Inverted terminal repetition

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. 5. Schematic representation of adenovirus replication. The linear viral genome with the 5 -linked, terminal protein, , 55K is shown associated with the 87K precursor to the terminal protein, 0, to which CMP has become covalently linked in the first step of the initiation reaction, priming. A new DNA chain is then elongated from this primer, displacing its parental homologue (steps 1 and 2 in the figure). This displaced strand is believed to circularize by virtue of the inverted terminal repetition, represented as a-a, to form a double-stranded, terminal segment that is identical to that of the parental DNA. Such a scheme was originally proposed by Rekosh et ai (1977) and has been modified to include the priming role of the precursor to the terminal protein discussed in the text.

WoLFSON, J., Dressler, D.. Adenovirus-2 DNA contains an inverted terminal repetition. Proc. nat. Acad. Sci. (Wash.) 69, 3054-3057 (1972). 

Lusby E, Fife KH, Bems KI. Ntrcleolide seqtrence of the inverted terminal repetition in adeno-assoeiated virus DNA. J Virol 1980 34 402-409. 

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...

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-... 

A second Drosophila transposon called mariner630 typifies the mariner / Tel transposon superfamily, which also contains members from nematodes,631 other invertebrates, fishes,632 amphibia,633 and possibly human beings.634 These transposons encode a transposase containing a D, D, D or D, D, E motif630 but no other proteins. They contain short 30-bp terminal inverted repeats and become inserted into host TA sequences.631 Movement of some repetitive sequences of the LINE635 and SINE636 families within the human genome may be assisted by mariner transposons.637... 

Characterization of a LINE-like element can be quite difficult. First, the repetitive region of the isolated clone is sequenced. Then a computer analysis is performed to determine the characteristics of the sequence, such as the presence of inverted or direct terminal repeats. If terminal repeats are not found it is still possible that the element is one of the terminal repeat class which has a deletion at one end. Further clones are then obtained from the library by using the repetitive portion of the clone as a probe. By way of cross-hybridization, regions of homology between the two isolates can be delineated. The sequence of portions of other isolates should then be determined to search for the ends of the element. 

Despite the TE classification used in projects around the world, some classes of TEs have remarkable features in their structures. Two examples are LTR class (TEs that present a Long Terminal Repeats) and TIR class (TEs presenting Terminal Inverted Repeats). For these cases, we could say, it is not difficult to produce computational applications for detecting these repeats - all is need is to search for repetitions, inverted or not, of character strings. But, for several other TE classes there is little (or even no) evident characteristic in their composition that could be used properly to construct computational tools. 

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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