Helical molecule, isolated

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. 

An isolated helical molecule is in essence a "one-dimensional crystal" because of its axial periodicity. Its Fourier transform (1, 2, 3) is therefore confined to layer lines and on each layer line it is a continous function proportional to Twhere... 

Restriction enzymes, also called restriction endonucleases, recognize specific base sequences in double-helical DNA and cleave, at specific places, both strands of that duplex. To biochemists, these exquisitely precise scalpels are marvelous gifts of nature. They are indispensable for analyzing chromosome structure, sequencing very long DNA molecules, isolating genes, and... 

Because of the double helical nature of DNA molecules, their size can be represented in terms of the numbers of nucleotide base pairs they contain. For example, the E. coli chromosome consists of 4.64 X 10 base pairs (abbreviated bp) or 4.64 X 10 kilobase pairs (kbp). DNA is a threadlike molecule. The diameter of the DNA double helix is only 2 nm, but the length of the DNA molecule forming the E. coli chromosome is over 1.6 X 10 nm (1.6 mm). Because the long dimension of an E. coli cell is only 2000 nm (0.002 mm), its chromosome must be highly folded. Because of their long, threadlike nature, DNA molecules are easily sheared into shorter fragments during isolation procedures, and it is difficult to obtain intact chromosomes even from the simple cells of prokaryotes. 

Figure 5.24 Model of hierarchical self-assembly of chiral rodlike monomers.109 (a) Local arrangements (c-f) and corresponding global equilibrium conformations (c -f) for hierarchical selfassembling structures formed in solutions of chiral molecules (a), which have complementary donor and acceptor groups, shown by arrows, via which they interact and align to form tapes (c). Black and the white surfaces of rod (a) are reflected in sides of helical tape (c), which is chosen to curl toward black side (c ). (b) Phase diagram of solution of twisted ribbons that form fibrils. Scaled variables relative helix pitch of isolated ribbons h hh /a. relative side-by-side attraction energy between fibrils eaur/e. Reprinted with permission from Ref. 109. Copyright 2001 by the National Academy of Sciences, U.S.A.

Conformational calculations are carried out on poly(di-n-hexylsilanes). The most significant finding from the energy calculations is that the a -trans conformation is not the lowest energy structure for the symmetrically alkyl-substituted silane polymers. A helical structure is preferred for the isolated molecule. 

When the chain length is dramatically increased, as in (28), podands are available which could imitate the helical ion channels believed to be available in membranes and so give information on the selective transfer of cations across such barriers. This type of ligand shows pronounced transfer of inorganic salt into organic phases and NMR studies indicate a likely helical coordination of the cation.33,218 Complexes have been isolated and the structure of (29)2KNCS has been solved.219 In this molecule, the podand wraps, in an S-shaped manner, within the dinuclear complex, and contains a KNCS unit within each loop of the S shape. 

The underwound state can be maintained only if the DNA is a closed circle or if it is bound and stabilized by proteins so that the strands are not free to rotate about each other. If there is a break in one strand of an isolated, protein-free circular DNA, free rotation at that point will cause the underwound DNA to revert spontaneously to the relaxed state. In a closed-circular DNA molecule, however, the number of helical turns cannot be changed without at least transiently breaking one of the DNA strands. The number of helical turns in a DNA molecule therefore provides a precise description of supercoiling. 

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