DNA: The Language of Life
DNA molecules are two-stranded structures that consist of phosphates, sugars, and bases arranged in a chain. There are four different bases: adenine (A), thymine (T), guanine (G), and cytosine (C). These bases are paired on either side of the molecule and only bond with their like pair, adenine to thymine and guanine to cytosine. For example, if one side of the strand contains AATG, they will be paired with TTAC on the opposing side. When DNA replicates, the chemical bonds that link the two sides break and new nucleotides join to the unwound strand, generating strands with the same sequences as the original. Mutations arise when an error in the copying occurs the wrong base joins to the strand.
DNA controls the production, timing, and quantity of proteins produced by each cell. When the cell begins to utilize the DNA codes to create proteins, enzymes called RNA polymerases unzip the strand and aid in the pairing of new bases onto the template strand. The new strand of RNA then exits the cell nucleus and the cell’s ribosomes translate the segment into a chain of amino acids, which then folds up and forms a protein. Different combinations of bases code for different amino acids, and each is represented by a three-base signal.
Sometimes more than one combination of bases leads to the same amino acid. For example, both AAA and AAG code for lysine. Therefore, a DNA replication error that led to a G at the third position rather than an A wouldn’t affect the code for lysine. This is known as a silent, or synonymous, change. However, if the third position had changed to a C, making the set AAC, that would change the amino acid to asparagine. This change could affect the protein produced, and is called a nonsynonymous change. These nonsynonymous changes are the basis for the diversity in a gene pool upon which evolution can act.
There are two kinds of DNA, named for their location within the cell. Nuclear DNA (sometimes called nDNA) is found within the cell’s nucleus and consists of the 23 pairs of chromosomes that make up our genome. Nuclear DNA is inherited from an organism’s parents, with each parent contributing 50% of the offspring genome, or one chromosome of each pair. This means that both parents’ lineages are represented by the DNA found within the nucleus.
The second type of DNA is called mitochondrial DNA (often called mtDNA) and is found within the cell’s mitochondria. MtDNA is a much smaller amount of DNA, and consists of a single chromosome that carries only 37 genes. Because of its small size, it is far easier to sample the complete mtDNA of an individual than it is to sample their full nuclear DNA genome. Importantly, mtDNA is directly passed from the mother to the offspring, so the genes passed down are reflective only of matrilineal heritage. This also makes mtDNA useful in studying relatedness over long periods of time, but can be limiting because it cannot detect paternal contributions to the genome.
Challenges in Extracting Ancient DNA
Working with ancient DNA can be challenging. It can be difficult to find sufficient material to work with after decomposition and fossilization have occurred and to eliminating contamination from modern human DNA. Distinguishing between modern human and ancient genetic material is particularly difficult when the ancient DNA comes from our close relatives.
The oldest DNA sample ever recovered to date is 700,000 years old and was recovered from an ancient horse (Millar and Lambert 2013). The oldest hominin whose DNA has been successfully sampled is a 400,000 year old Neanderthal (Meyer et al 2016). In both of these cases, and in many other cases of extraordinary DNA preservation, the DNA was recovered from fossils in extremely cold regions of the world. The ideal preservation condition for DNA is a cold and dry space with very little temperature fluctuation. Even in these circumstances, it takes a fair amount of luck in addition to extremely precise sampling technologies to retrieve DNA this old.
Organisms decompose after death. Water, oxygen and microbes break down DNA, which is a very fragile molecule. Therefore ancient DNA tends to be found in small quantities and is generally fragmentary and damaged. Still, it is sometimes possible to amplify the recovered DNA and obtain a viable sample for analysis. One key factor in harvesting ancient DNA is having technology that allows for the smallest of DNA samples to be detected and collected for study.
Contamination by modern DNA is a particularly difficult problem to solve. Many fossils have been handled by researchers for years and could be contaminated with DNA from hundreds of sources, especially since fossil excavation and subsequent handling does not often require gloves and wearing gloves can actually impede many non-DNA related aspects of fossil study. Contamination is difficult to detect because Neanderthals and humans share much of their genetic material, making some DNA sequences indistinguishable between the two species. Researchers have developed ways to analyze the results of ancient DNA sequencing efforts to determine whether contamination is likely and how much has occurred. Analysis of the results and efforts to keep labs and specimens free of modern DNA is very important as some researchers believe that the early studies of Neanderthal DNA included modern contaminants.
DNA codes for the proteins that control almost all aspects of an organism’s biology
Mitochondrial DNA consists of a small chromosome and is passed only from mother to child
Nuclear DNA consists of 23 pairs of chromosomes and are passed from both parents to the offspring
Both types of DNA have different advantages and drawbacks for further study
DNA preserves best in cold, dry environments