Polynucleotides, conformations

Sundaralingam M (1974) Principles governing nucleic acid and polynucleotide conformations. In Sundaralingam M, Rao ST (eds) Structure and conformation of nucleic acids and protein-nucleic acid interactions. Univ Park Press, Baltimore pp 487-524... 

The second model evaluation of folding patterns is based on the thermodynamic stability of polynucleotide conformations. Here, not only does this stability decide which of the many possible structures is formed (as in the preceding) but it also determines the fitness. The more stable is the optimal folding pattern for a particular sequence, the higher is its selective value ... 

From the above discussion, it appears that zinc may have its primary effect on zinc-dependent enzymes that regulate the biosynthesis and catabolic rate of RNA and DNA. In addition, zinc may also play a role in the maintenance of polynucleotide conformation. Sandstead et al. (99) observed abnormal polysome profiles in the liver of zinc-deficient rats and mice. Acute administration of zinc appeared to stimulate polysome formation both in vivo and in vitro. This finding is supported by the data of Femandez-Madrid, Prasad, and Oberleas (42), who noted a decrease in the polyribosome content of zinc-deficient connective tissue from rats and a concomitant increase in inactive monosomes. 

Zinc atoms in some of the enzyme molecules participate in catalysis and also appear to be essential for maintenance of structmre of apoen-zymes. Zinc also plays a role in stabilization of biomembrane structure and polynucleotide conformation. Inasmuch as zinc appears to have a protective influence in hepatic cellular damage induced by carbon tetrachloride poisoning, it is reasonable to suggest that zinc also may have a direct effect on free radicals. 

Many other polynucleotide conformations are possible, including the left-handed helical Z-DNA and more complicated structures thought to be involved in chain replication, together with supercoiling and more globular structures in single-stranded transfer RNA. 

Sundaralingam, M. The concept of a conformationally rigid nucleotide and its significance in polynucleotide conformational analysis Sundaralingam, M., Ed. Jerusalem, 1973, pp 417-456. 

Column 3 DNAs are identified by origin and are arranged in order of increasing %GC. Polynucleotides are arranged first of alt, deoxypolymers before ribopolymers, then in the order homopolynucleotides, helices involving interaction between different homopolynucleotides, and heteropolynucleotides and in alphabetical order of nucleotide bases. The abbreviations for polynucleotides conform to those proposed by the lUPAC-lUB convention [7011], except that the usual subscript is omitted. 

The hydration shell is formed with the increasing of the water content of the sample and the NA transforms from the unordered to A- and then to B form, in the case of DNA and DNA-like polynucleotides and salt concentrations similar to in vivo conditions. The reverse process, dehydration of NA, results in the reverse conformational transitions but they take place at the values of relative humidity (r.h.) less than the forward direction [12]. Thus, there is a conformational hysteresis over the hydration-dehydration loop. The adsorption isotherms of the NAs, i.e. the plots of the number of the adsorbed water molecules versus the r.h. of the sample at constant temperature, also demonstrate the hysteresis phenomena [13]. The hysteresis is i( producible and its value does not decrease for at least a week. 

The lUBMB Commission on Nomenclature has issued a number of recommendations dealing with areas of a more biochemical nature (72), such as peptide hormones (86), conformation of polypeptide chains (87), abbreviations for nucleic acids and polynucleotides (88), iron—sulfur proteins (89), enzyme units (90), etc. The Commission has also produced rules and recommendations for naming enzymes (91,92). 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

They did find that these compounds behaved kinetically as competitive inhibitors of polymerization of the normal substrates e.g., guanosine 5 -diphosphate. These authors suggested that the successful completion of the polynucleotide phosphorylase reaction requires that the nucleotide be capable of assuming the anti conformation. Also, Kapuler and Reich (53) have found that both 8-bromo- and 8-oxoguanosine 5 -triphosphates are very poor substrates in the E. coli RNA polymerase reaction and are competitive inhibitors with respect to guanosine 5 -triphosphate as a substrate. 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

The illustration opposite shows selected nucleic acid molecules. Fig. A shows various conformations of DNA, and Fig. B shows the spatial structures of two small RNA molecules. In both, the van der Waals models (see p. 6) are accompanied by ribbon diagrams that make the course of the chains clear. In all of the models, the polynucleotide backbone of the molecule is shown in a darker color, while the bases are lighter. 

TABLE 11.1. Association Constants of Various Nucleic Acids with Neomycin. From top to bottom, various polynucleotides with their conformational preference (B- to A-form) are listed in 10 mM sodium cacodylate, 100 mM NaCl, 0.1 mM EDTA, pH 6.8. RNA targets that have previously been shown to bind neomycin are also listed. These targets are examples of RNA secondary structures that show high-affinity binding to aminoglycosides. Solution conditions for RNA targets vary as shown... 

NUCLEOTIDES AND NUCLEIC ACIDS Abbreviations and symbols for nucleic acids, polynucleotides and their constituents /. Biol. Chem. (1970) 245, 5171-5176 Corrections, J. Biol Chem. (1971) 246, 4894 Abbreviations and symbols for the description of conformations of polynucleotide chains Eur. J. Biochem. (1983) 131, 9-15 Nomenclature for incompletely specified bases in nucleic acid sequences... 

This mixed sugar pucker conformation is associated with an extension of the -polynucleotide chain. 

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