Inverted terminal nucleotide sequence

Additional study of the termini of AAV DNA by Koczot et al. (1973) has shown that AAV DNA also contains an inverted terminal nucleotide sequence repetition of the type found in adenovirus DNA (Garon et al., 1972 WoLFSON and Dressler, 1972). This conclusion was based upon the fact that up to 70% of separated plus or minus strands of AAV DNA formed single-stranded circles when annealed and these circles were converted to linear molecules by exonuclease III digestion. It was hypothesized that such single-... 

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-... 

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). 

Ishino, M., Sawada, Y., Yaegashi, T., Demura, M. et al. (1987) Nucleotide sequence of the adenovirus type 40 inverted terminal repeat close relation to that of adenovirus type 5. Virology, 15, 414-416. 

Venkatesan S, Gershowitz A, Moss B. Complete nucleotide sequences of two adjacent early vaccinia virus genes located within the inverted terminal repetition. J Virol 1982 44 637-646. 

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 most essential and unique component in AAV is its inverted terminal repeats (ITRs) at both ends of the viral genome (57). In AAV-2, the ITR is composed of 145 self-complementary nucleotides (Fig. 2). This is an extremely GC (guanosine and cytosine)-rich sequence with a GC content of higher than 80% (the average GC content in human chromosomal DNA is less than 60% (58)). The overall structure ofthe ITR is a T-shaped hairpin with a three-way junction (Fig. 2). The A and A fragments form a duplex stem which terminates with two small palindromes (defined as B, B and C, C arms). Depending on the orientation of these two small palindromes, AAV ITRs can be classified as flip (B arm is closer to the 3 end) or flop (C arm is closer to the 3 end) (29). Biophysical studies have indicated that the ITR is composed of largely... 

Rho-dependent transcription termination signals in E coll also appear to have a distinct consensus sequence, as shown in Figure 37—6. The conserved consensus sequence, which is about 40 nucleotide pairs in length, can be seen to contain a hyphenated or interrupted inverted repeat followed by a series of AT base pairs. As transcription proceeds through the hyphenated, inverted repeat, the generated transcript can form the intramolecular hairpin structure, also depicted in Figure 37-6. 

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