Double Helix

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The sugar—phosphate backbones of the two strands spiral around the outside of the molecule.

The Francis Crick Papers

Phosphates are depicted in white and sugars in black. The base pairs gray are stacked down the center of the molecule, and their edges form the bottoms of the major and minor grooves. Reinhard Renneberg, The DNA double helix, recombinant DNA technology, the human genome project, and genetically modified organisms are now all part of popular culture.

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But what is the story behind these words? Understanding the language used to write these instructions and how these instructions were expressed lays the foundation for molecular biology.

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This journey led to a scientific revolution that took place in bacteria had been manipulated to harbor DNA sequences from completely unrelated organisms. Genetic engineering was born, leading to a new kind of biotechnology where any organism could be asked to carry and express any gene of natural or artificial origin. Genetic engineering has already saved the lives of millions of people around the world and the future of gene technologies is a true wonder. The DNA double helix can adopt more than one conformation Fig.

The B form most closely resembles the average structure of DNA under physiological conditions. Experimentally, this form is observed at high humidity. There are about 10 base pairs per turn of the helix. As expected, the major groove is wide, and the minor groove is narrow. The A form, on the other hand, is observed at low humidity. It has about 11 base pairs per turn. Compared with the B form, its major groove is narrower but deeper, and its minor groove is wider and shallower.

There are base pair to base pair variations in the structure. Also, the rotation per base pair is not a constant along the length of the DNA. Yet, the B form is a good approximation to the structure of cellular DNA and helps explain various macromolecular interactions and functions. The A structure is found in certain protein-DNA complexes.

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  5. Under certain conditions, DNA containing alternating purine and pyrimidine residues can adopt a left-handed structure. A prominent feature of the left-handed helix relates to the orientation of the purine base about the glycosidic bond.

    Rosalind Franklin and the Double Helix

    In nucleosides, rotation about the glycosidic bond allows the bases to occupy either of two principal positions— syn and anti Fig. In right-handed DNA, bases are always in the anti conformation. In left-handed DNA, pyrimidines do exist in the anti conformation, but the purine residues adopt the syn conformation. Nevertheless, left-handed DNA helices are only infrequently found in the cell. Syn and anti orientations of guanine and cytosine. Richard R. The DNA helix in solution will adopt a preferred helical repeat that is a function of the base composition as briefly mentioned in Chapter 1.

    On average, the helical repeat is about In linear DNA, in which the ends of the molecule are free to rotate, the DNA will adopt this preferred helical repeat of This helical repeat will also exist in nicked DNA in which the nick provides a swivel around which one strand can rotate about the other. The preferred helical repeat of a linear DNA molecule represents the lowest energy form of the molecule. When this state of helical twist exists in a covalently closed molecule, the molecule is relaxed and contains no supercoils.

    In the relaxed DNA shown in Figure 3. The linking number of relaxed DNA, L 0 , is defined as.

    DNA structure and replication

    The DNA molecule shown in Figure 3. One strand crosses the other 20 times in the plane of the page of this book. This linking number will be the same whether the DNA molecule exists in a linear, nicked, or covalently closed relaxed form. This may seem an obvious and unnecessary point to make but, as you will see, changes in temperature and salt concentration affect L 0 and introduce a new twist into the DNA structure story.

    The DNA double helix is usually thought of as a straight molecule. In fact, it must be bent or curved in many of its functional roles, especially when interacting with particular proteins. There has been much speculation on the nature of DNA bending in such situations as in the nucleosome component of chromatin which has base pairs wound around a histone protein core and closed-circular DNA, prior to determinations of nucleosome crystal structures.

    Some sequences have an inherent tendency to bend independently of there being any protein present. Intrinsic DNA bending and curvature was discovered Marini et al.

    These fragments showed highly anomalous gel electrophoresis behavior, with very slow migration through the gel, as if the DNA had a much higher molecular weight than was the case. The phasing is critical since it forces the tract to be always on the same side of the helix, thereby enabling the individual small bends associated with each tract to add up to a significant amount of total bending. It has been estimated Koo et al. A typical bending sequence, from kinetoplast DNA, is:. Two distinct structural models have been suggested to account for these observations of bending.

    In one, a combination of gel retardation and NMR studies have been used Nadeau and Crothers, , resulting in a structural model that has bending toward the minor-groove direction of the helix.

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    Abrupt changes in either tilt or roll can produce this situation. Thus, in the junction model, the A-tracts are themselves not bent. The structural basis for bending has been controversial, with there being continuing debate on the roles played by base-pair propeller twist, roll, buckle, and slide both within and flanking A-tracts themselves.

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    Figure 3. Schematic representations of bending models for A tract DNA. The advent of relevant crystal and NMR structures is providing structural data for distinguishing between these models, with increasing reliability for the various base and base-pair morphological parameters, although no bent structure is as yet available that even approaches atomic resolution. Charles Tanford, in Comprehensive Biochemistry , But proteins remained very much a part of the story.

    How many polypeptide chains? How big are they? Are they all alike? How are they linked? This circumstance got me involved in a controversy, quite unintentionally; I was not even aware of it at first. The ultimate substantive matter in question was the subunit composition of an enzyme, aspartate transcarbamylase, a critical regulatory component in the biosynthesis of nucleotides — DNA and RNA. But the controversy itself centered on just one person, Jacques Monod, one of the half dozen people closest to the very heart of molecular biology.

    He shared the Nobel Prize for biology or medicine in with two of his colleagues from the Pasteur Institute, but has never been one of my favorite scientists. One historian describes him as having a zest for combat and a flair for performance, but I was only rarely impressed by the relevance of his battles to scientific priorities.

    This meant taking on the arduous intellectual task of immersing themselves in all the fields of science involved: genetics, biochemistry, chemistry, physical chemistry, and X-ray crystallography. Drawing on the experimental results of others they conducted no DNA experiments of their own , taking advantage of their complementary scientific backgrounds in physics and X-ray crystallography Crick and viral and bacterial genetics Watson , and relying on their brilliant intuition, persistence, and luck, the two showed that DNA had a structure sufficiently complex and yet elegantly simple enough to be the master molecule of life.

    Other researchers had made important but seemingly unconnected findings about the composition of DNA; it fell to Watson and Crick to unify these disparate findings into a coherent theory of genetic transfer. The organic chemist Alexander Todd had determined that the backbone of the DNA molecule contained repeating phosphate and deoxyribose sugar groups. The biochemist Erwin Chargaff had found that while the amount of DNA and of its four types of bases--the purine bases adenine A and guanine G , and the pyrimidine bases cytosine C and thymine T --varied widely from species to species, A and T always appeared in ratios of one-to-one, as did G and C.

    Maurice Wilkins and Rosalind Franklin had obtained high-resolution X-ray images of DNA fibers that suggested a helical, corkscrew-like shape. Linus Pauling, then the world's leading physical chemist, had recently discovered the single-stranded alpha helix, the structure found in many proteins, prompting biologists to think of helical forms.

    Moreover, he had pioneered the method of model building in chemistry by which Watson and Crick were to uncover the structure of DNA. Indeed, Crick and Watson feared that they would be upstaged by Pauling, who proposed his own model of DNA in February , although his three-stranded helical structure quickly proved erroneous.