Biological Chemistry - Berezov T. T., Korovkin B. F. 1998

Chemistry of Nucleic Acids
Structure of Nucleic Acids
Tertiary Structure of Nucleic Acids

It is extremely difficult to isolate a native DNA molecule (Fig. 3.2) from most sources—particularly Chromosomes—due to the high susceptibility of DNA to tissue Nucleases and hydrodynamic degradation*.

Only certain viral, mitochondrial, and chloroplast DNAs have been successfully isolated in an intact (undamaged) state. Physical (specifically crystallographic) and physicochemical studies of these molecules have demonstrated that the DNA double helix can undergo further coiling in certain regions to form supercoils or an open circular conformation. It has also been shown that linear DNA can be derived from the circular form or exist naturally as such. Furthermore, single-stranded DNAs of both linear and circular forms have been discovered in certain Viruses (Fig. 3.3).

The formation of circular DNA molecules in Bacteria or animal Cell Mitochondria is frequently caused by the covalent joining of their open ends. It is well established that the superhelical (supercoiled) Structure enables the compact packaging of the enormous DNA molecule within a chromosome: instead of the 8 cm length it would span in an extended form, the human DNA molecule is packed so tightly that its length in the chromosome is reduced to 5 nm. Typically, DNA contains positive and negative supercoils generated by clockwise (right-handed) or counter-clockwise twisting of The Double Helix. The formation of such supercoils is catalyzed by specific Enzymes known as topoisomerases. These supercoils associate with Proteins (Histones) packed within the grooves, thereby ensuring the Stability of the tertiary Introduction/20.html">DNA Structure. The degree of supercoiling (the presence of supercoils) in a DNA molecule is generally determined by measuring Changes in the sedimentation constant under specific conditions. DNA Supercoiling can be disrupted by a single- or double-strand break in the double helix induced by DNase action or Treatment with intercalating agents. Intercalation refers to the insertion of flat aromatic rings between stacked Base Pairs of DNA. This process can be triggered by Antibiotics and Dyes; in intact Cells, it may involve the aromatic rings of Amino Acids, which presumably serves a distinct biological function in protein-nucleic acid recognition.

* A gentle method for isolating native DNA using proteinase K and SDS has been developed. The DNA preparation isolated from monkey Kidney cells had an unusually high Molecular Weight of 2 ∙ 10⁸; however, even in this case, the molecular weight is several orders of magnitude lower than the in vivo molecular weight of DNA, which is estimated at 10¹⁰–10¹¹.

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Fig. 3.2. Model of a DNA molecule.

Fig. 3.3. Tertiary Structure of DNA (schematic).

1 – linear single-stranded DNA (bacteriophage φX174 and other viruses); 2 – circular single-stranded DNA of viruses and mitochondria; 3 – circular double-stranded DNA helix.

Fig. 3.4. Tertiary structure of RNA in solution as a function of Ionic strength, Temperature, and medium pH (schematic) (after A.S. Spirin and L.P. Gavrilova).

a – compact rod, b – compact coil, c – extended chain.

Data on tRNA Structure indicate that native tRNA molecules share a generally similar tertiary structure, which is much more compact than the flat "cloverleaf" model due to the folding of various segments of the molecule. It is worth noting the existence of natural double-stranded RNAs in A number of viruses (reoviruses, wound tumor virus of plants, etc.) that share a structural Organization analogous to DNA. Under physiological values of pH, ionic strength, and temperature, conditions are established for the formation of multiple double-helical regions ("hairpins") in single-stranded messenger and Ribosomal RNAs, as well as the subsequent formation of complementary segments that largely determine the rigidity of their tertiary structure (Fig. 3.4). Currently, there is mounting evidence confirming The Importance of Van der Waals forces (dipole-dipole and London dispersion forces) between nitrogenous bases in stabilizing the overall spatial configuration of Nucleic Acids.