Polynucleotides, intramolecular

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. 

In a physicochemical study of oligo- or polynucleotides, it has been reported that Hypochromicity, depends on the degree of polymerization [61]. The value of native DNA is about 60%, which corresponds to the Hypochromicity, of the absorption of its mononucleotides [60]. The present result indicates that the purine rings may intramolecularly stack by themselves in an aqueous solution... 

Cleavage of nucleic acids refers to a reaction that results in the breakage of bonds in the phosphodiester backbone of a polynucleotide chain. There are two types of reactions resulting in the cleavage of either P-O or C-O bonds in the nucleic acid backboue (see Figure Id). Cleavage of the P-O bond occurs as a result of uucleophilic attack ou the phosphorus atom via either an intermolecular reaction with a H2O molecule hydrolysis) or an intramolecular reactiou involving the ribose 2 -OH transesterification). Of these two reactions, transesterification is specific to RNA (since DNA lacks a 2 -OH moiety) and can be catalyzed by many M- +... 

The presence of self-complementary sequences (called palindromes) within a single strand of polynucleotide can cause the palindromic portion of it to form intramolecular base pairs (Figure 4.27 and Figure 4.28). tRNAs and rRNAs have extensive base pairing of this type, although it can happen in DNA too. 

The families of alkanes, amides and carboxylic acids contain the constituents which comprise most of the amino acid residues of protein chains, and indeed the major motivation for deriving a consistent force field for these families was its potential application for biopolymers. However, a comprehensive consistent force field for biological molecules should include more groups e.g. aromatic and heterocyclic rings, carbohydrate, phosphate and sulfur groups it should also extend considerably the consistent analysis of intramolecular energy parameters pertaining to polypeptide and polynucleotide chains. This could be done fully only if more experimental data could be accumulated to supply the specific needs of the consistent force field analysis. 

RNA ligases catalyze the 3 —> 5 phosphodiester bond formation of RNA molecules with concomitant hydrolysis of ATP to AMP and PP . Initially detected as an activity that catalyzes the circularization of polyribonucleotides with 3 -OH and 5 -P ends (1), the RNA ligase is found in E. coli after infection by T-even (but not T-odd) bacteriophages. The enzyme can carry out intermolecular as well as intramolecular ligation reactions on ssRNA, ssDNA, or a variety of oligonucleotides and polynucleotides having 5 -P and 3 -OH termini. 

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