It is theorized that multivalent interaction can result in better affinity and selectivity than monovalent interaction in the design of high-performance ligands. Accordingly, biomolecular engineers are increasingly taking advantage of multivalent interactions to fabricate novel molecular assemblies, resulting in new functions for ligands or enhanced performance of existing ligands. Substantial efforts have been expended in using small molecules or epitopes of antibodies for designing multifunctional or betterperforming ligands. However, few attempts to use nucleic acid aptamers as functional domains have been reported. In this study, we explore the design of bivalent nucleic acid ligands by using thrombin and its aptamers as the model by which to evaluate its functions. By assembling two thrombin-binding aptamers with optimized design parameters, this assembly has resulted in the successful development of a nucleic acid-based high-performance bivalent protein inhibitor. Our experimentation proved (i) that the simultaneous binding of two aptamers after linkage achieved 16.6-fold better inhibition efficiency than binding of the monovalent ligand and (ii) that such an improvement originated from changes in the kinetics of the binding interactions, with a k off rate Ϸ1/50 as fast. In addition, the newly generated aptamer assembly is an excellent anticoagulant reagent when tested with different samples. Because this optimized ligand design offers a simple and noninvasive means of accomplishing higher performance from known functional aptamers, it holds promise as a potent antithrombin agent in the treatment of various diseases related to abnormal thrombin activities.anticogulation ͉ aptamers ͉ multivalent binding ͉ thrombin I n contrast to monovalent interaction, multivalent, or polyvalent, interactions involve the binding of multiple ligands of a biological entity, such as small molecules, oligosaccharides, proteins, nucleic acids (NAs), lipids, or aggregates of these molecules, to multiple binding pockets or receptors of a target, e.g., a protein, virus, bacterium, or cell (1). Polyvalency is ubiquitous in biology and has a number of benefits over monovalent interactions. For instance, polyvalent interactions collectively possess higher binding affinity than the corresponding monovalent interactions. That is, polyvalency results in a ''cooperative'' configuration in which the probability of rebinding of a dissociated monomer to the target is increased by the presence of other monomers bound to the same target. A classical example of this is demonstrated by the binding of galactoseterminated oligosaccharides to C-type mammalian hepatic lectins (2). In addition to increased binding affinity, polyvalent interactions also stand a better chance of providing higher selectivity in target recognition. Noticeably, a multivalent binder, despite being composed of weak homo-or heterogeneous ligands, can still have stronger binding property because of multiple binding events. A well known example of this phenomenon is taken fro...