Chemicals & Small Molecules

Hoechst S769121 (Nuclear Yellow) is a cell-permeable yellow-emitting fluorescent dye that strongly attaches to adenine-thymine-rich regions within double-stranded DNA's minor groove. This dye finds application in fluorescence microscopy, fluorometry, and flow cytometry for staining and measuring DNA content in live and fixed cells. It is frequently paired with retrograde tracers like True Blue for dual-color neuronal imaging. Additionally, Nuclear Yellow can photoconvert diaminobenzidine (DAB) into an electron-dense reaction product, extending its utility to light and electron microscopy.

Propidium iodide (PI) is a red-fluorescent nuclear and chromosome counterstain. It is not permeant to live cells, making it useful for detecting dead cells. PI binds to DNA by intercalating between the bases, with little or no sequence preference. In an aqueous solution, PI has a fluorescent excitation maximum at 493 nm (blue-green) and an emission maximum at 636 nm (red). It is commonly used in flow cytometry for cell viability and DNA content analysis, as well as in microscopy to visualize the nucleus and other DNA-containing organelles.

4-Di-16-ASP serves as a dialkylaminostyryl dye that fluoresces when inserted into membranes or diluted into organic solvents. Specifically, it uniformly labels neurons through diffusion in the plasma membrane. Notably, in intact tissue, the dye does not transfer from labeled to unlabeled cells, although some transfer may occur when the membrane is disrupted (e.g., after sectioning). Its excitation maximum is 492 nm, and its emission maximum is 607 nm.

Cy5 DIC18 is a far-red fluorescent carbocyanine dye used for cell membrane labeling both in vivo and in vitro. It diffuses laterally to stain the entire cell, making it suitable as an anterograde and retrograde neuronal tracer. Notably, in intact tissue, the dye does not transfer from labeled to unlabeled cells, although some transfer may occur when the membrane is disrupted (e.g., after sectioning). Initially, the dye is weakly fluorescent, but it becomes more pronounced once incorporated into membranes.

Cy3 DIC18 is an orange-red fluorescent carbocyanine dye widely utilized as a lipophilic tracer. Its long hydrocarbon chains integrate into cell membranes, rendering it weakly fluorescent until incorporation. DiI diffuses laterally to stain entire cells, making it effective for anterograde and retrograde neuronal tracing. In intact tissue, minimal transfer occurs between labeled and unlabeled cells, though slight transfer may happen post-membrane disruption, such as during sectioning.

DiO, lipophilic tracer is a green fluorescent and lipophilic carbocyanine dye. It is commonly used as an anterograde and retrograde neuronal tracer in both living and fixed tissues and cells. DiO uniformly labels neurons through diffusion in the plasma membrane, and while it does not transfer from labeled to unlabeled cells in intact tissue, some transfer may occur after membrane disruption, such as during sectioning.

DiR is a near-infrared fluorescent carbocyanine dye specifically designed for cell membrane labeling in both in vivo and in vitro applications. When applied, DiR diffuses laterally, effectively staining the entire cell. Its unique properties make it suitable as both an anterograde and retrograde tracer for neurons. Additionally, DiR can be combined with other tracers for multi-color studies and is useful for near-infrared imaging.

Laurdan is a membrane-permeable fluorescent probe that detects the physical state of surrounding phospholipids based on its localization and sensitivity to water molecules. Its generalized polarization values can identify the phospholipid phase, unaffected by polar head groups or pH.

RAPID DiI is a lipophilic dye that labels cell membranes by inserting its two long hydrocarbon (C18 carbon) chains into the lipid bilayer. It diffuses laterally to stain the entire cell and serves as an anterograde and retrograde tracer of neurons, with faster migration kinetics than DiI.