Polynucleotides stability

A Double Helical Polynucleotide Stabilized by three interbase Hydrogen Bonds... 

In addition to hydrogen bonding between the two polynucleotide chains the double helical arrangement is stabilized by having its negatively charged phosphate groups on the outside where they are m contact with water and various cations Na" Mg and ammonium ions for example Attractive van der Waals forces between the... 

Figure 13 7 The two-metal-ion mechanism for polynucleotide polymerases. One metal ion (usually Mg2+) activates the 3 -OH group of the primer terminus and stabilizes one of the partly negatively charged equatorial oxygen atoms of the phosphoryl group, whereas the other binds the phosphoryl oxygen and the oxygen atoms of the pyrophosphate leaving group. The two metal ions are 3.9 A apart. This mechanism fits both RNA and DNA polymerases. [Modified from T. A. Steitz, Nature, Lond. 391,231 (1998).]...

The first replicative units must have possessed considerably less information than the RNA viruses, which work with an optimized RNA-copying machinery. In the absence of efficiently adapted enzymes the accuracy of reproduction depends solely on the stability of the base pairs. Under these conditions the GC pair has a selective advantage over the AU pair of a factor of about 10. Model experiments show that for GC-rich polynucleotides the error rate per nucleotide can hardly be reduced below a value of 10-2. The first genes must accordingly have been polynucleotides with a chain length around 100 bases or less. 

Kakiuchi, N., Marck, C., Rousseau, N., Leng, M., De Clerq, E. and Guschlbauer, W. (1982) Polynucleotide helix geometry and stability. Spectroscopic, antigenic and interferon-inducing properties of deoxyribose-, ribose-, or 2 -deoxy-2 -fluororibose-containing duplexes of poly(inosinic acid), poly(cytidylic acid). J. Biol. Chem., 257, 1924-1928. 

Sletmoen M, Naess SN, Stokke BT (2009) Structure and stability of polynucleotide-(1, 3)-[beta]-D-glucan complexes. Carbohydr Polym 76(3) 389-399... 

Double helical structures may be constructed from complementary single-stranded polynucleotide chains sharing a common helical axis according to the procedure outlined below. The two strands of the complex are assumed to be regular helices defined by a common set of backbone and glycosyl torsion angles. The data presented here are limited to model poly(dA) poly(dT) double helices stabilized by Watson-Crick base pairs between anti parallel strands. 

While these "energies" are necessarily approximate, they afford a basis for clear discrimination between sterically allowed and sterically forbidden structures. The "energy" approach also offers a means to extrapolate experimental studies (nmr, X-ray, etc.) on the conformation of small model compounds to the polynucleotide level and to test the relevance of the data in a helical complex. In addition, the method provides a starting point for a refined potential energy analysis of double helical conformation and stability. 

Experiments have revealed that the microsystems of proteinoid and polynucleotide have stability in solution under changing temperature of pH such as is not possessed by particles composed of acidic proteinoid alone 2,54), The nucleoproteinoid microparticles have been viewed as models of evolutionary precursor of ribosomes 54). 

Note how many distances have to be uniform in order to properly align the hydrogen bonds that stabilize the DNA helix. Here the principle of bonding orbitals is continued to the next higher level of molecular association. The next step, the covalent linkage of the bases of nucleic acid to polynucleotides, is the moment when potential memory is produced from molecules that singularly have no meaning. 

RNA molecules form secondary structure by folding their polynucleotide chains via hydrogen bond formations between AU pairs and GC pairs. The thermochemical stability of forming such hydrogen bonds provides useful criterion for deducing the cloverleaf secondary structure of tRNAs that is, tRNA molecules are folded into DFI... 

The stability of polynucleotide systems and the conformational variability of nucleic acids are governed, inter alia, by noncovalent interactions [1], They lead to the... 

Polynucleotide polymerases, or nucleotidyl transferases, are enzymes that catalyze the template-instructed polymerization of deoxyribo- or ribonu-cleoside triphosphates into polymeric nucleic acid - DNA or RNA. Depending on their substrate specificity, polymerases are classed as RNA- or DNA-dependent polymerases which copy their templates into RNA or DNA (all combinations of substrates are possible). Polymerization, or nucleotidyl transfer, involves formation of a phosphodiester bond that results from nucleophilic attack of the 3 -OH of primer-template on the a-phosphate group of the incoming nucleoside triphosphate. Although substantial diversity of sequence and function is observed for natural polymerases, there is evidence that many employ the same mechanism for DNA or RNA synthesis. On the basis of the crystal structures of polymerase replication complexes, a two-metal-ion mechanism of nucleotide addition was proposed [1] during this two divalent metal ions stabilize the structure and charge of the expected pentacovalent transition state (Figure B.16.1). 

Polynucleotide polymerases attract much attention - not only because of their central role in DNA metabolism, which suggests an important link to various diseases like tumor growth, defects of the immune system, stress-associated mutagenesis, or viral infections. Several polymerases are indispensable tools for molecular biotechnology, and could be even more valuable if the range of substrates accepted, or their stability and activity, could be tuned to specific requirements. 

In addition to the reaction of mercaptopropionic acid, mixed anhydrides were also formed and identified starting from leucine and phenylalanine in the presence of Ca2+ ions, showing that RNAs can replace protein aminoa-cyl fRNA synthetase catalysts for amino acid activation. The formation of a detectable amount of aminoacyl S -phosphalc polynucleotide seems to be in contradiction with the instability predicted for aminoacyl adenylates (Table 1), however it can be explained by the low pH value increasing their stability and the fact that the selected RNA structures are likely to stabilize the mixed anhydride moiety of the covalent conjugate by favorable intramolecular interactions induced by folding. 

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