Omain biogenesis and maintenance and are further discussed in Section 5. 2.2. Less straightforward evidence in plasma membranes As shown in the previous Section, micrometric lipid domains are well-documented in artificial and highly specialized biological membranes. However, generalization of this concept to the plasma membrane of living cells is less straightforward and results haveAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptProg Lipid Res. Author manuscript; available in PMC 2017 April 01.Carquin et al.Pageremained doubted based on use of fluorescent tools (Section 2.2.1) and poor lipid fixatives (2.2.2) as well as imaging artifacts due to non-resolved membrane projections (2.2.3). 2.2.1. Use of fluorescent lipid probes–Whereas membrane labeling with fluorescent lipid probes represents a useful technique, it nevertheless presents the limitation that PMinserted probes can differentially partition as compared to endogenous lipids, depending on membrane lipid composition and on the fluorophore [62]. To minimize artifacts, at least two criteria should be considered: (i) probe insertion at trace level within the PM, as compared with endogenous lipid composition, to ensure preservation of membrane integrity and avoidance of cell surface perturbations, and (ii) verification that the probe is a qualitative bona fide reporter of its endogenous lipid counterpart. After a short description of available fluorophores, we will briefly review the mostly used fluorescent lipid probes: (i) fluorescent lipid analogs bearing an extrinsic fluorescent reporter; (ii) intrinsically fluorescent lipids; (iii) fluorescent artificial lipid dyes; and (iv) small intrinsically fluorescent probes for endogenous lipids (Fig. 3a,b). 2.2.1.1. Fluorophore grafting: Except for intrinsically fluorescent molecules (see Sections 2.2.1.3, 2.2.1.4 and 2.2.1.5), it is generally required to covalently link molecules (lipids themselves or PD150606 biological activity lipid-targeted specific proteins) to a fluorophore, in order to visualize membrane lipid organization. Among fluorophores, small organic dyes are generally opposed to big fluorescent proteins (EGFP, RFP, mCherry, Dronpa, a.o.). Most fluorophores used to label lipids are small organic dyes (Section 2.2.1.2) while both organic dyes and large fluorescent proteins are used to label lipid-targeted specific proteins (e.g. toxin fragments and proteins with phospholipid binding domain; see Sections 3.1.1 and 3.1.2). Among Losmapimod chemical information others, major organic dyes developed so far to label lipids are 7-nitrobenz-2-oxa-1,3diazol-4-yl (NBD) and 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY). One can also cite the red-emitting Rhodamine dye KK114 or the Cy dyes. To label proteins, most commonly used fluorophores are Alexa Fluor, Atto or Cy dyes. Labeling kits based on amine- or thiol-reactive organic dyes are available. The labeling of the thiol group of cysteines is a more selective method than the amine-reactive approach, allowing a greater control of the conjugation because thiol groups are not as abundant as amines in most proteins. While all organic dyes can be used in confocal microscopy, some dyes such as Alexa Fluor or Atto dyes have also been used to analyze living cells by super-resolution microscopy [63]. Indeed, such fluorophores have been shown to be reversibly photoswitched in the presence of thiol-containing reducing agents/thiol compounds. Interestingly, many organic dyes can be used in super-resolution micro.Omain biogenesis and maintenance and are further discussed in Section 5. 2.2. Less straightforward evidence in plasma membranes As shown in the previous Section, micrometric lipid domains are well-documented in artificial and highly specialized biological membranes. However, generalization of this concept to the plasma membrane of living cells is less straightforward and results haveAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptProg Lipid Res. Author manuscript; available in PMC 2017 April 01.Carquin et al.Pageremained doubted based on use of fluorescent tools (Section 2.2.1) and poor lipid fixatives (2.2.2) as well as imaging artifacts due to non-resolved membrane projections (2.2.3). 2.2.1. Use of fluorescent lipid probes–Whereas membrane labeling with fluorescent lipid probes represents a useful technique, it nevertheless presents the limitation that PMinserted probes can differentially partition as compared to endogenous lipids, depending on membrane lipid composition and on the fluorophore [62]. To minimize artifacts, at least two criteria should be considered: (i) probe insertion at trace level within the PM, as compared with endogenous lipid composition, to ensure preservation of membrane integrity and avoidance of cell surface perturbations, and (ii) verification that the probe is a qualitative bona fide reporter of its endogenous lipid counterpart. After a short description of available fluorophores, we will briefly review the mostly used fluorescent lipid probes: (i) fluorescent lipid analogs bearing an extrinsic fluorescent reporter; (ii) intrinsically fluorescent lipids; (iii) fluorescent artificial lipid dyes; and (iv) small intrinsically fluorescent probes for endogenous lipids (Fig. 3a,b). 2.2.1.1. Fluorophore grafting: Except for intrinsically fluorescent molecules (see Sections 2.2.1.3, 2.2.1.4 and 2.2.1.5), it is generally required to covalently link molecules (lipids themselves or lipid-targeted specific proteins) to a fluorophore, in order to visualize membrane lipid organization. Among fluorophores, small organic dyes are generally opposed to big fluorescent proteins (EGFP, RFP, mCherry, Dronpa, a.o.). Most fluorophores used to label lipids are small organic dyes (Section 2.2.1.2) while both organic dyes and large fluorescent proteins are used to label lipid-targeted specific proteins (e.g. toxin fragments and proteins with phospholipid binding domain; see Sections 3.1.1 and 3.1.2). Among others, major organic dyes developed so far to label lipids are 7-nitrobenz-2-oxa-1,3diazol-4-yl (NBD) and 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY). One can also cite the red-emitting Rhodamine dye KK114 or the Cy dyes. To label proteins, most commonly used fluorophores are Alexa Fluor, Atto or Cy dyes. Labeling kits based on amine- or thiol-reactive organic dyes are available. The labeling of the thiol group of cysteines is a more selective method than the amine-reactive approach, allowing a greater control of the conjugation because thiol groups are not as abundant as amines in most proteins. While all organic dyes can be used in confocal microscopy, some dyes such as Alexa Fluor or Atto dyes have also been used to analyze living cells by super-resolution microscopy [63]. Indeed, such fluorophores have been shown to be reversibly photoswitched in the presence of thiol-containing reducing agents/thiol compounds. Interestingly, many organic dyes can be used in super-resolution micro.
