Aptamers: Design, Theory, and Applications to Diagnosis and Therapy for Diseases

Abstract

Single-stranded DNA or RNA entities referred to as aptamers exhibit a strong affinity and specificity for attaching to specific targets. Owing to their special properties, which include simplicity of synthesis, low immunogenicity, and adaptability in targeting a variety of substances, these synthetic oligonucleotides have garnered a lot of interest. The function of aptamers can be altered by combining them with complementary oligonucleotides "antidotes," which are antisense to a particular aptamer sequence. Antidotes play an important role in several fields by specifically targeting the corresponding section of the aptamer. Nevertheless, even with their promising capabilities, the creation of antidotes to regulate or inhibit aptamer function continues to be a relatively unexamined field, constraining their secure and efficient application in medical environments. The review explores experimental methodologies for creating antidotes, the systematic design strategies for managing antidotes in aptamer-based therapies, and their therapeutic efficacy in counteracting disease biomarkers. Additionally, it highlights their diagnostic applications in biosensing and imaging, offering a promising alternative to traditional antibodies. It also investigates the progress, latest innovations, and potential medical uses of aptamer-antidote combinations. Its academic value lies in bridging the gap between theoretical design and practical applications, providing researchers and clinicians with a comprehensive resource to advance aptamer-based solutions in medicine and biotechnology.

Keywords: antidote; aptamer; reversible therapeutics.

FIGURE 1

Various application fields of aptamers and antidotes. Aptamers and antidotes can be utilized in diverse biomedical areas. Nucleic acid‐based aptamers have applications in several biomedical disciplines including biosensors, molecular imaging, drug delivery and gene therapy.

FIGURE 2

Pyroptosis combined with photothermal therapy. (A) Illustration of Apt/PPII/IR780‐NPs generation and (B) mechanism of enhancing liver cancer immunotherapy by inducing pyroptosis combined with photothermal therapy [98]. Copyright © 2024, Springer Nature.

FIGURE 3

The role of EpCAM–CS‐co‐PNVCL@IR780/IM NPs in inducing antitumor immunity through ferroptosis. Under NIR irradiation, EpCAM–CS‐co‐PNVCL@IR780/IMQ NPs induce ICD in tumor cells, and activate CTLs that release cytokines [99]. Copyright 2025, Elsevier.

FIGURE 4

The FIXa aptamer 9.3tC is capable of facilitating CPB. (A) This coagulation cascade illustrates how aptamer 9.3tC selectively inhibits FIXa (blue) whereas heparin (red) inhibits thrombin and FXa. (B) Anti‐FIXa aptamer's predicted secondary structure, and its interaction with antidote 5‐2C to regulate aptamer function [129]. Copyright 2006, Cell Press.

FIGURE 5

The mechanism of single‐molecule DNA antidotes reversal activity and scheme of thrombin‐binding RNA aptamer attached to RNA origami anticoagulant. (A) Schematic illustration of RNA origami anticoagulant (HEX01) interacting with single‐molecule DNA antidotes. The inset illustration shows the composition of mixed antidotes and single molecule DNA antidotes with and without spacers.(B) Two‐dimensional illustration of multivalent, thrombin‐binding RNA aptamers appended on RNA origami anticoagulant [134]. Copyright 2024, Molecular Therapy.

FIGURE 6

Graphical abstract of Cell‐Internalization SELEX against prostate cancer cells. (A) The mfold software was used to predict the secondary structure of the 36‐nt variant of the E3 aptamer. (B) The antidote oligonucleotide targets the region of the E3 aptamer shown in purple. (C) The E3 aptamer, which was identified through Cell‐Internalization SELEX against prostate cancer cells, has been reduced to 36 nt [142]. Copyright 2018, PNAS.

FIGURE 7

Graphical description of the synthesis of the PA–Dau–AuNPs complex and the antisense mechanism. Polyvalent aptamer blocks attached to AuNPs, enabling a rapid and effective reversal of the cytotoxic effects of the PA–Dau–AuNPs complex utilizing the antisense of the polyvalent aptamers [148]. Reproduced with permission from reference. Copyright 2016, Elsevier.

FIGURE 8

Through the use of an antidote, aptamers can reverse their attachment to cell surfaces, allowing for the efficient purification of cells and the production of cells in their natural state. The EGFR(+) cells were initially stained with the green fluorescent AF488‐SA‐E07 and subsequently sorted based on the E07/AF488+ signal. Then, an antidote treatment using mA9 was applied to remove the E07 stain, resulting in a population of ligand‐free unlabeled cells [135]. Copyright 2020, Cell Press.