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Supporting Information 1. Quantitative information from AFM topographic images in Figures 3, 4 and 5. SPB measurements of height (h), surface covering (C) and roughness (Ra) in absence and in presence of concentrations (100 and 200 µM)6-FQs. The h of the SPBs is the average from at least thirty line profiles that are parallel being the error for the measurements the standard deviation of the thirty data points. Ra is the average roughness of different areas for different random positions on the sample surfaces in each image. [FQs] µM CPX M3CPX M4CPX 0 100 200 h (nm) 5.7 ± 0.1 4.6 ± 0.2 4.2 ± 0.2 C (%) 79.0 77.1 75.6 Ra (nm) 0.141 0.140 0.126 h (nm) 5.6 ± 0.2 5.3 ± 0.3 4.9 ± 0.2 C (%) 67.6 71.2 71.2 Ra (nm) 0.165 0.168 0.180 h (nm) 5.5 ± 0.3 5.6 ± 0.3 5.71 ± 0.12 C (%) 57.0 52.8 52.3 Ra (nm) 0.168 0.159 0.125 2. In order to analyze the effect of ciprofloxacin on black lipid bilayers, membranes were prepared from a 1% (w/v) solution of diphytanoyl phosphatidylcholine (Avanti Polar Lipids, Alabaster, AL) in n-decane in a Teflon cell consisting of two aqueous compartments connected by a circular hole with an area of ca. 0.4 mm2 1,2 . The aqueous salt solutions (analytical grade; Merck, Darmstadt, Germany) were used unbuffered at pH 6. The temperature was kept at 20 ◦C throughout the experiments. The single-channel measurements were performed with a pair of Ag/AgCl electrodes (with salt bridges) switched in series with a voltage source and a current amplifier (Keithley; Keithley Instruments, Cleveland, OH). The amplified signal was monitored with a storage oscilloscope and recorded with a strip chart recorder. Small amounts of the stock solutions containing pure ciprofloxacin were added after the lipid membrane turned optically black to reflected light. For the zero current membrane potentials, the membranes were prepared in a 100 mM KCl solution and the eventual formation of pores was monitored . In concordance with these observations the ability of CPX to induce the formation of pores in bilayers was observed when CPX was added to the saline in teflon cells separated by black lipid bilayer membranes. Single channel recordings revealed the formation of transient pores with a short life (less than 0.1 seconds). Single channel conductance was hard to be measured due to the short life of pores but in any case was no higher than 2 nS in KCl 1M. Further experimental work should be done to establish critical experimental conditions allowing application of the method to determine the characteristics of transient channels formed by CPX in lipid bilayers. 3. The formation of pores observed in Figure 3 appears to depend on local CPX concentration and time of incubation. The below AFM image (A) shows a SPB formed by allowing the vesicles of E.coli to adsorb at room temperature for 40 min and further incubated for 20 extra min with 300 µM of CPX. The occurrence of 1 Benz R, Janko K, Boos W, Laüger P. Formation of large, ion- impermeable membrane channels by the matrix protein (porin) of Escherichia coli. Biochim Biophys Acta 1978;511:305–319. 2 Schmid A, Hancock REW. Ion selectivity of gram-negative bacterial porins. J Bacteriol 1985;162:722–727. several pores is demonstrated. The height of the holes could be estimated by cross section analysis (B). Strikingly this effect has not been observed neither for M3CPX nor for M4CPX at any of the concentrations assayed (100-300 µM) (see Figures 4 and 5). 4. Some of the events thought to occur in a hypothetical passive mechanism of entry of CPX into the bacterial cytoplasm: (A) bulk difussion until CPX reaches the surface of the biomembrane; (B) local accumulation (possibly on headgorups of acidic phospholipids); (C) insertion into the outer leaflet of the plasma membrane; (D) permetation of CPX though the bilayer.