Tandem repeat sequences

Kaneda S, Takeishi K, Ayusawa D et al. Role in translation of a triple tandemly repeated sequence in the 5 -untranslated region of human thymidylate synthase mRNA. Nucleic Acids Res 1987 15 1259-1270. 

Horie N, Aiba H, Oguro K et al. Functional analysis and DNA polymorphism of the tandemly repeated sequences in the 5 -terminal regulatory region of the human gene for thymidylate synthase. Cell Stmct Funct 1995 20 191-197. 

Kawakami K, Salonga D, Omura K, Park JM, Danenberg KD, Watanabe Y et al. Effects of polymorphic tandem repeat sequence on the in vitro translation of messenger RNA. Proc Am Assoc Cancer Res 1999 40 436 137. 

Kawakami K, Watanabe G. Identification and functional analysis of single nucleotide polymorphism in the tandem repeat sequence of thymidylate synthase gene. Cancer Res 2003 63 6004-6007. 

Mareuello E, Altes A, del Rio E et al. Single nucleotide polymorphism in the 5 tandem repeat sequences of thymidylate synthase gene predicts for response to fluorouracil-based chemotherapy in advanced colorectal cancer patients. Int J Cancer 2004 112 733-737. 

Variable number tandem repeat sequences tend to occur in clusters, with the number of repeats varying between individuals. 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

Second, it is important to consider whether a clone library will be representative of a particular repeated sequence. Besides the genetic factors, above, unusual patterns of restriction sites in some repeated sequences may influence their relative abundance in a library. This would be more likely for a tandemly repeated sequence or a very long repeated sequence than for short, interspersed repeated DNA sequences. Traditional A or plasmid libraries would be sufficient for most studies, but in certain situations it might be necessary to resort to DNA libraries of randomly frag-... 

Whereas all of the methods discussed thus far concern ectopic interactions between artificially constructed repeats, there have also been a number of studies designed to examine recombination between naturally occurring repeated sequences. Recombination between both dispersed and tandemly repeated sequences has been examined, and some of the approaches used are described below. 

Telomers seal the end of a chromosome. The telomers consist of simple, tandemly-repeated sequences. Typically one strand is G-rich and the other C-rich. A 15-residue long G-rich strand is added to the 3 end of the chromosomal DNA by the telomerase. This allows a primer to bind and initiate synthesis on the other strand.The telomerase maintains the lenght of the chromosome and prevents the loss of coding sequences. 

Telomerase is a ribonucleoprotein complex that exists in eukaryotic cells for the apparently sole purpose of synthesizing telomeric DNA, which consists of tandemly repeated sequences that contain clusters of G-residues and forms the ends of chromosomes. Telomerase comprises two essential core components, a protein subunit that has reverse transcriptase (RT) activity and an RNA sequence (hTR) that contains clusters of C-residues and serves as the template substrate for the RT (6). The G-rich DNA and C-rich RNA anneal to form a partial duplex with DNA as the primer. RT-mediated polymerization of dGTP and other complementary triphosphate substrates produces a DNA terminus that has been extended by around six nucleotides. The new end can become a substrate for either another round of telomerase-mediated elongation or primase/polymerase-mediated lagging-strand synthesis. 

DNA fingerprinting (genetic fingerprinting) The use of a pattern of DNA fragments obtained on restriction analysis of certain highly variable repeated DNA sequences, e.g. tandem repeat sequences which are virtually unique to an individual. This DNA profile , which can be detected in minute amounts of cells (e.g. in blood or semen), can be used in criminal cases and paternity suits. 

CA 27.29 is detected by a monoclonal antibody, B27.29, that is produced against an antigen in ascites of patients with metastatic breast carcinoma. The minimum epitope to which B27.29 reacts is the 8 amino acid sequence (SAPDTRPA) within the 20 amino acid tandem repeating sequence of the mucin core. The reactive sequence of the B27.29 overlaps with the sequence of DF3 used in the CA 15-3 assay. In inhibition studies using labeled MAb, B27.29 effectively competes with DF3 for binding to both CA 27.29 and CA 15-3 antigens. "... 

Debrauwere, H., C. G. Gendrel, S. Lechat, and M. Dutreix. 1997. Differences and similarities between various tandem repeat sequences Minisatellites and microsatellites. Biochimie 79 577-86. 

Kunz and coworkers reported the solid-phase synthesis of glycopeptides derived from the tandem repeat sequence of MUC4 with tumor-associated carbohydrate antigens. ... 

Following the N-terminal 80 residues, there is a tandem repeat of 12 amino acids in the rabbit and bovine MLCKs that is not present in chicken smooth muscle MLCK (Fig. 3). There are some differences in the size of the repeat in the two mammalian enzymes. Furthermore, the identity of the amino acid residues in this region is about 70%, which is the least conserved portion in smooth muscle MLCKs. The higher molecular masses of the mammalian MLCKs compared to the avian smooth muscle MLCK are primarily due to the presence of these tandem repeat sequences. 

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