Fundamentals of Molecular Biology - V.I. Rezyapkin 2009

Nucleic Acids
Secondary Structure of DNA

In 1953, the American geneticist J. Watson and the English physicist F. Crick proposed a model for the Introduction/11.html">Secondary Structure of DNA. According to this model, the Spatial Organization of DNA is a double helix.

The scientists made their discovery based on prior findings by other researchers. Specifically, E. Chargaff and subsequent researchers studying the Nucleotide Composition of DNA across various species drew the following Conclusions:

a) the nucleotide composition of DNA is identical in different Tissues of the same species;

b) the nucleotide composition of DNA varies among different species;

c) nucleotide composition is independent of age and diet;

d) the number of adenine residues in DNA always equals the number of thymine residues, and the number of guanine residues equals the number of cytosine residues.

Other researchers, R. Franklin and M. Wilkins, published an X-Ray Diffraction pattern obtained from the X-Ray Structural Analysis of DNA. X-ray structural analysis is widely used to study the spatial organization of molecules. The DNA double helix proposed by Watson and Crick (Fig. 1.2) successfully accounted for the findings of the aforementioned scientists.

The parameters of the DNA double helix proposed by Watson and Crick are outlined below:

a) DNA consists of two strands coiled into a right-handed double helix (Fig. 1.2B):

b) the strands within the DNA molecule are oriented antiparallel to each other (Fig. 1.2A);

c) the nitrogenous base moieties are oriented perpendicular to the axis of The Double Helix;

d) the pentose and phosphoric acid residues are located on the outer surface of the double helix;

e) DNA strands (Fig. 1.2B), when coiled into a double helix, form Major and minor grooves; the width of the major groove is 2.2 nm, and that of the minor groove is 1.2 nm;

f) there are 10 nucleotide pairs per turn of the helix;

g) a full turn of the helix is 3.4 nm long;

h) the diameter of the double helix is 1.8 nm;

i) the DNA strands are linked together by Hydrogen Bonds formed between guanine of one strand and cytosine of the other, or between thymine and adenine located on opposite strands;

j) two Hydrogen bonds are formed between thymine and adenine, whereas three hydrogen bonds are formed between guanine and cytosine (Fig. 1.3);

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Fig. 1.2. DNA parameters

The ability of guanine to interact exclusively with cytosine, and of adenine exclusively with thymine within the DNA molecule is referred to as complementarity, and the bases guanine and cytosine, as well as adenine and thymine, are called complementary bases. According to the complementarity principle, The sequence of one strand determines the sequence of the other. Thymine will always be opposite adenine, and cytosine opposite guanine. Thus, the DNA strands in the double helix are complementary to each other.

The double helix is additionally stabilized by base-stacking interactions. The bases are stacked vertically on top of one another with their planar surfaces in close proximity. As a result, hydrophobic interactions and dipole interactions of the $\pi$-bonds arise between them.

Fig. 1.3. Formation of hydrogen bonds between adenine and thymine, and between guanine and cytosine in the DNA molecule

Depending on environmental conditions and DNA composition, the parameters of the double helix may slightly differ from the original model proposed by Watson and Crick. Currently, several alternative DNA models have been described. Nevertheless, THE PRINCIPLE OF complementarity is preserved across all proposed models, and the DNA strands remain coiled into a double helix.

A-form of DNA

The A-form of DNA (Fig. 1.4) is formed at relatively low humidity. This structure is a right-handed helix. In this DNA conformation, there are 11 Base Pairs per helical turn. The distance between NUCLEOTIDES along the helical axis is 2.56 Å. The base pairs are tilted by 20^o.

Fig. 1.4. Various Forms of DNA

C-form of DNA

C-DNA is formed at high salt concentrations and humidity levels intermediate between those required for A- and B-DNA formation. The helical pitch of C-DNA is 30.9 Å, with 9.33 base pairs per turn. The base pairs are tilted at an angle of -8^o relative to the axis.

Z-form of DNA

The Z-form of DNA is a left-handed helix (Fig. 1.4). It was discovered in 1979 during structural studies of the hexanucleotide d(CG)3. This helix retains Watson-Crick base pairing, with 12 base pairs per turn of the Z-helix.

Circular double-stranded DNA molecules can exist in a supercoiled state. Supercoiling can occur as a result of local unwinding of the double helix. The resulting torsional stress is relieved by supercoiling. The transition of a circular DNA molecule into a supercoiled state and vice versa is mediated by topoisomerases:

DNA molecules may contain inverted repeats, known as palindromes:

Palindromes can form cruciform structures: