Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery

Abstract

Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.

Keywords: DNA origami; aptamers; drug delivery; gene regulation; medical imaging; modified triphosphates; neurodegenerative diseases; systematic evolution of ligands by exponential enrichment (SELEX).

Figure 1

Strategies for the construction of aptamers acting as smart contrast agents: (A) Response to a biochemical stimuli: An oligonucleotide is equipped with a Gd³⁺-DOTA complex. This oligonucleotide is complementary to part of the aptamer and upon binding to the target, the structural reorganization causes the Gd³⁺-DOTA-labeled strand to dissociate from the duplex, which in turn increases the relaxation time and thus the brightness of the MRI signal [46]; (B) Vectoring to intended target: An aptamer is equipped with a contrast agent and will vector the probe directly to the intended target.

Figure 2

(A) Hypothetical secondary structure of the sgc8 aptamer and the ¹⁸F-label; and (B) positron emission tomography (PET) images of a mouse model with HCT116 tumors, white arrows represent the HCT116 xenograft [65].

Figure 3

(A) Chemical structure of the main biogenic monoamine neurotransmitters; and (B) amino acid sequence of neuropeptide Y [96].

Figure 4

Schematic depiction of the formation of Aβ fibrils: BACE1 cleaves APP (Aβ sequence numbers are shown only) in the extracellular domain and the resulting fragment remains membrane-bound where it is cleaved by the γ-secretase complex into Aβ peptides (only the main Aβ40 and Aβ42 isoforms are shown). Monomeric Aβ peptides then aggregate to form oligomers and eventually β-fibrils. The cellular prion protein PrP^C can also bind to Aβ oligomers [78,119].

Figure 5

(A) Schematic representation of the aptamer-gated DNA nanorobot [151]: the aptamer (magenta) is locked in a double-stranded form by a partially complementary sequence (yellow) and both are grafted on the nanorobot. The payloads (either gold nanoparticles (shown) or antibody fragments) are constrained to remain within the DNA construct and only the recognition of intended target by the aptamer (green) will unlock the DNA nanorobot and enable the delivery of the payload; (B) AFM images of a DNA origami-aptamer construct in the presence of a non-target protein (hLDH; left-hand side) and presence of the target protein (PfLDH; right-hand side) [152]; (C) AFM analysis of a DNA origami equipped with a split aptamer system in the closed (left-hand side) and open (right-hand side) forms [153].

Figure 6

Illustrative examples of aptameric-based systems used as drug delivery systems: (A) encapsulation of aptamer-drug complexes in liposome [205]; (B) antibody-aptamer pincers (AAPs) for selective targeting of HER2 and delivery of DOX [208]; (C) streptavidin serves as the core for the connection of two anti-PSMA aptamers and two siRNA molecules [209]; (D) delivery of the 5-fluorouracil (5-FU; shown in red) drug connected to an aptamer-oligonucleotide scaffold via a photo-cleavable linker (shown in blue) [210]; and (E) chemical structures of tobramycin (red) and DOX (blue).

Figure 7

Chemical structures of base-modified nucleoside triphosphates used in selection experiments of aptamers with an expanded chemical repertoire.

Figure 8

Chemical structures of the unnatural base pairs Ds Px and dP dZ used in the expansion of the genetic code.

Figure 9

Chemical structures of sugar and phosphate modified nucleotides.