For PCR work and plasmid DNA storage which water is best to use? Can ultra pure water (DNase and RNase free) serve the purpose of nuclease free water? What is the difference?
In practice, milliQ water suffices for most standard PCR (you don't need to buy nuclease free water or DEPC-treat your water). Contamination by unwanted DNA is often more of a hazard than nuclease contamination (these are typically denatured by the high temperatures used in PCR). If you want to exercise an abundance of caution, use nuclease free water.
While DNA can be stored in water, unbuffered water is not great for long-term stability. It is better practice to choose a Tris-buffered solution such as TE or Qiagen's EB buffer (essentially 10mM Tris, pH 8.5). Here, molecular biology grade reagents (DNAse free) are recommended.
In practice, milliQ water suffices for most standard PCR (you don't need to buy nuclease free water or DEPC-treat your water). Contamination by unwanted DNA is often more of a hazard than nuclease contamination (these are typically denatured by the high temperatures used in PCR). If you want to exercise an abundance of caution, use nuclease free water.
While DNA can be stored in water, unbuffered water is not great for long-term stability. It is better practice to choose a Tris-buffered solution such as TE or Qiagen's EB buffer (essentially 10mM Tris, pH 8.5). Here, molecular biology grade reagents (DNAse free) are recommended.
I have never encountered any problem with milliQ water in DNA manipulations. However as Suggested by Daniel Cohen, Buffer is good for DNA storage. For PCR and restriction digestions, MilliQ water is suffice!!
TE buffer is usually useful for long term sample storage. However for your regular work sterile milliQ water is the best. One minute thing you have to observe in your TE buffer before storage, is the pH. Sometimes due to wrong pH adjustment in your buffer may input adverse impact during PCR reaction. The pH should be maintained at 8-8.5.
I think both are referring to the same thing.
Although in our lab, what we do is we autoclave milliQ water and use this for our working solutions. But for long term storage, I agree with everyone else, TE buffer is best.
"DNase-free, RNase-free water" is the same thing as "nuclease-free" water since DNase and RNase are the exact "nucleases" in question. Whether you trust the company or not is most likely the concern. I don't think too many companies are untrustworthy. But I am an optimist.
For NGS we usually prefer elution in TE Buffer but for PCR DNA eluted in Autoclaved milliQ work best
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