Question

3. What is the common label used to detect amplicons if you use agarose gel electrophoresis?

5. I ordered an 18-mer oligonucleotide primer from Fisher Scientific. What is an 18-mer?

8. You begin a PCR with 20 copies of the DNA template. After 5 cycles, approximately how many copies of amplicon do you have?

Answer 1

3.

A common label used to detect DNA separated by Agarose Gel Electrophoresis is Ethidium Bromide (EtBr).

EtBr is an intercalating agent, which binds to the hydrophobic region of the DNA Nitrogenous bases by sandwiching between adjacent bases. When seen under UV light, EtBr fluoresces, which can be detected to 'visualize' DNA on an Agarose Gel.

4.

The suffix -mer is used to designate the length of DNA sequences. An 18-mer sequence has 18 nucleotides. The -mer suffix comes from the Greek Meros, or Part and is commonly used in Chemistry to denote the number of repeats in a structure. Aside from nucleotides, proteins are often referred to as monomers, dimers or trimers, which also has the same meaning. A DNA molecule that has n nucleotides, is an n-mer.

8.

Since there were 20 copies originally, each round doubles the number of copies in the previous round of replication.

Number of copies after round 1 = 20 * 2 = 40
Number of copies after round 2 = 40 * 2 = 80
Number of copies after round 3 = 80 * 2 = 160
Number of copies after round 4 = 160 * 2 = 320
Number of copies after round 5 = 320 * 2 = 640

Or,

Number of copies after 5 rounds, beginning with 20 copies = 20 * 2⁵ = 20 * 32 = 640