Amphipathic antimicrobial peptides can destroy bacteria cells by inducing membrane permeabilization, forming one strategy for innate defense by various organisms. However, although the antimicrobial peptides are considered a promising alternative for use against multidrug-resistant bacteria, large-scale screening of potential candidate antimicrobial peptides will require a simple, rapid assay for antimicrobial activity. Here, we describe a novel fluorescence resonance energy transfer (FRET)-based assay system for antimicrobial peptides which takes advantage of pH-related changes in FRET efficiency due to the instability of enhanced yellow fluorescent protein versus the stability of enhanced cyan fluorescent protein in a reduced-pH environment. We successfully showed that quantification of antimicrobial activity is possible through a difference of FRET efficiency between ECFP-EYFP fusion molecules released from disrupted Escherichia coli in an extracellular environment (pH 6) and those retained in an intracellular environment (pH ϳ7). Thus, we herein suggest a new simple, effective, and efficient pH-controlled FRET-based antimicrobial peptide screening method applicable to high-throughput screening of candidate peptide libraries.Conventional chemical-based antibiotics, such as penicillin, usually destroy bacteria by blocking synthesis of the bacterial cell wall or by disrupting the translational machinery (3, 4). However, due to the wholesale use of chemical antibiotics over the past decades, many bacteria have become antibiotic resistant. Amphipathic peptides, which have both hydrophilic (cationic) and hydrophobic properties, have been found in organisms ranging from bacteria to humans; many of these peptides have antibiotic properties, including effects against multidrugresistant bacteria. Although the mechanism of antimicrobial peptides (AMPs) action is not clearly understood, the AMPs are generally believed to bind lipopolysaccharide on gramnegative bacteria or lipoteichoic acid on gram-positive bacteria. This charge-based binding perturbs the fundamental structure of bacterial membranes, forming transient pores that eventually lead to bacterial lysis (5, 17).Owing to the potential superiority of AMPs as antibiotics, many researchers have sought to screen potential candidate peptides from various types of organisms. However, the traditional screening methods used to test AMP candidates have proven time consuming and laborious, limiting the effectiveness of these studies. To overcome these limitations, we here introduce a novel fluorescence resonance energy transfer (FRET)-based assay for rapid and high-throughput screening of AMPs. In general, FRET is the distance-dependent transfer of energy from a donor fluorophore to an acceptor fluorophore (12). For this process to occur, the distance between two fluorophores should be 2 to 6 nm, and the emission spectrum of the donor must overlap with the excitation spectrum of the acceptor by more than 30% (15). These requirements have been used to develop FRET-based fl...