Nucleotide sequence permutation

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...

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). 

Altschul, S. R, and Erickson, B. W. (1985). Significance of nucleotide sequence alignments A method for random sequence permutation that preserves dinucleotide and codon usage. Mol. Biol. Evol. 2, 526-538. 

The RNA oligomers studied by these authors [115, 116] are several evolved sequences (hepatitis delta virus), synthetic polymers (poly-U), and various random RNA sequences. The random sequences are obtained from the HDV sequence by a permutation of the nucleotides in which base composition is fixed [115, 116]. The lengths of all RNA oligonucleotide fragments are 85 nucleotides [115, 116],... 

---