DEPC water vs nuclease free water, when does it actually matter which one you use
i see this come up a lot and wanted to write out a clear answer because the standard response of "they're basically the same" isn't totally accurate and neither is "they're completely different."
DEPC treated water works by having diethyl pyrocarbonate inactivate RNases through covalent modification. the DEPC is then removed by autoclaving. it works well for a lot of RNA applications but there is a catch. residual DEPC can interfere with downstream reactions especially coupled transcription and translation systems. more importantly DEPC reacts with Tris and imidazole so DEPC treated water is not suitable for Tris based buffers.
commercially produced nuclease free water is usually made with WFI grade or high purity water, sterile filtered, manufactured under conditions that prevent nuclease introduction. no DEPC concerns. most commercial NFW gets tested for DNase, RNase, and protease activity and the COA confirms absence.
practical rule of thumb: for Tris based buffers, PCR, RT-PCR, in vitro transcription, use commercial NFW. for most other RNA work either is fine but commercial NFW is lower risk and more convenient.
one thing i'd add from experience: not all NFW is equal and if you're having unexplained RNA issues, actually test your water, don't just trust the COA. we had a supplier lot issue that took forever to trace. switched to Biologix after that and it's been consistent but the testing point stands regardless of who you buy from.
happy to answer questions on this.