One of the assumptions of molecular biology from an evolutionary perspective is that the triplet nature of the genetic code is a traditional form of two-nucleotide coding. In other words, it is assumed that protein coding using three nucleotides is an evolutionary modification of coding based on two nucleotides. In this sense, one might expect that the mRNA UUU codon, which encodes the formation of the amino acid Phenylalanine, might have been previously represented by the two-nucleotide UU codon encoding the same amino acid. In fact, such speculation makes sense, and the following paragraphs aim to use compelling biological evidence for this thesis.
It is now well known that DNA consists of four nucleotides (A, T, G, and CD), and every three variations of these nucleotides create a particular amino acid. In this regard, there is the Central Dogma of Molecular Biology, which determines that DNA through transcription gives rise to mRNA, which through translation is converted into the amino acid sequence of a polypeptide. According to the law of mathematics, coding four elements into three sites could yield 43 variants or 64 combinations of nucleotides. If only two nucleotides were enough for coding, with no change in the number of monomers forming the DNA, this would result in 42 variants or only 16, which is exactly four times less.
In this sense, the first intuitive argument is that the diversity of protein molecules used to be significantly lower and their amino acid composition scarcer. Chemical evolution continues to add to the number of emerging substances, but earlier, when life was just beginning, it is highly likely that the three-nucleotide code was redundant. Cells did not expend as much energy to use triplets because protein molecules were meaningfully simpler.
In addition, the genetic code is degenerate, which means that the same amino acid is encoded by several codons at once. For example, a study of the mRNA table makes it clear that lysine is encoded by two triplets at once (AAA and AAG) and serine by six (AGU, AGC, UCA, UCG, UCU, UCC). In fact, almost all functional amino acids, except for Methionine, Tryptophan, are encoded by at least two codons. It can be seen that the first and second nucleotide are always the primary fixatives, while the quality of the third nucleotide in the codon can vary. This leads to the idea that two nucleotides are historically more fundamental.
At the same time, the effect of frameshift on the posttranslational outcome has been investigated. In particular, it is estimated that deletion or alteration of the first or second nucleotide in a codon always resulted in an inability to create a protein (Hardison, 2021). Alternatively, changing the third nucleotide only affected the final quality of the amino acid but still led to its formation. From this, one can conclude that the nucleotide was initially based on the use of two nucleotides, but over time, biochemical evolution led to the importance of the third.
The first phase of the PCR technique involves the most intense heating of the DNA strand, causing the hydrogen bonds that form the complementary helical complex to break down. Thus, the helix is converted into a mixture of two linear stranded nucleotide chains simultaneously in solution. It is noteworthy that the nucleotide composition of the mixture does not differ in this case because no qualitative changes in the molecule, except for the breaking of the bond between the nucleotides, occurred. In other words, if the initial DNA sample had a GC composition equal to 70%, then the amount of guanine and cytosine in the already unpaired DNA strands will remain unchanged even after the whole molecule is destroyed.
In the experiment under consideration, it is proposed to use two samples of DNA, one of which contains 70% of GC and the other containing only 45%. At this point, one can conclude that the two molecules are not related since the composition of close biological genera and, even more so, the species of GC is very similar (Machado, & Gram, 2017). An essential feature of using guanine and cytosine specifically for this characteristic of any nucleotide chain is the presence of three hydrogen bonds between the C and G pair. As it is known from the kinetics of chemical reactions, a more significant number of bonds usually requires more input energy to break them. In other words, a DNA molecule with 70% GC is more resistant to degradation and denaturation, which means that more effort is required to break it.
A reasonable conclusion can then be drawn that DNA with 70% GC will require higher temperatures to break the entire molecule, in contrast to DNA with almost 1.6 times lower proportion of G and CD nucleotides. In other words, the first DNA sample could be used at higher annealing phase temperatures, as opposed to the second sample, which would require less heat input. However, in either variant, temperatures as low as 100°C may be sufficient to separate the helix of the nucleotide chains.
References
Hardison, R. (2021). Genetic code. Libre Texts. Web.
Machado, H., & Gram, L. (2017). Comparative genomics reveals high genomic diversity in the genus Photobacterium.Frontiers in Microbiology, 8, 1-8. Web.