The blue-fluorescent DAPI nucleic acid stain preferentially stains dsDNA; it appears to associate with AT clusters in the minor groove.DAPI is a popular nuclear counterstain that is used in multicolor fluorescent techniques. Its blue fluorescence stands out in vivid contrast to green, yellow, or red fluorescent probes of other structures. DAPI stains nuclei specifically, with little or no cytoplasmic labeling. . The DAPI dilactate form may be somewhat more water soluble. The counterstaining protocols are compatible with a wide range of cytological labeling techniques—direct or indirect antibody-based detection methods, mRNA in situ hybridization, or staining with fluorescent reagents specific for cellular structures. DAPI can also serve to fluorescently label cells for analysis in multicolor flow cytometry experiments. Staining buffer (100 mM Tris, pH 7.4, 150 mM NaCl, 1 mM CaCl2, 0.5 mM MgCl2, 0.1% Nonidet P-40). A 1 mL volume will be required for each cell sample. To make a 5 mg/mL DAPI stock solution (14.3 mM for the dihydrochloride or 10.9 mM for the dilactate), dissolve the contents of one vial (10 mg) in 2 mL of deionized water (dH2O) or dimethylformamide (DMF). The less water-soluble DAPI dihydrochloride may take some time to completely dissolve in water and sonication may be necessary.
First, read Dr. Upadhyay response above, which explains DAPI quite well. From a techniques perspective, DAPI dilacetate should go into water, so I is strange it doesn't easily go into solution. Maybe your using a different less soluble form? In either case try dissolving in DMF or DMSO (DAPI is stable in either chemical), then dilute in H2O before use. If it doesn't solubilize in DMF/DMSO, then buy fresh DAPI as the kind your using is bad.
First you make a stock solution of 1 mg/ml (dissolved in water or PBS) and then you dilute the solution 1:5000. If you are left with a colloidal liquid, leave if for 5 to 10 min in 60 degrees heated water bath. You can also use sonication and heating to better help the dissolving process.