# Biosensors Based on Bivalent and Multivalent Recognition by Nucleic Acid Scaffolds
## 1 Introduction  
Bivalent or multivalent interactions are the most prevalent binding modes found in various biological systems. Many biomolecular components adopt multivalent interactions to overcome weak, monovalent, non-covalent interactions and to make their biomolecular interactions stronger and more specific, ultimately enabling the occurrence of desired biological processes [1]. For example, antibodies use two antigen recognition parts for immune response, and viruses utilize multivalent interactions to attach themselves to host cells [2, 3]. In addition, cells use many multivalent receptors for cell signaling [4]. These examples indicate that bivalent and multivalent interactions are an indispensable part of biological processes that should be understood and utilized for the development of biotechnologies. Inspired by these observations, the concept of multivalent interactions has been applied to the design of artificial molecular constructs capable of multivalent binding. In such constructs, multiple ligands connected to each other are placed at specified positions to mimic the pattern of receptors in the target [1, 5]. Such a design endows the construct with positive cooperativity in its binding; thus, the construct more strongly and selectively binds to the target biomolecules. Owing to their attractive features, such as enhanced binding capability, multivalent biomolecular interactions have been considered a useful strategy for the study of biology, biotechnology, and pharmaceutical drug design [6, 7]. In particular,multivalent interactions are expected to provide new, advanced strategies for the design of biosensors targeting macromolecules with multiple binding modes. Among diverse polymer candidates, nucleic acids have been considered promising scaffolds for the design of biosensors based on multivalent displays of ligands for several reasons (Figure 1). First, nucleic acid helices based on Watson-Crick base pairs have constant base-pair distances of 3.4 A. The distance between ligands can be precisely controlled by introducing ligands into designated positions of nucleotides [8; 9; 10; 11]; strategies involving such ligand-nucleotide conjugation are well known [12]. Second, helical structures of nucleic acids provide rigidity that enables the predictable design of ligand displays. Third, nucleic acids readily provide secondary structures of diverse shapes, such as A-helices, B-helices, hairpins, and quadruplexes [13]. Such structural diversity enables ligand arrays of numerous shapes and patterns to be prepared on 2D or 3D nanostructures [14; 15]. Lastly, nucleic acids can readily convert biomolecular interaction signals into specific forms of output, mainly nucleic acid strands. To date, many types of DNA nanodevices, including those that perform DNA computing and DNA nanomachines, commonly initiated by inputting a nucleic acid strand, have been invented [16; 17; 18]. The integration of DNA-based multivalent recognition and nanodevices would facilitate the design of biosensors that amplify the signals of multivalent interactions. Accordingly, nucleic acid scaffolds are the most promising materials for the design of multivalent-based biosensors. Various types of biosensors have been designed and constructed on nucleic acids to reveal the bivalent or multivalent interactions of biological macromolecules. This review focuses on the design strategies of biosensors rather than their biological targets. We first explore basic biosensor designs and recent examples of biosensors based on bivalent and multivalent biomolecular interactions directed by nucleic acid hybridizations and structures. Then, we discuss the design principles of nucleic acid scaffolds that can precisely recognize a target through bivalent or multivalent interactions. Various strategies for obtaining readable signals (e.g., fluorescence) from bivalent or multivalent biomolecular interactions are then discussed.