Double helix, for DNA

The most famous stracture in aU chemistry is the Watson-Crick double helix for DNA (figure 12.3). The discovery of this structure by James Watson and Francis Crick in 1953 was the beginning of molecular biology. An amazing number of insights about the nature of life have been derived from this structure. 

For quantitative structure-activity relationship (QSAR) studies a three-dimensional model of a DNA-quinoIone complex was built using molecular modeling techniques. It was based on the intercalation of quinolone into the double helix of DNA. It was concluded that the intercalation model is consistent with most available data on the structure of the quinolone complex. This predicted... 

DNA, short for deoxyribonucleic acid, is the coding machinery of life. The beauty of DNA is in its simplicity that results in the complexity of life. The double helix of DNA is made of the chemicals adenine (A), guanine (G), thymine (T), and cytosine (C). These chemical are bound in long stretches as AT and CG pairs,... 

MECHANISM FIGURE 26-1 Transcription by RNA polymerase in E. coli. For synthesis of an RNA strand complementary to one of two DNA strands in a double helix, the DNA is transiently unwound, (a) About 17 bp are unwound at any given time. RNA polymerase and the bound transcription bubble move from left to right along the DNA as shown facilitating RNA synthesis. The DNA is unwound ahead and rewound behind as RNA is transcribed. Red arrows show the direction in which the DNA must rotate to permit this process. As the DNA is rewound, the RNA-DNA hybrid is displaced and the RNA strand extruded. The RNA polymerase is in close contact with the DNA ahead of the transcription bubble, as well as with the separated DNA strands and the RNA within and immediately behind the bubble. A channel in the protein funnels new nucleoside triphosphates (NTPs) to the polymerase active site. The polymerase footprint encompasses about 35 bp of DNA during elongation. 

The replication of DNA Double helix of DNA unwinds. Each single strand serves as a template for the formation of a new DNA strand containing the complementary sequence. Two daughter double helices are formed, each containing one of the parent strands. 

The two strands of DNA are held together by the molecular attractions that occur between nucleotides. Because of their molecular structures, however, the nucleotides are particular in the attractions they have for each other. Guanine and cytosine, for example, are best attracted to each other, while adenine and thymine are best attracted to each other. Accordingly, within the DNA double helix for each adenine on one strand there is a thymine on the opposing strand to which it is attracted. The number of adenines and thymines in DNA, therefore, is always the same. 

Watson and Crick also found that the two complementary strands of DNA are coiled into a helical conformation about 20 A in diameter, with both chains coiled around the same axis. The helix makes a complete turn for every ten residues, or about one turn in every 34 A of length. Figure 23-27 shows the double helix of DNA. In this drawing, the two sugar-phosphate backbones form the vertical double helix with the heterocyclic bases stacked horizontally in the center. Attractive stacking forces between the pi clouds of the aromatic pyrimidine and purine bases are substantial, further helping to stabilize the helical arrangement. 

A very suggestive route to knots is through multiply ravelled species in the form of helices, the double helix for example. The double helix itself attracts great interest in itself as a beautiful object. In the age of genetics, we are almost constantly bombarded with images of the DNA double helix. Indeed, many authors refer to this intertwined structure when describing their work on helices, simply because it is a beautiful object that demonstrates intricate function with relative simplicity of structure. 

In 1953 Thomas J. Watson and F. N. C. Crick proposed the double helix for the structure of DNA [10]. Even after this was postulated, the problem of a more precise structure of DNA remained. Many studies were begun during this period of time to characterize the electronic structure of the components of DNA, experimentally from spectroscopic studies and theoretically from quantum mechanics. Indeed, there were questions as to whether the components of DNA were acceptors or donors of electrons [11]. 

The pKa for the proton on N -1 of guanine is typically 9.7. When the pH approaches this value, the proton on N-1 is lost (see Figure 1.16). Because this proton participates in an important hydrogen bond, its loss substantially destabilizes the DNA double helix. The DNA double helix is also destabilized by low pH. Below pH 5, some of the hydrogen bond acceptors that participate in base-pairing become protonated. In their protonated forms, these bases can no longer form hydrogen bonds and the double helix separates. Thus, acid—base reactions that remove or donate protons at specific positions on the DNA bases can disrupt the double helix. 

Figure 28.27 Replication fork. A schematic view of the arrangement of DNA polymerase III and associated enzymes and proteins present in replicating DNA. The helicase separates the two strands of the parent double helix, allowing DNA polymerases to use each strand as a template for DNA synthesis. Abbreviation SSB, single-strandbinding protein.

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