The invention describes the preparation and use of fluorescent stains for nucleic acids derived from unsymmetrical cyanine dyes, dimmers, trimers, or tetramers. In particular, the invention describes unsymmetric cyanine dyes, dimmers, trimer and tetramers having a water soluble substituent. The dyes of the invention possess superior fluorescent properties when complexed with nucleic acids, and have utility in any application which requires detection of nucleic acids, such as detection of nucleic acids in solution, in gels, in blots, in microarrays, and in bacteria and cells, and for use in analysis of cell structure, membrane integrity, and function. The presence of the water soluble substituent results in improved water soluability and stability, resulting in improved detection of nucleic acids.