Duplex linear monomers

C below the Tm of duplex AAV DNA. These duplex linear monomers did form duplex circular monomers and hnear dimers when exposed to annealing conditions. Thus, anneahng of intact linear AAV single polynucleotide chains led to the formation of two types of duplex linear monomers (1) those without cohesive single-stranded termini, and (2) those with cohesive single-stranded termini. 

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...

Fig. 5- Duplex AAV linear monomers which did not form circles or oligomers when exposed to annealing conditions (< 1 %) were digested to the extent of 1 % using exonuclease III and annealed in 2 X SSC (0.30 M NaCl, 0.03 M Na citrate) at either 45° C ( ) or 55° C (o) for various periods of time. The percentage of circles and dimers formed is plotted. (No dimers were observed at 55° C)...

Nevertheless, the RNA World hypothesis would seem to answer most of the questions raised above how can an essentially linear molecule be autocatalytic, how can it synthesize proteins, and how can it replicate Autocatalysis can occur because RNA can adopt a wide range of secondary and tertiary structures that position RNA monomers into a preorganized sequence and link them together, it can apply the same flexibility to bind other small molecules and catalyse their polymerization, and it could form weakly interacting sense and antisense duplexes. The main problem is... 

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