immunoassay-like analyses. Aptamers are selected from combinatorial libraries of oligonucleotides by affinity methods. Until now, technological limitations have precluded the development of smart aptamers. Here, we report on two kinetic capillary electrophoresis techniques applicable to the selection of smart aptamers. Equilibrium capillary electrophoresis of equilibrium mixtures was used to develop aptamers with predefined equilibrium dissociation constants (Kd), while nonequilibrium capillary electrophoresis of equilibrium mixtures facilitated selection of aptamers with different dissociation rate constants (k(off)). Selections were made for MutS protein, for which aptamers have never been previously developed. Both theoretical and practical aspects of smart aptamer development are presented, and the advantages of this new type of affinity probes are described.

Signaling aptamers created using fluorescent nucleotide analogues

A new approach to creating fluorescent signaling aptamers using fluorescent nucleotide analogues is presented. The fluorescence quantum yield of nucleotide analogues such as 2-aminopurine strongly depends on base stacking interactions when incorporated into double or single stranded DNA. This property is used to generate a binding-specific fluorescence signal. Aptamers for human alpha-thrombin, immunoglobulin E, and platelet-derived growth factor B were modified with fluorescent nucleotide analogues in positions that undergo conformational changes. The resulting signaling aptamers show a specific, binding-induced increase in the fluorescence signal of up to 30-fold. Conformation-changing positions in these aptamers were identified by screening a set of modified aptamer sequences that each included a fluorescent nucleotide analogue at a different position. The positions for these modifications were estimated by modeling the aptamer secondary structure. It is likely that this approach to producing fluorescent signaling aptamers is of general use for protein-binding aptamers because of their "induced fit" binding mechanism.

Aptamer-based detection of plasma proteins by an electrochemical assay coupled to magnetic beads

The DNA thrombin aptamer has been extensively investigated, and the coupling of this aptamer to different transduction principles has demonstrated the wide applicability of aptamers as bioreceptors in bioanalytical assays. The goal of this work was to design an aptamer-based sandwich assay with electrochemical detection for thrombin analysis in complex matrixes, using a simple target capturing step by aptamer-functionalized magnetic beads. The conditions for the aptamer immobilization and for the protein binding have been first optimized by surface plasmon resonance, and then transferred to the electrochemical-based assay performed onto screen-printed electrodes. The assay was then applied to the analysis of thrombin in buffer, spiked serum, and plasma and high sensitivity and specificity were found. Moreover, thrombin was generated in situ in plasma by the conversion of its precursor prothrombin, and the formation of thrombin was followed at different times. The concentrations detected by the electrochemical assay were in agreement with a simulation software that mimics the formation of thrombin over time (thrombogram). The proposed work demonstrates that the high specificity of aptamers together with the use of magnetic beads are the key features for aptamer-based analysis in complex matrixes, opening the possibility of a real application to diagnostics or medical investigation.

Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3

We previously described a cis-acting RNA-cleaving deoxyribozyme known as pH3DZ1 that exhibits optimal catalytic activity at pH 3.0 (Zhongjie Liu, Shirley H. Mei, John D. Brennan, and Yingfu Li. J. Am. Chem. Soc. 125, 7539 (2003)). This DNA catalyst was made of a 99-nucleotide (nt) catalytic domain covalently linked to a 23-nt DNA–RNA chimeric substrate containing a single ribonucleotide as the cleavage site. In the present work, we conducted an extensive sequence examination of this deoxyribozyme via nucleotide truncation and reselection experiments, with a goal to minimize its size and identify the nucleotides that are crucial to its catalytic function. A trans-acting deoxyribozyme that can process an external substrate was also successfully designed. Stretches of 30 and 17 nucleotides from the 5′ and 3′ ends of the trans catalyst, respectively, were found to be completely dispensable; in contrast, few nucleotides could be deleted internally without producing a detrimental effect. The reselection experiment led to the discovery of 7 and 5 absolutely conserved nucleotides located at the 5′ and 3′ ends of the minimized catalyst, respectively, separated by a 31-nt element in which 14 highly conserved nucleotides were scattered among 17 variable nucleotides. The shortened deoxyribozyme and the original catalyst showed a similar pH profile with the optimal activity at pH 3; however, the minimized deoxyribozyme still exhibited strong catalytic activity at pH 2.5, while the full-length catalyst was barely active at this pH. Finally, it was found that this deoxyribozyme generated two cleavage fragments, one with 2′,3′-cyclic phosphate and the other with 5′-OH.Key words: DNA, deoxyribozyme, RNA cleavage, in vitro selection, catalysis.

