Nucleic Acids with Proteins

These studies demonstrate that Cu(II) has substantial effects on the structure of polynucleotides as well as on the intermolecular packing of complexes of nucleic acids with proteins or polypeptides. 

Nucleoproteins. These are combinations of nucleic acids with protein. These compounds are found in cell nuclei. 

These interactions are frequently ionic in character. The coulombic forces of interaction between macroions and lower molecular weight ionic species are central to the life processes of the cell. For example, intermolecular interactions of nucleic acids with proteins and small ions, of proteins with anionic lipids and surfactants and with the ionic substrates of enzyme catalyzed reactions, and of ionic polysaccharides with a variety of inorganic cations are all improtant natural processes. Intramolecular coulombic interactions are also important for determining the shape and stability of biopolymer structures, the biological function of which frequently depends intimately on the conformational features of the molecule. 

Covalent bonding of modified nucleic acids with proteins in study of specific protein-nucleic interactions 05UK84. 

Metal ion interactions also play an important role in the binding of nucleic acids with proteins, influencing denaturation stability and protein synthesis and thus keeping the inherited information. 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Figure 16.2 The icosahedron (top) and dodecahedron (bottom) have identical symmetries but different shapes. Protein subunits of spherical viruses form a coat around the nucleic acid with the same symmetry arrangement as these geometrical objects. Electron micrographs of these viruses have shown that their shapes are often well represented by icosahedra. One each of the twofold, threefold, and fivefold symmetry axes is indicated by an ellipse, triangle, and pentagon, respectively.

With remarkable accuracy, Democritus in the fifth century B.C. set the stage for modem chemistry. His atomic theory of matter, which he formulated without experimental verification, still stands, more or less intact, and encapsulates the profound truth that nature s stunning wealth boils down to atoms and molecules. As science uncovers the mysteries of the world around us, we stand ever more in awe of nature s ingenious molecular designs and biological systems nucleic acids, saccharides, proteins, and secondary metabolites are four classes of wondrous molecules that nature synthesizes with remarkable ease, and uses with admirable precision in the assembly and function of living systems. 

There exist numerous reports on the interaction of noble metal nanoparticles, especially those of gold, with DNA. The reason for this intense work in most cases is the use of gold nanoparticles for the analysis of nucleic acids, or proteins. In any case, the interactions between the two... 

Potentiometric and H-NMR methods were combined in the studies of the interaction of [Pd(en)(H20)2]2+ and [Pd(pic)(H20)2]2+ (pic = 2-picolylamine) with monodentate ligands containing nitrogen or sulfur donor atoms. The ligands represent the side chain residues of nucleic acids and proteins.178... 

The complete complex of nucleic acid and protein, packaged in the virus particle, is called the virus nucleocapsid. Although the virus structure just described is frequently the total structure of a virus particle, a number of animal viruses (and a few bacterial viruses) have more complex structures. These viruses are enveloped viruses, in which the nucleocapsid is enclosed in a membrane. Virus membranes are generally lipid bilayer membranes, but associated with these membranes are often virus-specific proteins. Inside the virion are often one or more virus-specific enzymes. Such enzymes usually play roles during the infection and replication process. 

Virus infection obviously upsets the regulatory mechanisms of the host, since there is a marked overproduction of nucleic acid and protein in the infected cell. In some cases, virus infection causes a complete shutdown of host macromolecular synthesis while in other cases host synthesis proceeds concurrently with virus synthesis. In either case, the regulation of virus synthesis is under the control of the virus rather than the host. There are several elements of this control which are similar to the host regulatory mechanisms, but there are also some uniquely viral regulatory mechanisms. We discuss various regulatory mechanisms when we consider the individual viruses later in this chapter. 

The analysis of extraterrestrial matter is concentrated on the detection of nucleic acid and protein building blocks, i.e., N-heterocycles and amino acids. The search for such compounds began immediately after the fall of the Murchison meteorite. Twenty-two amino acids were detected in it as early as 1974 eight of them pro-teinogenic, ten which hardly ever occurred in biological material, and four which were unknown in the biosphere. Up to now, about 70 amino acids have been identified (Cronin, 1998), the most common being glycine and a-aminoisobutyric acid. The latter is a branched-chain amino acid with the smallest possible number of carbon atoms. The most frequently found amino acids occur in concentrations of... 

A technical challenge with this step is to achieve RNA extraction of uniform quality and efficiency for each fraction. This is because the amount of RNA in each sucrose gradient fraction varies considerably and the high concentration of sucrose in the bottom fractions interferes with phase separation in typical phenol-based extraction steps. To address these problems, we spike each fraction with an aliquot of a foreign (control) RNA, which can be used later to correct for differences in RNA recovery (and reverse transcription efficiency) between samples. We then remove sucrose from the samples by precipitation of total nucleic acid and protein with ethanol. To purify RNA, a standard Trizol (Invitrogen) extraction is performed as outlined later (also see product insert). 

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