Natural terminal repetition

Fig. 4. A model of the nucleotide sequence arrangement contained within AAV DNA, Two nucleotide sequence permutations are illustrated. Plus and minus strands may anneal to form duplex linear monomers with (3 and 4) or without cohesive 3 or 5 termini (1 and 2). Duplex linear monomers with cohesive termini can then form duplex circular monomers or duplex linear oligomers. In the figure the terminal repetitions are depicted as symmetrical nucleotide sequences. In the inset two alternative types of terminal repetitions are illustrated the first has the inverted repetition subterminal to the natural repetition, the second illustrates the possibility that a strand may have either an inverted or a natural terminal repetition...

There are three possible models to account for the data which indicate the existence of both inverted and natural terminal nucleotide sequence repetition in the population of purified AAV DNA molecules (Fig. 4). One possible structure would be that the terminal nucleotide sequence repetition is symmetrical. This possibility would be in accord with the fact that the lengths determined for both types of terminal repetition are similar. Two other alternatives are possible. The first is that the inverted and natural terminal repetitions occupy different positions along the genome. In that case the data of Berns and Kelly would probably tend to overestimate the length of the inverted nucleotide sequence repetition if it were subterminal. Likewise the estimate of the length of the natural terminal repetition (1%) by Gerry et al. would be too great if the natural terminal repetition were subterminal. An unlikely third alter-... 

Figure 20. C-NMR spectra from a perfused mouse liver at SS C. (c) C natural abundance background of this liver, accumulated before the substrate was added. The substrate, 8 mM [3- C]alanine and 20 mM unlabelled ethanol, was then added at 0 minutes and again at 120 minutes, and a series of C-NMR spectra were taken, (b) Spectrum measured during the period 150-180 minutes (a) C-NMR spectrum of the perfusate after the perfusion was terminated, at 240 minutes this spectrum consisted of 5000 scans. The pulse repetition times were 0.5 seconds for b and c and 2 seconds for a. Abbreviations pci, oCl, ]9C3.5, aC4, pC6, aC6, PC2, C2.5 and aC3, the carbons of the glucose anomers Glu C2, glutamate C-2 Gin C2, glutamine C-2 Asp C2, aspartate C-2 Ala C2, alanine C-2 LacC3, lactate C-3 CB, cell background peak W, X, Y and Z, unknowns AA Ca, acetoacetate CHj and / -HB Ca, -hydroxybutyrate CHj (from [31]).

There are some general features of a free radical reaction. Free radical reactions take three distinct, identifiable steps. The first is formation of the free radical that can happen by enzyme catalysis, homolysis, thermolysis, radiation, light induction, combustion and pyrolysis, or other means. The second step, called propagation, is the heart of a free radical reaction. In this step, free radicals are repeatedly regenerated and can react with neutral molecules to produce new free radicals. If there is no intervention, two free radicals can react to form a neutral molecule and the reaction is terminated, which represents the third step in the general reaction scheme. Because of this repetitive nature of the reaction, free radical reactions are called chain reactions and are often represented as a cyclic process [Nagendrappa (27A78)]. 

The current model of the purified DNA is that it is a linear single polynucleotide chain containing a limited number of nucleotide sequence permutations, the start points of which occur within a region representing less than 6% of the genome, and also containing a terminal nucleotide sequence repetition (either inverted, natural, or both). 

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