PCR Mastermix Preparation
A PCR Master Mix is just a way to speed up your pipetting. Instead of preparing 10 different reactions of 20ul each (for example) you prepare one reaction of 200ul and then you split it into 10 tubes. This also reduces distraction errors (it is less likely to forget to pipet once 100ul that 20 times 5ul). Also, less plastic (pipet tips) is used.

Some tips:

Given the error of some pipettes, it's generally good to count for an extra reaction every 10. For example, if you need to run 10 PCR, make a Master Mix for 11.

If you are planning to run the same PCR on different templates (which is often the case) then you don't need to add the template in your Mix.

Negative and positive controls should always be included. 

The negative control of a PCR reaction is often done by substituting the template DNA with water. The negative control should not show any amplification band. This guarantees that you don't have DNA contaminants in your mix and that you primers do not amplify each other.

A positive control is a reaction that is expected to work. In this case, if your positive control shows amplification but your sample don't, you know it is not because of some component in the reaction behaving unexpectedly (Polymerase, buffer, etc..).

Let's make a practical example.

Let's say I want to amplify the same target sequence from 10 different DNA samples.

The 1X reaction looks like something like:

**PCR 1X**

Template     1ul
Primer F     1ul
Primer R     1ul
H2O         10ul
MgCl2        2ul
dNTPs        2ul
Buffer 10X   2ul
Polymerase   1ul


Now, considering the positive and negative controls, and 10% extra volume, I would prepare a Master Mix for 13 reactions. Of course, the template must be excluded.

**Master Mix 13X:**


Primer F     13ul
Primer R     13ul
H2O         130ul
MgCl2        26ul
dNTPs        26ul
Buffer 10X   26ul
Polymerase   13ul


Now aliquot 19ul in the 12 tubes, add 1ul of the right template to each of them (in the C- just add 1ul H2O) and run it!

There are cases in which you may want amplify different targets sequences from the same DNA. In this scenario, you want to include the template in the Master Mix, since it is the same for all the reactions, but you want to add the primers separately since each reaction will contain a specific set of primer to amplify a specific sequence.