# Biosensors Based on Bivalent and Multivalent Recognition by Nucleic Acid Scaffolds
## 2 Biosensors Based on Bivalent Binding Modes
### Biosensors Based on Steric Strain-Induced Distance Change  
In contrast to strategies based on nucleic acid displacement, a biosensor's response to changing distances between binding sites has been studied by a few groups. Among them, in 2015, the [PERSON] group reported a DNA-based beacon for antibody detection [95]. The beacon consists of a DNA hairpin bearing a fluorophore and quencher pair and two additional single-stranded tails that serve as antigen-carrying oligonucleotides. In a relaxed state, the beacon forms a hairpin structure, and the resulting close proximity between the fluorophore and quencher quenches the fluorescence. However, in the presence of target antibodies, steric strain induced by the bivalent binding of the antibody to the  
Figure 10: Scheme of a cancer cell identification system based on bivalent interactions between cells and aptamers. Fluorescence signaling is enabled by a hybridization chain reaction (HCR). Adapted with permission from _J. Am. Chem. Soc._ 2019, 141, 12738–12743, doi:10.1021/jacs.9b05470. Copyright (2019) American Chemical Society [90].  
Figure 9: Scheme of a protein sensor based on DNA displacement and a catalytic DNA circuit for signal amplification. Adapted with permission from _J. Am. Chem. Soc._ 2013, 135, 2443–2446, doi:10.1021/ja311990w. [[https://pubs.acs.org/doi/full/10.1021/ja311990w](https://pubs.acs.org/doi/full/10.1021/ja311990w)]([https://pubs.acs.org/doi/full/10.1021/ja311990w](https://pubs.acs.org/doi/full/10.1021/ja311990w)) (accessed on 31 January 2021). Copyright (2013) American Chemical Society [83].  
beacon opens the hairpin, rapidly restoring the fluorescence (Figure 11, top). Through this distance-dependent strategy, antibodies or proteins at low nanomolar concentrations were detected rapidly and selectively, even in complex samples. Furthermore, this method was also applicable to the sensing of a monovalent protein or the simultaneous sensing of two different antibodies through AND logic gate operation (Figure 11, bottom). More recently, the same strategy was adopted for the detection of a single antibody in a DNA origami nanoantenna [96].  
DNA structural changes due to bivalent interactions have also been applied to other concepts. In 2017, the same group reported DNA-based nanomachines that can release nucleic acid cargo strands upon bivalent binding to a target antibody [97]. The DNA nanomachine has a DNA triplex structure, where a clamp-like structure holds a cargo strand inside through both Watson-Crick and Hoogsteen base pairs. Because each side of the clamp-like structure is conjugated with a specific antigen, the nanomachine can bind to the antibody through bivalent interactions. In the triplex structure, the cargo strand, bearing a fluorophore and quencher at each end, becomes fluorescent owing to the spatial distance between its fluorophore and quencher components. In the presence of the antibody, however, the clamp-like structure is disturbed by the steric strain-induced distance change between the two antigens, and the fluorescence signal decreases (Figure 12). Through this process, the antibody-powered DNA nanomachine enables the rapid and highly specific detection of three different target antibodies on the nanomolar scale. In addition, steric strain-induced strategies have been introduced into protein sensors utilizing the binding-induced dissociation of kissing loops [98].  
Figure 11: The structure and principle of a DNA-based beacon for the detection of antibodies. The antibody exerts steric strain on the beacon and changes the distance between a fluorophore and quencher. Reproduced by permission from John Wiley & Sons Ltd.: _Angew. Chem. Int. Ed._ 2015, 127, 13412-13416, doi:10.1002/ange.201505179. Copyright (2015) [95].  
Figure 12: Conceptual scheme of antibody-powered DNA nanomachine capable of antibody detection [97].