Selection of fluorescent aptamer beacons that light up in the presence of zinc

Development of DNA aptamers using Cell-SELEX

In the past two decades, high-affinity nucleic acid aptamers have been developed for a wide variety of pure molecules and complex systems such as live cells. Conceptually, aptamers are developed by an evolutionary process, whereby, as selection progresses, sequences with a certain conformation capable of binding to the target of interest emerge and dominate the pool. This protocol, cell-SELEX (systematic evolution of ligands by exponential enrichment), is a method that can generate DNA aptamers that can bind specifically to a cell type of interest. Commonly, a cancer cell line is used as the target to generate aptamers that can differentiate that cell type from other cancers or normal cells. A single-stranded DNA (ssDNA) library pool is incubated with the target cells. Nonbinding sequences are washed off and bound sequences are recovered from the cells by heating cell-DNA complexes at 95 degrees C, followed by centrifugation. The recovered pool is incubated with the control cell line to filter out the sequences that bind to common molecules on both the target and the control, leading to the enrichment of specific binders to the target. Binding sequences are amplified by PCR using fluorescein isothiocyanate-labeled sense and biotin-labeled antisense primers. This is followed by removal of antisense strands to generate an ssDNA pool for subsequent rounds of selection. The enrichment of the selected pools is monitored by flow cytometry binding assays, with selected pools having increased fluorescence compared with the unselected DNA library. The procedure, from design of oligonucleotides to enrichment of the selected pools, takes approximately 3 months.

Using aptamers to visualize and capture cancer cells

Since diseased cells exist in exceedingly low concentration at the early stage of cancer, highly sensitive imaging and detection methods are required. By improving the methods for capturing and visualizing cancer cells, clinicians can diagnose metastatic relapse, stratify patients for therapeutic purposes, monitor response to drugs and therapies, and track tumor progression. Therefore, using advanced biotechnological and analytical methods combined with cell-SELEX (systematic evolution of ligands by exponential enrichment)-based aptamers, we improved the capture and visualization of diseased cells in a manner that is inexpensive, simple, sensitive, and fast. This multiplexed cancer detection platform therefore improves our control over a range of clinical exigencies, including cancer diagnosis, therapeutic modalities, and drug delivery systems.

Aptamer-DNAzyme hairpins for amplified biosensing

Engineered nucleic acid hairpin structures are used for the amplified analysis of low-molecular-weight substrates (adenosine monophosphate, AMP) or proteins (lysozyme). The hairpin structures consist of the anti-AMP or antilysozyme aptamer units linked to the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The HRP-mimicking DNAzyme sequence is protected in a "caged", inactive structure in the stem regions of the respective hairpins, whereas the loop regions include a part of the respective aptamer sequence. The opening of the hairpins by the analytes, AMP or lysozyme, through the formation of the respective analyte-aptamer complexes, results in the self-assembly of the active HRP-mimicking DNAzyme. The DNAzyme catalyzes the H(2)O(2)-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the colored ABTS(*-), thus providing the amplified optical detection of the respective analytes. The engineered aptamer-DNAzyme hairpin structures reveal significantly improved analytical performance, as compared to analogous fluorophore-quencher-labeled hairpins.

Synthetic biology: understanding biological design from synthetic circuits

An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems - from synthetic promoters to the control of cell-cell interactions - has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics.

The second wave of synthetic biology: from modules to systems

Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering. Efforts in synthetic biology have largely focused on the creation and perfection of genetic devices and small modules that are constructed from these devices. But to view cells as true 'programmable' entities, it is now essential to develop effective strategies for assembling devices and modules into intricate, customizable larger scale systems. The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies.

Nucleic acid aptamers for biosensors and bio-analytical applications

Oligonucleotides were once considered only functional as molecules for the storage of genetic information. However, the discovery of RNAzymes, and later, DNAzymes, unravelled the innate potential of oligonucleotides in many other biological applications. In the last two decades, these applications have been further expanded through the introduction of Systematic Evolution of Ligands by EXponential enrichment (SELEX) which has generated, by repeated rounds of in vitro selection, a type of molecular probe termed aptamers. Aptamers are oligonucleic acid (or peptide) molecules that can bind to various molecular targets and are viewed as complements to antibodies. Aptamers have found applications in many areas, such as bio-technology, medicine, pharmacology, microbiology, and analytical chemistry, including chromatographic separation and biosensors. In this review, we focus on the use of aptamers in the development of biosensors. Coupled with their ability to bind a variety of targets, the robust nature of oligonucleotides, in terms of synthesis, storage, and wide range of temperature stability and chemical manipulation, makes them highly suitable for biosensor design and engineering. Among the many design strategies, we discuss three general paradigms that have appeared most frequently in the literature: structure-switching, enzyme-based, and aptazyme-based designs.

Application and analysis of structure-switching aptamers for small molecule quantification

Modern tools for the analysis of cellular function aim for the quantitative measurement of all members of a given class of biological molecules. Of the analyte classes, nucleic acid measurements are typically the most tractable, both on an individual analyte basis and in parallel. Thus, tools are being sought to enable measurement of other cellular molecules using nucleic acid biosensors. Of the variety of potential nucleic acid biosensor strategies, structure-switching aptamers (SSAs) present a unique opportunity to couple sensing and readout of the target molecule. However, little has been characterized about the parameters that determine the fidelity of the signal from SSA biosensors. In this study, a small molecule biosensor based on a SSA was engineered to detect the model small molecule, theophylline, in solution. Quantitative theophylline detection over nearly three orders-of-magnitude was achieved by scintillation counting and quantitative PCR. Further analysis showed that the biosensor fidelity is primarily controlled by the relative stability of the two conformations of the SSA.

Applications of aptamers as sensors

Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.

Mutational analysis of a signaling aptamer suggests a mechanism for ligand-triggered structure-switching

Structure-switching signaling aptamers are nucleic acids that change shape upon binding to a specific ligand. Previously, we applied a new in vitro selection strategy to isolate structure-switching RNA aptamers responsive to the aminoglycoside antibiotic tobramycin. Here, we report the results of mutational analysis, secondary structure modeling, and ligand-specificity studies that suggest a mechanism for tobramycin-triggered structure switching.