Double helix base composition

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

Application of Equation 17 to the two systems discussed here shows that dissolution of / -lactoglobulin in 40% 2-chloroethanol in the final conformation assumed by the protein in this medium stabilizes the system since (d/x2(e)/dm3) = —6,000 cal/mole protein/mole 2-chloroethanol in 1000 grams of water. This means that in this system the protein has a stronger affinity for the alcohol than for water relative to the bulk solvent composition. As a result, excess alcohol is found in the domain of the protein. Exactly the opposite is true for the DNA in salt system. Here, the obtained values of D result in a destabilization of the system by the salt since (dfi2ie /dm3) = 50-100 cal/(mole/A) of DNA per mole of salt in 1000 grams of water. For a double helix of 100 base pairs this amounts to a destabilization of the order of 10 kcal/mole of salt added. As pointed out above, this results in excess water in the domain of the macromolecule —i.e.9 in preferential hydration of the DNA. 

The examination of crystallized DNA fragments of varying base composition show sequence-dependent variations in the double helix while emphasizing the A, B and Z forms as structurally distinct families. Variation occurs in the orientation of each base pair to the next by rotation about the X axis or tilt, the Y axis or roll or the Z axis or twist of the helix. Bases in a pair may also rotate in opposition producing variations in buckle, propeller and opening (Fig. 7-5). 

Firstly, the determination of the base composition of DNA from a number of sources had shown that while the overall base composition varied widely, there was always the same amount of A as of T, and the same amount of G as of C. Secondly, high-quality X-ray photographs of DNA fibres were consistent with a helical structure composed of either two or three polynucleotide chains. The major physiological form of the DNA double helix is the B-DNA described by the X-ray pictures of Rosalind Franklin, with 10 base parrs per turn (Figure 3.18),... 

Aladan substitution of internal core amino-acid residues provides an approach to characterise the physical characteristics of protein cores. Steady-state fluorescence alone can provide initial insight to the immediate environment of Aladan in the protein core. However, time-resolved fluorescence spectroscopy can be used to understand variations in protein core composition and structure as a function of time through the characterisation of Aladan fluorescence intensity and /max changes that are caused by small fluctuations in the relative permittivity, e, of the protein interior with time (fs-ps timescale). Such spectroscopy is possible since fluorescence lifetimes, Tr, are typically in the ns range (see Section 4.5). Also, time-resolved fluorescence spectroscopy can be performed with non-covalently linked extrinsic fluorophores such as ethidium bromide (EtBr). This fluorophore intercalates between the bases of DNA or RNA double helix and in so doing acquires a substantial increase in (j) and hence fluorescence intensity at /max (595 nm). Should there be a disruption or collapse in double-helical structure, then intercalation fails and fluorescent intensity drops... 

The X-ray diffraction pattern of DNA demonstrated the helical structure and the diameter. The combination of evidence from X-ray diffraction and chemical analysis led to the conclusion that the base pairing is complementary, meaning that adenine pairs with thymine and that guanine pairs with cytosine. Because complementary base pairing occurs along the entire double helix, the two chains are also referred to as complementary strands. By 1953, studies of the base composition of DNA from many species had already shown that, to within experimental... 

The number of base pairs per turn of the double helix, 70, is rigorously fixed under given ambient conditions. However, upon changing the ambient conditions (temperature, composition of solvent, etc.), it can vary. Therefore, the number of supercoils r, in contrast to the Lk value, is a topological invariant of DNA only under fixed ambient conditions. 

The Watson-Crick model was based on molecular modeling and two lines of Watson-Crick model experimental observations chemical analyses of DNA base compositions and math- double-helix model for the ematical analyses of X-ray diffraction patterns of crystals of DNA. 

In the computer model of this triple helix, there is more coverage of the hydrophobic surfaces, since each "step" of the helix is almost 50% longer. This may well be why the triple helix is possible when a double helix does not form under any conditions we examined. The triple helix is of the normal composition, with a central purine and two pyrimidine strands, one with Watson-Crick base pairing and one with Hoogsteen base pairing. Our further work is aimed at a more detailed understanding of this structure in our compounds. 

In the investigations performed to date on double-stranded DNA, it has been presumed that the relaxation behavior of each P nucleus is the same as all others. However, that presumption is probably not precisely correct. Work has indicated that the preferred conformation of the nucleotide units in the helix varies somewhat with base composition and sequence (e.g., Wang et al, 1979 Wing et al, 1980 Levitt and Warshel, 1978 Keepers et ai. 1982). The relaxation of P depends on the magnitude of the P-H intemuclear distances that may vary with conformation of the monomeric unit. It should be anticipated that variations, perhaps small, in P relaxation values from DNAs with different composition will be reported in the future. 

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