Xiangling Xiong

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 °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 ∼3 months.

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.

Aptamer-Enabled Efficient Isolation of Cancer Cells from Whole Blood Using a Microfluidic Device

Circulating tumor cells (CTC) in the peripheral blood could provide important information for diagnosis of cancer metastasis and monitoring treatment progress. However, CTC are extremely rare in the bloodstream, making their detection and characterization technically challenging. We report here the development of an aptamer-mediated, micropillar-based microfluidic device that is able to efficiently isolate tumor cells from unprocessed whole blood. High-affinity aptamers were used as an alternative to antibodies for cancer cell isolation. The microscope-slide-sized device consists of >59,000 micropillars, which enhanced the probability of the interactions between aptamers and target cancer cells. The device geometry and the flow rate were investigated and optimized by studying their effects on the isolation of target leukemia cells from a cell mixture. The device yielded a capture efficiency of ~95% with purity of ~81% at the optimum flow rate of 600 nL/s. Further, we exploited the device for isolating colorectal tumor cells from unprocessed whole blood; as few as 10 tumor cells were captured from 1 mL of whole blood. We also addressed the question of low throughput of a typical microfluidic device by processing 1 mL of blood within 28 min. In addition, we found that ~93% of the captured cells were viable, making them suitable for subsequent molecular and cellular studies.

Smart Multifunctional Nanostructure for Targeted Cancer Chemotherapy and Magnetic Resonance Imaging

Targeted chemotherapy and magnetic resonance imaging of cancer cells in vitro has been achieved using a smart multifunctional nanostructure (SMN) constructed from a porous hollow magnetite nanoparticle (PHMNP), a heterobifunctional PEG ligand, and an aptamer. The PHMNPs were prepared through a three-step reaction and loaded with the anticancer drug doxorubicin while being functionalized with PEG ligands. Targeting aptamers were then introduced by reaction with the PEG ligands. The pores of the PHMNPs are stable at physiological pH, but they are subject to acid etching. Specific binding and uptake of the SMN to the target cancer cells induced by aptamers was observed. In addition, multiple aptamers on the surface of one single SMN led to enhanced binding and uptake to target cancer cells due to the multivalent effect. Upon reaching the lysosomes of target cancer cells through receptor-mediated endocytosis, the relatively low lysosomal pH level resulted in corrosion of the PHMNP pores, facilitating the release of doxorubicin to kill the target cancer cells. In addition, the potential of using SMN for magnetic resonance imaging was also investigated.

Semiquantification of ATP in live cells using nonspecific desorption of DNA from graphene oxide as the internal reference.

In this aritcle, we have developed an interesting imaging method for intracellular ATP molecules with semiquantitation. While there has been a lot of work in understanding intracellular events, very few can come close to quantitation or semiquantitation in living cells. In this work, we made an effective use of nanomaterials, graphene oxides, both as a quencher and a carrier for intracellular delivery. In addition, this graphene oxide also serves as the carrier for reference probes for fluorescent imaging. An ATP aptamer molecular beacon (AAMB) is adsorbed on graphene oxide (GO) to form a double quenching platform. The AAMB/GO spontaneously enters cells, and then AAMB is released and opened by intracellular ATP. The resulting fluorescence recovery is used to perform ATP live-cell imaging with greatly improved background and signaling. Moreover, a control ssDNA, which is released nonspecifically from GO by nontarget cellular proteins, can serve as an internal reference for ATP semiquantification inside living cells using the intensity ratio of the AAMB and control. This approach can serve as a way for intracellular delivery and quantitative analysis.

DNA-guided metal-nanoparticle formation on graphene oxide surface.

Over the last decade, DNA has been widely employed as a scaffold to form inorganic metallic nanoparticles (MNPs). The unique programmable structure provided by Watson-Crick base pairing and the tunable properties of DNA have been used for growth and positioning of nanoparticle structures. This has enabled new synthetic strategies, such as DNA-metallization,[1-8] DNA-mediated nanoparticle synthesis,[9-15] and DNA-controlled positioning of nanoparticles,[16-17] to create novel, efficient and useful miniaturized optical sensors, electronic devices, circuits and medical theranostic kits. The remarkable molecular recognition properties and self-assembly capabilities of DNA have been intensively utilized for several years. For example, DNA-directed inorganic nanowire particles have been studied for observing conformational changes of double-stranded DNA by addition of metal ions [1]. Moreover, the assembly of nanocrystals of semiconductor materials using DNA as a template has been examined to overcome insulation of DNA in electronic circuits.[18] Thus, the binding affinity of metal ions to oxygen-containing mono/di/tri-phosphate groups and N bonds of bases prevents excessive deposition on DNA with increases in concentration. [19] In addition to its ability to self-assemble, DNA has also been used to produce unique dispersed nanoparticles and to control the positions of these particles on programmable DNA scaffolds. As an example, DNA/RNA sequence, structure and composition have been used to fine tune the size, shape and physicochemical properties of nanoparticles and to generate biocompatible and easily functionalizable nanomaterials. [11-12]

