What is the best way to store DNA?

 short-term storage (weeks) 4 degree centigrade in Tris-EDTA

 Medium-term storage (months) -80 degree centigrade in Tris-EDTA
 Long-term storage (years) -80 degree centigrade as a precipitate in ethanol
 Long-terms storage (decades) -164 degree centigrade or dried.

If you want to use multiple time, then you can store with aliquot to avoid freeze thaw.

The shearing of DNA occurs when stored in -80 degree, so its safe to store in -20 for long term storage. And
make aliquot of your DNA sample so you don't need to freeze thaw it every time.

One thing to avoid: acidic solutions.

In TE buffer they keep much better.

Although DNA is quite stable, it can degrade in certain condition. so, avoid those conditions
1. DNAse contamination: use autoclave miliQ water for TE buffer.
2. frequently Freeze thaw: make the aliquot or store @ 4 degree C.
3.Avoid Water for storage: use TE buffer pH 7.4. (avoid high salt strength during pH maintenance of buffer.)
For very long-time storage use -80 freezer

Why sodium hydroxide is used for DNA digestion to do genotyping?

In DNA isolation or extraction, NaOH ( Sodium hydroxide) is used as alkaline lysis buffer. It basically helps in
dissolving the cell membrane so that the inner components of the cell including the DNA come out. The
dissolution process happens when NaOH along with SDS (Sodium Dodecyl Sulphate) breaks the hydrogen
bonding (H bonds) between the two strands of the double stranded DNA helix and denatures them into a
single strand. This method is called the Alkaline Lysis method.

Why PCR is generally performed upto 40 cycle?

Polymerase chain reaction, or PCR, uses repeated cycles of heating and cooling to make many copies of a
specific region of DNA. First, the temperature is raised to near boiling, causing the double -stranded DNA
to separate, or denature, into single strands. When the temperature is decreased, short DNA sequences
known as primers bind, or anneal, to complementary matches on the target DNA sequence. The primers
bracket the target sequence to be copied. At a slightly higher temperature, the enzyme Taq polymerase,
binds to the primed sequences and adds nucleotides to extend the second strand. This completes the first
cycle. In subsequent cycles, the process of denaturing, annealing and extending are repeated to make
additional DNA copies. After three cycles, the target sequence defined by the primers begins to
accumulate. After 40 cycles, as many as a billion copies of the target sequence are produced from a single
starting molecule.

Why we need Mg to do PCR?

PCR Reaction Components

A few changes have to be made in order to replicate DNA in a lab reaction. In place of helicase, a PCR
reaction simply uses heat to break the bonds between the nitrogenous bases. Human DNA polymerase is not
stable enough to withstand these temperatures. A similar molecule called Taq polymerase, or thermostable
polymerase, is used in its stead, because it can withstand the heat requirements of PCR. Additionally, a PCR
reaction requires free nucleotides, a buffer, and magnesium.
The Role of Magnesium Chloride

Magnesium chloride is the preferred method of adding magnesium to a PCR experiment. Thermostable
polymerase requires the presence of magnesium to act as a cofactor during the reaction process. Its role is
similar to that of a catalyst: the magnesium is not actually consumed in the reaction, but the reaction cannot
proceed without the presence of the magnesium.
Effects of Abundant Magnesium

The more magnesium that is added to a PCR reaction, the quicker the reaction will proceed. However, that is
not necessarily a good thing. If too much magnesium is present, the DNA polymerase will work too quickly
and often make errors in the copying process. This will lead to many different strands of DNA being produced
that do not necessarily represent the original sample that was provided.
Effects of Scarce Magnesium

If magnesium is in limited supply in a reaction, it will not go as quickly as it should if at all. You may attempt
to run a 40 cycle PCR but not get the amount of copies you intended. Each cycle of PCR doubles the amount
of DNA in the test tube exponentially. So while you start off with a small amount, you end up with many
times that initial amount in the end. If there is not enough magnesium, some of the DNA polymerase will not
be activated and it will not work. However, the heat will have taken apart the DNA that is already present and
it will not be rejoined. Therefore, the entire experiment can be ruined if there is not enough magnesium
present.