Calculation for PCR Composition

The calculation below is for a general conventional PCR calculated to help beginners.

S.N.	PCR Component	Initial Concentration	Final Concentration	Final Volume (in µL)
1.	PCR Buffer	10 X	1 X	2.5
2.	MgCl₂	25 mM	2 mM	2
3.	dNTPs	10 mM	200 µM	0.5
4.	Forward Primer	10 µM	0.4 µM	1
5.	Reverse Primer	10 µM	0.4 µM	1
6.	DNA Template	–	–	1
7.	Nuclease Free Water	–	–	16.8 µL
8.	Taq DNA Polymerase	5 U/µL	1 U/25 µL	0.2
	Total			25 µL

Notes:

The concentration of PCR buffer may vary, however, the aim is to make it 1 X at the final volume.
The concentration of Magnesium Chloride can vary from one PCR experiment to another depending upon the primer design and sequence being amplified. The concentration ranges from 1.5 mM to 6 mM. Magnesium Chloride primarily determines the DNA polymerase activity meaning, the higher the concentration of magnesium higher will be the polymerase activity, lower the concentration lower will be the polymerase activity. In other words, increasing the concentration of magnesium will increase the activity of polymerase, however this also increases its sensitivity but decreases specificity. This means there is a higher chances of smear as the DNA gets amplified at a non-specific site as well. In other words, increasing the concentration of magnesium will increase sensitivity while decreasing specificity while decreasing the concentration of magnesium will increase specificity while decreasing sensitivity. One of the ways to optimize the PCR composition is through an increase or decrease of MgCl2 concentration. If you are having a problem with no band after PCR, you could increase the concentration of MgCl₂ while if you suffer from non-specific bands after PCR, you need to decrease MgCl₂ concentration.
Increasing the amount of dNTPs, primers or DNA polymerase does not increase the amount of PCR products after a certain point as limiting factors like degenerating polymerases restrict the productivity.
However, one of the key parameters for optimizing the PCR is through variations with additional supplements to PCR buffer like Ammonium or potassium salts and concentrations of Magnesium Chloride, DNA or DNA polymerase.
Final Calculations can be made using following formula:

S₁* V₁ = S₂ * V₂

where,

S₁: Initial Concentration

S₂: Final Concentration

V₁: Initial Volume

V₂: Final Volume.

Example: (For calculating MgCl₂ with Initial Concentration = 25 mM, Final Concentration = 2 mM; Initial Volume to take = Unknown; Final Volume: 25 ul)

25 mM * Initial Volume to take = 2 mM * 25 ul

Initial Volume to take = 2 * 25 / 25
= 2 ul

For further information:

PCR Optimization for Beginners: A Step by Step Guide