Nucleic acid scattering densities

An alternative procedure, called molecular replacement, uses information about known structures that are believed to be similar to that of the species being investigated. The known structure is used to estimate the electron density of the unknown structure, which is then refined and improved. Another method of dealing with the phase problem is to introduce atoms which absorb radiation in the region of the incident X-rays, leading to a process called anomalous scattering . For proteins, a popular method is to replace S by Se by using selenomethionine in place of methionine. For nucleic acids, iodouracil or iodocytosine can be used in place of thymine and cytosine respectively. 

Scattering properties of nucleic acid residues. The electron densities correspond to unhydrated residue volumes. Residue volumes were calculated using V = 0.66 ml/g for ribose and the summations of molar atomic volumes for the bases as given below, and using v = 0.52 ml/g for RNA, whereupon the phosphate volume was best determined from the difference as 0.06 nm. The final v for RNA is 0.515 ml/g and for DNA is 0.529 ml/g assuming a unit weighting of the four bases... 

The term reflects the curvature of the Stuhrmann parabola and is always positive (Fig. 5). Since it is a second-order term and is defined mainly by R% values measured in low Ap (where counting statistics are usually weaker and sample impurity effects are larger), the inherent accuracy of is less than that oi Rc and a. Physically, it corresponds to the displacement of the centre of scattering within the particle as the contrast is varied, i.e. corresponds to the distance between the centres of the shape Py(r) and the fluctuations pp(r). Typical systems where might be measurable include protein-detergent, protein-nucleic acid and proto-nated-deuterated protein complexes (Section 4). If a particle can be divided into two components 1 and 2 with distinctly different scattering densities, the separation between 1 and 2 can be calculated [47] ... 

To a first approximation, the sizes of isometric viruses can be estimated by comparing the experimental maxima and minima with the theoretical curves calculated for spheres and hollow spheres [492-494,504]. However, viruses are composed of protein shells and nucleic acid cores (with carbohydrate and lipid in more complex viral structures), so a full analysis requires the explicit consideration of non-uniform scattering densities. In addition, the principle of icosahedral symmetry in the assembly of the protein shell means that, at large Q, deviations from spherical symmetry will influence the scattering curve. The separation of the scattering curve... 

Many of the physical properties of polynucleotides are changed upon alteration of their structure this allows for the application of a wide range of techniques in such studies. Hydrodynamic properties such as viscosity, sedimentation coefficients, and buoyant density can all be readily monitored. Light and low-angle X-ray scattering are also well understood. Changes in spectroscopic properties are also conveniently studied. These have all been summarized in Physical Chemistry of Nucleic Acids [28], and the major effects which are discussed in this book are briefly reviewed below. 

A spectrophotometric test for purity may be made by measuring the optical density at 260 m/i, the wavelength of the absorption maximum of nucleic acid and thus of the phages. Extraneous nucleic acid will increase the absorbency index per particle (see Sec. IV, 6). A correction must be made for light scattering. 

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