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.

High‐Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild‐Type and B.1.1.7 SARS‐CoV‐2 in Unprocessed Saliva

“…The results indicate that the dimeric aptamer approach can produce aptamers with significantly enhanced affinity for the trimeric spike protein, presumably via bivalent recognition. [ 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ] Figure 1 B shows binding curves derived from dot‐blot assays using the full trimeric spike proteins of SARS‐CoV‐2 (representative dot blot assay results are provided in Figure S2). In comparison to the substantial affinity enhancement observed for the heterodimeric aptamer DSA1N5 (≈99‐fold; Table S2), the two homodimeric aptamers showed much reduced affinity enhancements relative to their monomeric counterparts (Table S2).…”

“…To derive a high‐affinity DNA aptamer, we took advantage of a well‐established strategy of engineering bivalent or multivalent aptamers through ligation of two or more monomers,[ 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ] given the fact that the full spike protein is a homotrimeric protein and each SARS‐CoV‐2 virus expresses ≈30 spikes on its surface. [ 48 , 49 ] We hypothesized that generation of dimeric aptamers from the best members in the collection of the diverse monomeric S1 protein‐binding aptamers developed recently by our groups [38] may provide an aptamer with sufficient affinity to achieve this goal.…”

Design Strategies for Electrochemical Aptasensors for Cancer Diagnostic Devices

“…For successful operation in biological matrices, the aptamer selection is also performed in the natural environment in which they are planned to be used, in order to ensure the optimum binding properties of the aptamers in clinical samples [ 13 ]. The aptamers can be also readily engineered into bi-specific dimer aptamers [ 14 , 15 ]. Construction of “multivalent” aptamers, dimers in their simplest form, capable of binding to multiple protein binding sites, essentially improves the biorecognition and affinity properties of the aptamers.…”

Charge-Transfer Interactions Stabilize G-Quadruplex-Forming Thrombin Binding Aptamers and Can Improve Their Anticoagulant Activity

“…Starting from large pools of random-sequence oligonucleotides, aptamers are generally identified through a reiterative fishing procedure based on affinity chromatography, known as SELEX (systematic evolution of ligands by exponential enrichment) [4][5][6][7][8]. Notably, aptamers exhibit several advantages compared to antibodies [1,2], and, for this reason, have gained interest as agents of choice in both diagnostic [9][10][11] and therapeutic [12][13][14][15][16][17] applications. However, the biomedical use of aptamers still proceeds slowly; just a few candidates have entered clinical trials [14,[18][19][20].…”