Nucleotide sequence repetition

Waring M. and Britten R.J. (1966). Nucleotide sequence repetition a rapidly reassociating fraction of mouse DNA. Science 154 791-794. 

Sheared duplex fragments with nucleotide sequence repetition at single strand break points... 

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). 

Combinatorial Hbraries are limited by the number of sequences that can be synthesized. For example, a Hbrary consisting of one molecule each of a 60-nucleotide sequence randomized at each position, would have a mass of >10 g, weU beyond the capacity for synthesis and manipulation. Thus, even if nucleotide addition is random at all the steps during synthesis of the oligonucleotide only a minority of the sequences can be present in the output from a laboratory-scale chemical DNA synthesis reaction. In analyzing these random but incomplete Hbraries, the protocol is efficient enough to allow selection of aptamers of lowest dissociation constants (K ) from the mixture after a small number of repetitive selection and amplification cycles. Once a smaller population of oligonucleotides is amplified, the aptamer sequences can be used as the basis for constmcting a less complex Hbrary for further selection. 

Examples of a polymorphism include single nucleotide substitutions, insertions and deletions of nucleotides, and repetitive sequences. While most polymorphisms are harmless and part of normal human genetic variations, studies have established links between certain gene polymorphisms and metabolic alterations or human diseases. 

The genes that respond to a specific hormone contain identical HRE (Fig. 1.6). Normally, it is a matter of short nucleotide sequences pentamers or hexamers. In the case of the ER, the sequences are found repeated in inverse order in the same strand of DNA (palindromic, or symmetrically legible sequences 5 GGACA-nnn-ACAGG 3 n is any nucleotide). In the case of the thyroid hormones and retinoic acid, the HRE at times are presented like two repeated sequences in the same order (direct repetition GGACA-GGACA). 

Hancock, J.M. and Armstrong, J.S. (1994) SIMPLE34 an improved and enhanced implementation for VAX and SUN computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Cabios 10, 67-70. 

Figure 10.2. Removal of noncoding repetitive elements with RepeatMasker. The nucleotide sequence encoding human lysozyme is submitted to RepeatMasker and the sequence with masked(X) noncoding repetitive elements is returned (partial sequence is shown here).

D. Parley, J. Travis, and G. Salvesen. Die human neutrophil elastase gene. Aialysfe of the nucleotide sequence reveals three distinct classes of repetitive DNA. BioL Chem Hoppe-Styier 57t 737 (1989). 

Low-complexity sequence. The phrase low-complexity sequence refers to stretches of nucleotide or protein sequence that are repetitive or simple in composition (11). Extreme examples include runs of As in a nucleotide sequence such as the poly-A tails of eukaryotic mRNAs, or the poly-proline tracts found in some... 

These results provided the first evidenee for physical recombination of mitochondrial DNA in crosses of wild-type yeast eells, indieated that recombination was very frequent in crosses and shed some light on mitochondrial segregation. They also provided examples of reeombination phenomena in an interspersed system of unique and repetitive nucleotide sequences. 

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. 

Pech M, Igo-Kemenes T, Zachau HG (1979) Nucleotide sequences of a highly repetitive component of rat DNA. Nucleic Acids Res 7 417 - 432... 

A technique in which an individual s DNA is analysed to reveal the pattern of repetition of certain short nucleotide sequences, called short tandem repeats (STRs), throughout the genome. This pattern is claimed to be... 

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