Double helix featuring hydrogen bonds

Figure 5. A stereo view of the gellan double-helix featuring the intrachain hydrogen bonds (thin dashed lines), interchain hydrogen bonds (thick dashed lines), potassium ions (filled circles), and water molecules (open circles) and the six ligands attached to each potassium ion (thin lines).

Fig. 16. An unusual interrupted helix from subtilisin (residues 62-86), in which the helical hydrogen bonds continue to a final tum that is formed by a separate piece of main chain. Such interrupted helices (broken on one side of the double helix) are apparently a fundamental feature of nucleic acid structure as illustrated by tRNA, but are exceedingly rare in protein structure.

The important features of the Watson and Crick model are as follows. The DNA consists of a double helix whereby two polynucleotide chains are coiled around a common axis (figure 3.18). The bases are on the inside of the helix whereby a base on one chain hydrogen bonds with a base on the other chain. There is a very specific pairing of bases (figure 3.17) adenine (A) must pair with thymine (T) whereas guanine (G) must pair with cytosine (C). These pairs fit perfectly into the space available on the inside of this helix whose dimensions are consistent with the X-ray fibre diffraction pattern. 

The two intertwined polynucleotide chains of the DNA double helix run in opposite (antiparallel) directions. Thus, each end of the double helix contains the 5 end of one chain and the 3 end of the other. The sugar-phosphate backbone is on the outside of the helix, and the bases point inward. The unique feature of the Watson and Crick structure is the way in which the chains are held together to form the double helix. They theorized that the DNA structure is stabilized by hydrogen bonding between the bases that extend inward from the sugar-phosphate backbone (see I Figure 11.8). The spacing in the interior of the... 

When the Watson-and-Crick structure was published, Pauling immediately saw the beauty and validity of it, and he undertook a small-molecule crystal-structure investigation (SP 117) that revealed the detailed configuration of the hydrogen bonding between pyrimidines and purines—the bonding feature that is the basis for complementariness between the two DNA strands in the double-helix structure. 

In sunmary, a model for G-C destabilization has been derived from nucleotide hydrogen exchange studies that is consistent with thermodynamic considerations of H-bond strength and DN4 stability. This model contains the point of view that DN4 stability may depend on the weakness of the interbase oxygen-to-amino H-bonds If the nucleobase aminos were strong H-bond donors a stable double helix could not be formed, due to the competition of water for the donor sites. Sequence specific interactions of protein cationic sidechains, or non-specific interactions of small cations, both with the G(N-7) site accessible to solvent in the large helical groove, would decrease the interbase proton lifetime and allow a drastic increase in solvent (water) interaction of G-C-rich sequences exclusively. A central feature of the model s extension, the requirement for simultaneous interaction of... 

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