A “Primer” on DNA and the Consequences of Mutation

We can’t talk about Molecular Diagnostics without possibly talking about DNA, and with DNA, comes mutation. Much of the work I do revolves around searching for specific variants in a patient’s DNA sequence. We all have mutations in our DNA, but does that mean we all are affected negatively? Absolutely not. Spontaneous mutations occur during normal process such as DNA replication and repair within our cells. They also can arise from exposure to ionizing radiation, UV exposure, and chemical agents. Some mutations are passed down through reproductive cells. Mutations can be categorized as harmless or sometimes hurtful giving rise to gene defects, copy number variants, metabolic deficiencies, and cancer, while others result in positive effects.

Where do mutations occur?

Somatic mutations occur in cells that aren’t reproductive in nature. These mutations for the most part do not have a blatant effect on the organism because our normal body cells are able to counteract the mutated cells. However, sometimes mutations in somatic cells can affect division of cells, which has the potential to result in forms of cancer. On the contrary, germ-line mutations occur in reproductive cells and have the possibility of being passed down through generations, resulting in the presence of the mutation in all of the organism’s cells.

Understanding DNA

A T G C bases, along with a sugar, and a phosphate group combine to form a polymer of nucleotides. This polymer backbone of alternating sugar and phosphates is what we call DNA (Deoxyribonucleic Acid). DNA is transcribed to RNA (Ribonucleic Acid) which instead of Thymine (T) contains a Uracil (U). Finally, RNA is translated to protein.

Pyrimidines	Purines
Single-ringed organic bases	Double-ringed organic bases
Thymine (T) Cytosine (C) Uracil (U)	Adenine (A) Guanine (G)
Hydrogen Bonds Between Complimentary Strands of DNA
Adenine bonds Thymine   A = T(U) Guanine bonds Cytosine   G ≡ C	Two Hydrogen Bonds Three Hydrogen Bonds

Amino acids are the triplet codons that make up proteins. It is extremely important to become familiar with the codon table. You don’t need to memorize it, however you should at a minimum know what triplets code for START and STOP codons. You will quickly see that there are multiple codes for a single amino acid. This becomes important when considering the effects of mutation:

Like I mentioned earlier, many of the tests I perform involve screening for variants in DNA sequence. I accomplish this through different methods, which I will touch on in future blog posts. We could easily discuss mutations for hours and hours, but for now, it’s probably most important to gain a quick (and simple) understanding of the types of mutations and what the resulting effects can be. For the sake of demonstration, let us consider the following normal (wild type) sequence pattern:

Transition Mutations occur when mispairing results in a purine being replaced with a different purine, or a pyrimidine replaced with a different pyrimidine:

A→G

C→T

Transversion Mutations occur when a purine is replaced with a pyrimidine or vice versa:

A→T

C→G

Missense Mutations have the ability to result in a change in the amino acid. This happens when the codon triplet is altered, and the amino acid sequence of the encoded protein is changed:

Sometimes, Missense Mutations are silent:

Frame shift mutations can result from either a single base insertion or a single base deletion.

Nonsense mutations are exactly what they are called… Nonsense! Here, a base substitution changes an amino acid into a stop codon. Nonsense mutations result in abnormal termination of translation and the protein product is shortened:

Chromosomal Abnormalities

Sometimes changes in the actual chromosomal structure or number take place in the cells. These changes can result in deletions, duplications, inversions, and translocations of chromosomes. Chromosomal deletions and insertions are simply the loss or gain of chromosomal material. Inversions result from the removal, flipping, and then reconnection of the chromosomal material within the same chromosome.

Translocations are more complicated and involve switching of genetic material between two chromosomes. A reciprocal translocation occurs when parts from two different chromosomes exchange. We call a reciprocal translocation “balanced” when there isn’t a gain or loss of genetic material between the chromosomes (both chromosomes remain fully functional). An “unbalanced” reciprocal translocation affects an offspring’s phenotype due to extra or missing genes.

This information I have touched on is very general, however, it doesn’t mean it is not of importance. These basic concepts are the fundamentals needed to begin understanding mutation as they will provide us with the framework for recognizing the needs and importance of molecular diagnostic testing!

---

Test your Molecular Knowledge

1. What amino acids do the following codons code for:
   1. GAU
   2. AUG
   3. UAG
   4. CAG
   5. UGA
2. Classify the following mutations:
   1. T→A
   2. T→C
   3. AGA→UGA
   4. AGA→AAA
   5. AGA→CGA

Answers

1 a) Aspartic Acid b) Methionine (start) c) Stop codon d) Glutamine e) Stop codon. 2 a)Transversion b) Transition c) Nonsense d) Missense e) Silent

-LeAnne Noll, BS, MB(ASCP)^CM is a molecular technologist at Children’s Hospital of Wisconsin and was recognized as one of ASCP’s Top Five from the 40 Under Forty Program in 2015.