Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition

Abstract

Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.

Keywords: G-quadruplex; aptamer; design; dimerization; molecular recognition; multivalency; protein target; therapy.

Figure 1

Schematic representation of the secondary structure of the L-selectin targeting aptamers. (a) Structure of the monomeric aptamers LD201* and mΔ1, as predicted by the mfold software for nucleic acid folding prediction [64]. The blue box in LD201* sequence represents the nucleotides removed in the truncated mΔ1 analogue (G3-C8 and G33-C34); (b) structure of the mΔ1 dimer in which two aptamer units are linked with poly(dA) linkers of different length. Figures were adapted from Riese et al. [61] with permission.

Figure 2

Schematic representation of the G-quadruplex folding topology adopted by T30695-I2 (a), 93del (b) and T30177-I11 (c) in K⁺-solutions as proposed by Do et al. [75], Phan et al. [76] and Mukundan et al. [77], respectively. For both T30695 and T30177, NMR spectra were obtained from derivatives including a single guanine-to-inosine substitution at position 2 or 11, respectively. (d) Schematic representation of the TEL-ODNs as monomers (A) and dimers (B). Figures were reproduced from refs [75,76,77,78] with permission.

Figure 3

Schematic representation of the G-quadruplex structure formed in solution by the homodimeric RA-36 (a) and heterodimeric HD1-22 (b) thrombin-targeting aptamers. Figures were redrawn from Amato et al. [109] and Müller et al. [110] respectively.

Figure 4

Schematic representation of the possible G-quadruplex structures of AS1411 (a) and NMR-derived G-quadruplex structures adopted by AT11 (b) and AT11-L0 (c) in K⁺-solutions as described by Dailey et al. [161], Do et al. [165], and Carvalho et al. [166] respectively. Figures were reproduced from refs [154,165,166] with permission.

Figure 5

Schematic representation of the secondary structure of the monomeric and dimeric- vitronectin-targeting aptamers VBA-01 (a) and DVBA-01 (b) as predicted by the mfold software for nucleic acid folding prediction [64]. In DVBA-01 structure, red boxes indicate potential Dox-binding sites. Figures were redrawn from Stuart et al. [177].

Figure 6

Schematic representation of the prostate-specific membrane antigen (PSMA)-targeting dimeric aptamer including two SZTI01 motifs linked by a duplex DNA “bridge” containing CG sequences appended to the ends of the dA₁₆ or T₁₆ bases (depicted as red and green, respectively). Red boxes indicate potential Dox-binding sites. Figure was redrawn from Boyacioglu et al. [178].

Figure 7

Schematic representation of the secondary structure of the monomeric and dimeric mIgM-targeting aptamers: TD05 (a), TD05.1 (b), TD05.17 (c), bivalent TD05.17, i.e., L-BVA.8S (d), trivalent TD05.17, i.e., L-TVA.8S (e) and tetravalent TD05.17, i.e., L-TetVA.8S (f). Nucleobases in red color are LNA residues. Figures were redrawn from Mallikaratchy et al. [185].

Figure 8

Schematic representation of the mIgM-targeting dimeric R1.2 aptamer. Figure was redrawn from Batool et al. [191].

Figure 9

Schematic representation of the secondary structure of the monomeric and dimeric TCR-CD3-targeting aptamers: ZUCH-1 (a), OSJ-T1 (b), OSJ-T3_LNA-OMe with LNA and 2′-OMe RNA residues (c), bivalent OSJ-T3_LNA-OMe (d). LNA and 2′-OMe RNA nucleobases are marked in red and blue, respectively. Figures were adapted from Freage et al. [195] with permission.

Figure 10

Schematic representation of the secondary structures of VEa5 (a) and its truncated aptamers del5-1 (green box) and SL₂-B (b), as predicted by the mfold software for nucleic acid folding prediction [64]. Figures were redrawn from Hasegawa et al. [211] and Kaur et al. [212], respectively.