SELEX and dynamic combinatorial chemistry interplay for the selection of conjugated RNA aptamers

SELEX (for Systematic Evolution of Ligands by Exponential enrichment) has proven to be extraordinarily powerful for the isolation of DNA or RNA aptamers that bind with high affinity and specificity to a wide range of molecular targets. However, the modest chemical functionality of nucleic acids poses some limits on the versatility of aptamers as binders and catalysts. To further improve the properties of aptamers, additional chemical diversity must be introduced. The design of chemical modifications is not a trivial task. Recently, dynamic combinatorial chemistry (DCC) has been introduced as an alternative to traditional combinatorial chemistry. DCC employs equilibrium shifting to effect molecular evolution of a dynamic combinatorial library of molecules. Herein, we describe an original process that combines DCC and SELEX for the in vitro selection of modified aptamers which are conjugated to chemically diverse small-molecules. Its successful application for the selection of small-molecule conjugated RNA aptamers that bind tightly to the transactivation-response (TAR) element of HIV-1 is presented.

Aptamers-based assays for diagnostics, environmental and food analysis

Aptamers are single stranded DNA or RNA ligands which can be selected for different targets starting from a huge library of molecules containing randomly created sequences. Aptamers have been selected to bind very different targets, from proteins to small organic dyes. In addition to the very important aspect of having an unlimited source of identical affinity recognition molecules available due to the selection process, aptamers can offer advantages over antibodies that make them very promising for analytical applications. The use of aptamers as therapeutic tools is nowadays well established. On the contrary, the analytical application of aptamers in diagnostic devices or in systems for environmental and food analysis, is still under investigation and the scientific community still need further research to demonstrate the advancements brought by this new kind of ligands. This review will focus on these latter applications with particular attention to the detection of food pathogens, terrorism threat agents, thrombin and cytokines.

Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors

We have fabricated label-free protein biosensors based on aptamer-modified carbon nanotube field-effect transistors (CNT-FETs) for the detection of immunoglobulin E (IgE). After the covalent immobilization of 5'-amino-modified 45-mer aptamers on the CNT channels, the electrical properties of the CNT-FETs were monitored in real time. The introduction of target IgE at various concentrations caused a sharp decrease in the source-drain current, and a gradual saturation was observed at lower concentrations. The amount of the net source-drain current before and after IgE introduction on the aptamer-modified CNT-FETs increased as a function of IgE concentration. The detection limit for IgE was determined as 250 pM. We have also prepared CNT-FET biosensors using a monoclonal antibody against IgE (IgE-mAb). The electrical properties of the aptamer- and antibody-modified CNT-FETs were compared. The performance of aptamer-modified CNT-FETs provided better results than the ones obtained using IgE-mAb-modified CNT-FETs under similar conditions. Thus, we suggest that the aptamer-modified CNT-FETs are promising candidates for the development of label-free protein biosensors.

SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways

Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target. The procedure can be used to infer the strongest binders for a given DNA or RNA binding protein, and the highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic and therapeutic applications. Recently, important new modifications of the SELEX protocol have been proposed. In particular, a modification of the standard SELEX procedure allows generating a dataset from which protein-DNA interaction parameters can be determined with unprecedented accuracy. Another variant of SELEX allows investigating interactions of a protein with nucleic-acid fragments derived from the entire genome of an organism. We review here different SELEX-based methods, with particular emphasis on the experimental design and on the applications aimed at inferring protein-DNA interactions. In addition to the experimental issues, we also review relevant methods of data analysis, as well as theoretical modeling of SELEX.

Aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells

We have extended the use the aptamer-conjugated nanoparticles for the collection and detection of multiple cancer cells. The aptamers were selected using a cell-based SELEX strategy in our laboratory for cancer cells that, when utilized in this method, allow for the selective recognition of the cells from complex mixtures including fetal bovine serum samples. Aptamer-conjugated magnetic nanoparticles were used for the selective targeting cell extraction, and aptamer-conjugated fluorescent nanoparticles were employed for sensitive cellular detection. Employing both types of nanoparticles allows for selective and sensitive detection not possible by using the particles separately. Fluorescent nanoparticles amplify the signal intensity versus a single fluorophore label resulting in improved sensitivity. In addition, aptamer-conjugated magnetic nanoparticles allow for extraction and enrichment of target cells not possible with other separation methods. Fluorescent imaging and a microplate reader were used for cellular detection to demonstrate the wide applicability of this methodology for medical diagnostics and cell enrichment and separation.

Analytical performances of aptamer-based sensing for thrombin detection

Aptamer-based assays represent a modern and attractive approach in bioanalytical chemistry. The DNA thrombin aptamer has been extensively investigated, and the coupling of this aptamer to different transduction principles has demonstrated the wide applicability of aptamers as bioreceptors in bioanalytical assays. The goal of this work was to critically evaluate all the parameters that can influence the sensor performances by using the thrombin aptamer immobilized onto piezoelectric quartz crystals. The optimization of the immobilization and the binding protocol was of paramount importance, and improvements in analytical performances could be obtained by optimizing simple steps in immobilization and assay conditions. Moreover, the work demonstrated the possibility of using aptamer-based sensors in complex matrixes, opening the possibility of a real application to diagnostics or medical investigation.

A mathematical analysis of SELEX

Systematic evolution of ligands by exponential enrichment (SELEX) is a procedure by which a mixture of nucleic acids that vary in sequence can be separated into pure components with the goal of isolating those with specific biochemical activities. The basic idea is to combine the mixture with a specific target molecule and then separate the target-NA complex from the resulting reaction. The target-NA complex is then separated by mechanical means (for example by filtration), the NA is then eluted from the complex, amplified by polymerase chain reaction (PCR) and the process repeated. After several rounds, one should be left with a pool of [NA] that consists mostly of the species in the original pool that best binds to the target. In Irvine et al. [Irvine, D., Tuerk, C., Gold, L., 1991. SELEXION, systematic evolution of nucleic acids by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 222, 739-761] a mathematical analysis of this process was given. In this paper we revisit Irvine et al. [Ibid]. By rewriting the equations for the SELEX process, we considerably reduce the labor of computing the round to round distribution of nucleic acid fractions. We also establish necessary and sufficient conditions for the SELEX process to converge to a pool consisting solely of the best binding nucleic acid to a fixed target in a manner that maximizes the percentage of bound target. The assumption is that there is a single nucleic acid binding site on the target that permits occupation by not more than one nucleic acid. We analyze the case for which there is no background loss (no support losses and no free [NA] left on the support). We then examine the case in which such there are such losses. The significance of the analysis is that it suggests an experimental approach for the SELEX process as defined in Irvine et al. [Ibid] to converge to a pool consisting of a single best binding nucleic acid without recourse to any a priori information about the nature of the binding constants or the distribution of the individual nucleic acid fragments.

Electrochemical strategies for the label-free detection of amino acids, peptides and proteins

Electrochemical methods for the detection of amino acids, peptides, and proteins in a variety of media are reviewed. Label-free strategies in which the detection is based on the inherent electrochemical properties of the analyte are discussed. Various processes such as direct or mediated (in solution or immobilised) redox processes and interfacial ion transfers have been employed for the electrochemical detection and determination of the target analytes. The various methods covered encompass voltammetry at uncoated and modified electrodes and at immiscible liquid-liquid interfaces, potentiometry at polymer membrane electrodes and electrochemical impedance spectroscopy. The determination of the target analytes in complex biological matrices is discussed. The various approaches highlighted here illustrate the rich capabilities of electrochemical methods as simple, low-cost, sensitive tools for the determination of these important biological analytes at trace and ultra-trace levels.