| Overview
Blue fluorescent DNA stain that is commonly used in fluorescent microscopy. It is frequently used as a nuclear stain to stain nuclei. It is excited by UV light.
Hoechst 33342 is cell permeable and has greater cell permeability than Hoechst 33258. The stain can be used on both live and fixed cells and is often used as an alternative to DAPI.
Hoechst 33342 binds to the AT-rich regions of the minor grove in DNA which renders it specific for nuclear chromatin. Its fluorescent intensity depends on the DNA content, chromatin structure and the position of the cell within the cell cycle.
Uses and applications
There is little fluorescent overlap with other commonly used small-molecule fluorophores / fluorescent proteins that emit in the green / red range. This makes it suitable for a wide range of applications.
Counterstain
Hoechst 33342 is commonly used as a counterstain in fluorescent imaging.
Cell cycle studies / Apoptosis
Hoechst 33342 can stain the condensed nuclei of apoptotic cells to allow the identification of chromatin condensation and fragmentation. It is commonly used with propidium iodide to distinguish normal/live apoptotic and dead cell populations [5]. It can additionally be used in conjunction with arcidine orange (AO) to distinguish apoptotic cells.
Incorporation of Brdu into DNA has a quenching effect on Hoechst fluorescence. Hoechst 33342 is also used in combination with BrdU to monitor cell cycle progression.
Stem cells
Combination of the Hoechst 33342 stain with surface-marker phenotyping allows the characterisation of a sub-population of stem cells termed the ‘side population’ (SP). | 
Understanding purity and quality - a guide for life scientists