Nanoparticle-mediated IgE-receptor aggregation and signaling in RBL mast cells

Complex cell behaviors are usually triggered by multivalent ligands that first bind to membrane receptors and then promote receptor clustering, thus altering intracellular signal transduction. While it is possible to produce such altered signal transduction by synthetic means, the development of chemically defined multivalent ligands of effectors is sometimes difficult and tedious. Specifically, the average spacing between two binding sites within an antibody and the average distance between receptors on the cell membrane are usually larger than most organic molecules. In this study, we directly address these challenges by demonstrating how gold nanoparticles (AuNPs) of precisely controlled mean diameters can be easily synthesized and surface-modified with dinitrophenyl (DNP) at an equally well-controlled ligand density or spacing. We found that both nanoparticle size and surface ligand density play key regulatory roles in the process of membrane antibody-receptor (IgE-Fc epsilonRI) binding and cross-linking, which, in turn, leads to degranulation and consequent release of chemical mediators on rat basophilic leukemia cells. In addition, by adjusting DNP-AuNP architecture, we discovered that our conjugates could either promote or inhibit cellular activation. Thus, these results demonstrate that nanoparticles serve not only as simple platforms for multivalent binding but also as mediators for key biological functions. As such, the findings we report here may provide insight into the use of nanoparticles as a comprehensive tool for use in detailed receptor/ligand interaction studies and in the design of nanoscale delivery and therapeutic systems.

DNA Aptamer-Mediated Cell Targeting

One important issue using cells as therapeutics is targeted delivery. Engineering cell surfaces to improve delivery efficiency is thus of great interest. Here we report a simple, efficient and effective way to modify the cell surface with target-specific ligands, i.e., DNA aptamers, while minimizing the effects on the modified cells. We demonstrated that after incubating with lipo-aptamer probes (shown in expansion), immune cells (red) recognize cancer cells (blue) in the cell mixture, and kill cancer cells.

Aptamer Conjugated Multifunctional Nanoflowers as a Platform for Targeting, Capture and Detection in Laser Desorption Ionization Mass Spectrometry

Although many different nanomaterials have been tested as substrates for laser desorption and ionization mass spectrometry (LDI-MS), this emerging field still requires more efficient multifuncional nanomaterials for targeting, enrichment, and detection. Here, we report the use of gold manganese oxide (Au@MnO) hybrid nanoflowers as an efficient matrix for LDI-MS. The nanoflowers were also functionalized with two different aptamers to target cancer cells and capture adenosine triphosphate (ATP). These nanoflowers were successfully used for metabolite extraction from cancer cell lysates. Thus, in one system, our multifunctional nanoflowers can (1) act as an ionization substrate for mass spectrometry, (2) target cancer cells, and (3) detect and analyze metabolites from cancer cells.

Self-assembled aptamer-based drug carriers for bispecific cytotoxicity to cancer cells.

Monovalent aptamers can deliver drugs to target cells by specific recognition. However, different cancer subtypes are distinguished by heterogeneous biomarkers and one single aptamer is unable to recognize all clinical samples from different patients with even the same type of cancers. To address heterogeneity among cancer subtypes for targeted drug delivery, as a model, we developed a drug carrier with a broader recognition range of cancer subtypes. This carrier, sgc8c-sgd5a (SD), was self-assembled from two modified monovalent aptamers. It showed bispecific recognition abilities to target cells in cell mixtures; thus broadening the recognition capabilities of its parent aptamers. The self-assembly of SD simultaneously formed multiple drug loading sites for the anticancer drug doxorubicin (Dox). The Dox-loaded SD (SD-Dox) also showed bispecific abilities for target cell binding and drug delivery. Most importantly, SD-Dox induced bispecific cytotoxicity in target cells in cell mixtures. Therefore, by broadening the otherwise limited recognition capabilities of monovalent aptamers, bispecific aptamer-based drug carriers would facilitate aptamer applications for clinically heterogeneous cancer subtypes that respond to the same cancer therapy.