Depend on what you are planing to do with your DNA. TE buffer is good for preserving your DNA samples but the EDTA can have some effect on your downstream application such as PCR. Anyway DNA is very stable molecule and even nuclease free water will do just fine

Depend on what you are planing to do with your DNA. TE buffer is good for preserving your DNA samples but the EDTA can have some effect on your downstream application such as PCR. Anyway DNA is very stable molecule and even nuclease free water will do just fine

Phosphate buffer just holds correct pH. TE buffer, i addition inhibits DNAses thanks to EDTA. I agree with Amr T. M. Saeb - my favourite solution for DNA elution is pure deionized water.

I think that as Amr T. M. Saeb said it depends on what you want to do with your DNA. To my knowledge for qualitative approaches like end-point PCR it might be okay, but forget it for quantification techniques. I use TE with commercial solid phase extraction kit and I never faced any problems with downstream PCR even when I do do qPCR. If you use such kit, take care to follow manufacturers instructions to maximize desorption yields.

I agree that it really depends what you want to do with the DNA later. Storing DNA in pure nuclease-free water, as some suggest, is fine. However, I would only recommend it for short-term storage, not if you want to keep the DNA for several years. It also depends a little bit on the type of DNA. Circular plasmids are less susceptible to degradation than linear DNA (PCR fragments, primers etc.), as they are not providing free ends that exonucleases could attack. I, personally, store DNA in TE buffer, but instead of the more common 1 mM EDTA, I include only 0.1 mM EDTA. I never had any problems with PCR applications or restriction digests, even if I had to add a large volume of DNA. Phosphate buffer, in turn, is probably better than pure water for DNA storage, as it at least keeps the pH. However, phosphate buffer will not protect your DNA from degradation, as it lacks EDTA.

In the publication of Rossen et al. 1992, it was figured that an EDTA concentration of 0.1 mM in the master mix of a PCR did not affect the reaction, whereas of 1 mM led to inhibition

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We will often store our DNA in 5 mM Tris.  Most mini-prep kits provide EB (Elution Buffer) which is just 10 mM Tris, so we dilute that by half in distilled H2O. 

Also, remember that EDTA is chelating agent that catches divalent ions such as MG2+

So in your protocol and depending on how downstream in your application, you need to figure out if ionic strength is a factor. For example, some restriction enzymes do require cofactors.  If it is a factor, then you'll want to switch to the phosphate buffer.  This is a general rule of thumb.  However,as some people pointed out, you can effectively dilute out the effects of EDTA.   

I always use TE buffer though in some kits DNA can be stored in Tris pH 8.5.I think 10mM Tris with 0.1 mM EDTA is a good option for ensuring good enzymatic reactions for cloning