Fundamentals of Molecular Biology - V. I. Rezyapkin 2009

Nucleic Acids
Physicochemical Properties of DNA

Denaturation

DNA denaturation is caused by Chemical factors (such as urea, guanidine hydrochloride, acids, and alkalis) as well as physical factors (Temperature). Denaturation results in the disruption of the Introduction/11.html">Secondary Structure of DNA. Once the denaturing agent is removed, the secondary structure can be restored—a process known as renaturation:

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As noted above, elevated temperatures lead to DNA denaturation, or melting. This process is accompanied by an increase in the optical density of DNA solutions at a wavelength of 260 nm, a phenomenon referred to as the hyperchromic effect. The maximum increase in optical density upon complete degradation of DNA into mononucleotides at this wavelength is approximately 80%.

Fig. 1.5 shows the plot of the optical density of a DNA solution at a wavelength of 260 nm versus temperature. This relationship is sigmoidal (S-shaped) in nature and is determined by the DNA composition. A DNA molecule consisting exclusively of poly-d(AT) melts at lower temperatures than one composed of poly-d(GC). This is because two Hydrogen Bonds form between A and T, whereas three hydrogen bonds form between G and C.

A crucial characteristic of DNA is its melting temperature, which is defined as the temperature at which the increase in optical density reaches half of the maximum increase observed upon complete denaturation. As seen from Fig. 1.5, the melting temperature of poly-d(AT) DNA is 66 °C, while that of poly-d(GC) DNA is 85 °C. Natural DNAs have a melting temperature above 66 °C and below 85 °C because they contain all four nitrogenous bases in varying proportions across different living organisms. For instance, human DNA has a melting temperature of 81–82 °C, whereas that of E.coli is 90.5 °C.

Fig. 1.5. Optical density of a DNA solution at 260 nm as a function of temperature

Upon cooling the DNA solution (annealing), the original secondary structure may be restored in accordance with THE PRINCIPLE OF complementarity.

If a mixture of different DNA molecules is first melted and then annealed, Hybridization between the DNA molecules can occur provided there is sufficient similarity in their primary structures (Fig. 1.6).

Fig. 1.6. Hybridization between different DNA molecules

The higher the similarity between DNA molecules, the greater the degree of hybridization. Based on the hybridization results between DNAs from different species, evolutionary relationships can be inferred. The higher the degree of hybridization, the closer the phylogenetic relationship between the analyzed species.

Hybridization can also occur between DNA and RNA molecules, provided homologous nucleotide sequences are present (Fig. 1.7).

Fig. 1.7. Hybridization between DNA and RNA