L buffered formalin, and undifferentiated colonies were counted to calculate the colony forming efficiency by dividing with the initial sorted number of cells. Primary isolated mNSC or cultured neurospheres were dissociated in single cell suspension and treated with the nonspecific-MB to set the sorting gate for a high and low population of neurospheres. The Sox2-MB-treated primary isolated mNSC or cultured neurospheres were sorted into a Sox2MBhigh and Sox2-MBlow population. 350 cells in triplicate were plated into a 96-well plate using a FACSAria II (BD Bioscience). The sorted cells were either fixed with 10 natural buffered formalin after 1 wk of culture and imaged (Inverted motorized IX81 microscope, Olympus) or Title Loaded From File continued to be serially passaged. Sphere forming efficiency was calculated by manually counting all the spheres and then divided with the initial number of sorted cells. Population doublings (PD) was calculated using the following formula: PD = Log(N/N0)/Log(2), where the N0 is the number of seeded cells and N was the calculated number of cells at the time of passaging using a hemocytometer. 5 minutes before the sort of primary isolated NSCs, 5 mL of Annexin-V-Cy5 (Biovision, LuBioScience) was added to 500 mL of MB treated cells. Annexin-V negative cells were selected prior to setting the gates for Sox2-MBhigh and Sox2-MBlow populations (Figure 4 A and G).***p,0.001). All the error bars represent the standard error of the mean (S.E.M.).Results Sox2-MBs detect their targets and discriminate between Sox2-positive and Sox2-negative cellsFour different MBs targeting Sox2 (Sox2-MBs) were designed (Figure 1B). To determine their sensitivity to their complementary target sequences, we measured Cy3 emission from the candidate Sox2-MBs in vitro in the presence and absence of their targets (Figure 1C and 1D). For all MBs assayed, a difference of 12-fold or more in Cy3 fluorescence was seen between the presence and absence of the complementary sequences, indicating functional molecular beacon reporting for all four candidates. We then assayed if our Sox2-MBs could be used to distinguish between Sox2-negative and Sox2-positive cell populations (i.e. if the MBs would recognize their targets in the complex milieu in vivo within the cell). As a model system to study the activity of our beacon, we choose mES, which are known to express Sox2. MEFs were used as negative control. Sox2 expression was first confirmed by RT-PCR (Figure 2A). MBs were delivered to cells using as a delivery vehicle the cationic micelles, consisting of a hydrophobic core, a hydrophilic corona of poly(ethylene glycol), and a cationic poly(ethylene imine) chain embedded in the corona [12]. As expected, when Sox2negative MEFs were treated with the candidate Sox2-MBs or nonspecific-MB and analyzed by flow cytometry, neither showed a fluorescence signal (Figure 2B, Figure S1A). In contrast, when the Sox2-MBs were incubated with mES cells, two of the MBs (Sox2MB1 and Sox2-MB3) clearly displayed an increase in fluorescent as detected by microscopy (Figure S2), whereas the nonspecific-MB (Sox2-MB2 and Sox2-MB4) did not show fluorescence over background in both the feeder cultures and the mES colonies. Similar results were obtained by flow cytometry: Sox2-MB1 and Title Loaded From File Sox2-MB3 showed a 2.6 and 4.6-fold higher mean fluorescence signal as compared with the nonspecific-MB (Figure 2C, Figure S1B). Based on these results from microscopy and flow cytometry, we selected Sox2-MB3 for fu.L buffered formalin, and undifferentiated colonies were counted to calculate the colony forming efficiency by dividing with the initial sorted number of cells. Primary isolated mNSC or cultured neurospheres were dissociated in single cell suspension and treated with the nonspecific-MB to set the sorting gate for a high and low population of neurospheres. The Sox2-MB-treated primary isolated mNSC or cultured neurospheres were sorted into a Sox2MBhigh and Sox2-MBlow population. 350 cells in triplicate were plated into a 96-well plate using a FACSAria II (BD Bioscience). The sorted cells were either fixed with 10 natural buffered formalin after 1 wk of culture and imaged (Inverted motorized IX81 microscope, Olympus) or continued to be serially passaged. Sphere forming efficiency was calculated by manually counting all the spheres and then divided with the initial number of sorted cells. Population doublings (PD) was calculated using the following formula: PD = Log(N/N0)/Log(2), where the N0 is the number of seeded cells and N was the calculated number of cells at the time of passaging using a hemocytometer. 5 minutes before the sort of primary isolated NSCs, 5 mL of Annexin-V-Cy5 (Biovision, LuBioScience) was added to 500 mL of MB treated cells. Annexin-V negative cells were selected prior to setting the gates for Sox2-MBhigh and Sox2-MBlow populations (Figure 4 A and G).***p,0.001). All the error bars represent the standard error of the mean (S.E.M.).Results Sox2-MBs detect their targets and discriminate between Sox2-positive and Sox2-negative cellsFour different MBs targeting Sox2 (Sox2-MBs) were designed (Figure 1B). To determine their sensitivity to their complementary target sequences, we measured Cy3 emission from the candidate Sox2-MBs in vitro in the presence and absence of their targets (Figure 1C and 1D). For all MBs assayed, a difference of 12-fold or more in Cy3 fluorescence was seen between the presence and absence of the complementary sequences, indicating functional molecular beacon reporting for all four candidates. We then assayed if our Sox2-MBs could be used to distinguish between Sox2-negative and Sox2-positive cell populations (i.e. if the MBs would recognize their targets in the complex milieu in vivo within the cell). As a model system to study the activity of our beacon, we choose mES, which are known to express Sox2. MEFs were used as negative control. Sox2 expression was first confirmed by RT-PCR (Figure 2A). MBs were delivered to cells using as a delivery vehicle the cationic micelles, consisting of a hydrophobic core, a hydrophilic corona of poly(ethylene glycol), and a cationic poly(ethylene imine) chain embedded in the corona [12]. As expected, when Sox2negative MEFs were treated with the candidate Sox2-MBs or nonspecific-MB and analyzed by flow cytometry, neither showed a fluorescence signal (Figure 2B, Figure S1A). In contrast, when the Sox2-MBs were incubated with mES cells, two of the MBs (Sox2MB1 and Sox2-MB3) clearly displayed an increase in fluorescent as detected by microscopy (Figure S2), whereas the nonspecific-MB (Sox2-MB2 and Sox2-MB4) did not show fluorescence over background in both the feeder cultures and the mES colonies. Similar results were obtained by flow cytometry: Sox2-MB1 and Sox2-MB3 showed a 2.6 and 4.6-fold higher mean fluorescence signal as compared with the nonspecific-MB (Figure 2C, Figure S1B). Based on these results from microscopy and flow cytometry, we selected Sox2-MB3 for fu.