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Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing

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As biotechnology is rapidly developing, a plethora of generated aptamers now can bind many kinds of targets, ranging from simple inorganic molecules to large protein complexes, and even entire cells. With distinctive advantages, aptamers become ideal candidates for diagnostic and therapeutic applications, purification of target molecules from complex mixtures, biosensor design, etc. A research team, of which the members are from University of California San Diego and Sichuan University, reviewed selected research activities related to nucleic acid-based aptamer techniques, as well as limitations and possible approaches to overcome these limitations.

Aptamers are short single-stranded DNA- or RNA-based oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity. Nucleic acid aptamers, with a length in the range of 10–100 nucleotides (nt), are identified from an in vitro selection process, systemic evolution of ligands by exponential enrichment (SELEX).

The selection of aptamers involves two steps: upstream screening and downstream truncation. A typical SELEX process flow for aptamer screening includes repetition selection cycle and amplification. Cell-SELEX identifies aptamers that specifically bind to a certain cell type based on unique cell membrane extracellular characteristics. And several methods have been developed for aptamer truncation, such as the "rational truncation" approach and the hybridization inhibition approach.

Aptamers as Sensors for Biomarker Discovery

Conventional approaches for biomarker discovery use mass spectrometry or monoclonal antibody (mAb), which are inadequate in regard to membrane proteins. Aptamers can target cells through the exponential enrichment process, which generates a highly specific DNA sequence by multiple rounds of selection. The cell-SELEX screening method has been effectively demonstrated to discover molecules as biomarker candidates, but the identified protein targets still need to be further characterized and validated.

Aptamers as Molecular Imaging Probes

Several aptamer-based molecular beacons have been designed, such as structure-switching signaling aptamer applied for real-time activation and amplification for fluorescence imaging and targeting therapy. Optical molecular imaging with aptamer-based probes are also a hot topic, which has already been used to image disease associated biomarkers. In addition, aptamer-nanomaterials probes have also been used in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI).

Aptamers as Vehicles for Drug Delivery

With great biocompatibility, the use of aptamer-polymer hybrid delivery system is considered as attractive materials for clinical application, which have shown promise in clinical applications for drug delivery. Besides, several aptamer-based bioconjugate systems including liposome, dendrimer hybrid, gold-nanostars, single-walled carbon nanotubes (CNT), gold nanoparticle-hybridized graphene oxide (AuNP-GO), superparamagnetic iron oxide nanoparticles (SPION), quantum dots, and gold nanoparticles (GNPs) for drug delivery, imaging or therapy have been reported.

Aptamers as Potential Drugs

On one hand, in the clinic of cancer therapy, aptamer-based therapeutics is gaining momentum, which can be used as conventional therapeutic drugs in the same way as monoclonal antibody. On the other hand, since the first DNA thrombin aptamer was isolated in 1992, recent research has found that the rapid onset of action and short half-life in vivo suggest that the thrombin aptamer may be useful in anticoagulation with extracorporeal circuits and acute clinical settings like surgical interventions.

Aptamer-Based Programmable Hydrogels

Aptamer-functionalized hydrogels can be programmed to release various and multiple therapeutics when needed through specific nucleic acid recognition and complementary hybridization process, as well as to control cell capture and release. In addition, it has also been used as an artificial extracellular matrix (ECM) for cell adhesion without affecting cell viability.

Aptamers in Precision Cancer Medicine

Recently, several research groups have reported aptamer-based tumor marker discovery platforms with versatile development potential or multiplexing capabilities. Novel technologies using aptamers continue to evolve in precision medicine, providing enormous opportunities for tumor-related biomarker discovery and detection.

This article also listed some unanswered questions about aptamer-based drug targeting and delivery systems, such as how to efficiently and rapidly select aptamers of high affinity to the disease-associated targets, how to engineer aptamers to maintain their correct conformation and structure on the surface of nanoparticles or liposomes, the influence of shape or size of the nanoparticles to the target binding ability of aptamers, and how to improve in vivo biostability of aptamers.

Aptamers are highly attractive and promising tools for various kinds of biotechnology, covering functional characterization of biomolecules, disease detection, therapeutic intervention as drug carriers, and the pharmaceutical lead compounds. More potential is expected to be unveiled about aptamers in the future research.

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