Can alcohol precipitation give 100% recovery of DNA? - (Sep/17/2007 )
I probably can do this empirically, but let's say we begin with a pure DNA sample and then precipitate it with ethanol or isopropanol, can we still recover all of the initial amount?
Would the recovery be dependent on factors such as:
-size of DNA (eg. smaller vs large fragments
-Ethanol vs isopropanol
-Precipitation time and temperature
-others?
j
salt form, Na+, Ca2+, Mg2+ or NH4+
Just googled and found this:
Alcohol Precipitation of DNA
The major considerations in using alcohols to precipitate DNA are:
Temperature: -20°C is optimal, but 0°C can be used for >20 ng/mL
2) Amount: For small amount of DNA (<100 ng, i.e. too little to reliably see a pellet) the use of glycogen (1 μL of a
20 mg/mL stock: Roche) will increase yield and allow visualization of the pellet.
3) Time: Optimal precipitation requires >1 hr at -20°C.
4) Speed of centrifuge (>12,000 rpm): Important for small amounts or small oligos.
5) Mg [10 uM] helps pellet oligos (<100 bp).
6) Avoid precipitates: EDTA (>10 mM) and Ca (>1 mM) will precipitate at the concentrations indicated in alcohol
solutions. SDS will also precipitate with salts other than NaCl.
7) Choice of alcohol: Isopropanol has the advantage of requiring less volume (from 0.6 vol to 1 vol. of isopropanol is
added to 1 volume of DNA/salt soulution compared to 2 vol. of ethanol). However isopropanol has the disadvantage
of coprecipitating more salts and is less volatile (so it air dries slower) compared to ethanol.
8) Choice of salt:
NaOAc, pH5.2, [0.3M]: This is the standard. (10x Stock concentration = 3 M)
NaCl [0.2M]: SDS is more soluable in NaCl (Stock conentrations vary 1M - 5M)
NH4OAc [2 - 2.5M]: Less coprecipitation of dNTPs, good for purifying oligos. However, NH4+ inhibits
polynucleotide kinase).
LiCl [0.8M]: Soluble in a higher concentration of ethanol which is useful for the precipitation of RNA.
However Cl- inhibits the initiation of protein synthesis and RNA will display varying solubility based on
size.
Would the recovery be dependent on factors such as:
-size of DNA (eg. smaller vs large fragments
-Ethanol vs isopropanol
-Precipitation time and temperature
-others?
j
no never you could have 100% back it is caused by alot of things for example you might use one of those 99.9% EtOH on lab and if only youre EtOH contains 0.1% water it will solve your DNA and it is not possible to gather all.
and as you mention all of the item could change its efficiency.
cheers,
akhshik.