Molecular beacons (MBs) are stem-loop structured oligonucleotides capable of sensitive and specific nucleic acid detection. However, large-scale usage of MBs for high throughput applications has been hindered by the many expensive and tedious chemical modifications. In this paper, we reported a new class of fluorescent protein-based molecular beacons (FP-MBs) based on zinc finger protein-guided assembly. The design consisted of a single oligonucleotide which forms a hairpin structure with an extending arm on both ends for the attachment of two different fluorescent proteins upon simple mixing. This new design allows for simplified MB assembly and modifications for awide range of applications. (C) 2014 Wiley Periodicals, Inc.