Friday, March 27, 2015

Mnemonic for nucleotide nomenclature

This information is procured from "Nucleotide Nomenclature and Symbol" (In Biological Sciences).

Mnemonic for nucleotide nomenclature and symbol. The letters cap and underlined are the symbols. E.g. W represents Adenine and Thymine (or W = A or T), K represents Guanine and Thymine (K = G or T).

Thursday, March 26, 2015

Information unfriendly commercial companies

I get it, that secret ingredients are what makes commercial companies thrive.
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Unfortunately, kits with minimal information is not helping students understand the concept behind workability of the kit (or approach). It is a disservice to Science and knowledge.
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I never liked companies that provided less-to-no information about their products. I shun away from these companies to save myself from being made into a technical person who follow instructions.
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Some companies are friendlier while others are protective of self-interest.
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For those who want to learn more about kits, the ideal place to look would be via patent files. Google is one place to start.
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Just to share.

Thursday, March 5, 2015

Estimate the molecular/formula weight of DNA based on its length in base pair (bp)

This is just an estimation, i.e. 650.
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How to calculate Molarity and Number of DNA molecules
  • Calculate the molecular weight of DNA molecule
A double stranded DNA of 100 bp will have an estimated molecular/formula weight = 100 bp x 650/bp = 65,000. Note that 650 is the molecular weight of one base pair.
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  • Calculate the Molarity of DNA solution
To calculate molarity of DNA, e.g. 100 µg/ml (equivalent to 0.1 g/l) of 100 bp DNA will corresponds to 0.1/65000 Molar = 1.5 µM DNA (equivalent to 1.5 µmol/l).
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  • Calculate the number of DNA molecules in a volume of DNA solution
To calculate the numbers of DNA molecules in 1 µl (equivalent to 1 x 10^-6 l) of 1.5 µM DNA, use the Avagadro number to convert mol to the number of molecules. First, determine the mol of DNA in 1 µl of 1.5 µmol/l DNA solution, e.g. 1.5 x 10^-6 x 10^-6 = 1.5 x 10^-12 mol. Next, determine number of DNA molecules, e.g. 1.5 x 10^-12 x 6.023 x 10^23 = 9.03 x 10^11 DNA molecules. That is equivalent to 0.9 trillion DNA molecules.
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  • Calculate the number of DNA molecules based on mass
If I have a mass of DNA molecule, e.g. 135 pg of 500 bp dsDNA, how many DNA molecules is there? First, determine the molecular weight, i.e. 500 bp x 650/bp = 325,000. Note that 135 pg is equivalent to 135 x 10^-12 g. Next, determine the mol of DNA, i.e. 135 x 10^-12 / 325,000 = 4.15 x 10^-16 mol. In a mole, there is 6.023 x 10^23 molecules, thus the amount of DNA molecules is 4.15 x 10^-16 x 6.023 x 10^23 = 250 million DNA molecules.
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This is for my own reference.