Helical structure in polynucleotides

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

Whereas proteins have their low energy absorption band at 280 nm, polynucleotides typically have maxima at 260 nm (38,500 cm ). A phenomenon of particular importance in the study of nucleic acids is the hypochromic effect. In a denatured polynucleotide the absorption is approximately the sum of that of the individual components. However, when a double helical structure is formed and the bases are stacked together, there is as much as a 34% depression in the absorbance at 260 nm. This provides the basis for optical measurement of DNA melting curves (Fig. 5-45).45,86 The physical basis for the hypochromic effect is found in dipole-dipole interactions between the closely stacked base pairs.7,86,87... 

The nucleic acids are among the most complex molecules that you will encounter in your biochemical studies. When the dynamic role that is played by DNA in the life of a cell is realized, the complexity is understandable. It is difficult to comprehend all the structural characteristics that are inherent in the DNA molecules, but most biochemistry students are familiar with the double-helix model of Watson and Crick. The discovery of the double-helical structure of DNA is one of the most significant breakthroughs in our understanding of the chemistry of life. This experiment will introduce you to the basic structural characteristics of the DNA molecule and to the forces that help establish the complementary interactions between the two polynucleotide strands. 

Double helix. A structure in which two helically twisted polynucleotide strands are held together by hydrogen bonding and base stacking. 

While these "energies" are necessarily approximate, they afford a basis for clear discrimination between sterically allowed and sterically forbidden structures. The "energy" approach also offers a means to extrapolate experimental studies (nmr, X-ray, etc.) on the conformation of small model compounds to the polynucleotide level and to test the relevance of the data in a helical complex. In addition, the method provides a starting point for a refined potential energy analysis of double helical conformation and stability. 

While the complementary double helical structure explained how particular sequences of bases could be used to store a genetic instruction it was not immediately clear how replication occurred or, indeed, how these instructions were used. Later work by Gamow linked DNA base pair sequences to protein synthesis [15] but it was not until 1961, when Nirenberg and Matthaei demonstrated that cell-free protein synthesis relied upon synthetic or natural polynucleotides [16], that the final link was made. The information held within the linear DNA sequence is replicated every time a cell divides. Replication is possible because of the unique double helical structure of DNA as shown in Fig. 2.7. 

One well-established observation is that, under conditions where single-stranded polynucleotides give rise to a d.c. polarographic reduction wave, both native DNA and other double-helical natural and synthetic polynucleotides are inactive 22 23,46-47, 58,59,61) Tjjjs js rea(ji]y interpretable in that, in such helical structures, the adenine and cytosine residues are located in the interior of the helix, and hydrogen bonded in complementary base pairs (see below). Z-DNA, in which cytosine residues are at the surface of the helix, is of obvious interest in this regard, and the B - Z transition in the synthetic poly(dG dC) has been investigated with the aid of differential pulse polarography and UV spectroscopy 60). 

These results lead to the following scheme for the cooperative disordering of these polynucleotides by Cu(II). Initial increments of Cu(II) bind to phosphate and stabilize the helical structure, as the initial increase in rotation in Figure 4 demonstrates. As the concentration of polymer-bound Cu(II) increases, crosslinking to bases takes place. Such crosslinks may be within the same polymer strand or between different strands. Once such crosslinking has begun, additional cooperative cross-... 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

While the importance of IR and Raman spectroscopy for the structural elucidation of purine bases has diminished over the last few decades, its advantages for the study of oligo- and polynucleotides in particular with respect to base pairing is apparent. The IR absorption spectrum of a single-stranded polynucleotide is very similar to that of its component nucleotides, but drastic changes occur on formation of hydrogen-bonded helical structures. 

The analysis obtained with classical polarographic methods corresponds roughly with those reached by the pulse-polarographic technique, but the sensitivity is much lower. The difference between the polarographic behaviour of single-stranded and double-helical form of polynucleotides makes possible the study of the conformation of nucleic acids [81,82,108-113]. Polarography can be utilized also in the study of structural changes of polynucleotides under the influence of the temperature [112,114,115] or irradiation [116]. The photodynamic destabilisation of DNA has been described [117]. 

There is a large variability possible in the structures of double stranded DNA due to the fact that (compared to polypeptides) many more bonds can be rotated in the backbone of each monomer (Scheme 14). The most common and physiologically most important structure is the B-DNA helix. It consists of two polynucleotide chains running in opposite direction which coil around a common axis to form a right-handed double helix. In the helix, the phosphate and deoxyribose units of each strand are on the outside, and the purine and pyrimidine bases on the inside. The purine and pyrimidine bases are paired by selective hydrogen bonds adenine is paired with thymine, and guanine with cytosine (Scheme 15). The structure is very flexible and can form a supercoil with itself, or around proteins. It can form a left-handed supercoil around histones to form nucleosomes which assemble in yet another helical structure to form chromatin. ... 

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