A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats

Gel networks that mimic the properties of naturally occurring mammalian elastin have been synthesized for the development of novel biomaterials. Hydrogels with controllable and predictable mechanical properties are pursued for use in drug encapsulation and delivery systems, as scaffolds for tissue engineering and for the development of prosthetic implantable devices. The techniques of genetic engineering and microbial expression have been used to produce a 90KD recombinant protein based starting material that was polymerized into a solvent swollen gel network by the introduction of covalent bifunctional crosslinks at regularly spaced lysyl residues. SEM methods have been used to describe solvent and temperature dependent structural features.The polypeptide precursor to the elastin-mimetic gels, poly[(VPGVG)4VPGKG], was obtained through bacterial expression (pET system) of an oligomerized gene coding for tandem repeats of the monomer. Gel networks were formed by crosslinking the protein with a bifunctional NHS-ester in both water and anhydrous DMSO. For conventional below-lens SEM studies, samples were dehydrated in an ethanol gradient, critical point dried from CO2(l), mounted on stubs with carbon tape and sputter coated with a 4-6 nm layer of Au/Pd.

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A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae.

Genetics ◽

10.1093/genetics/135.3.711 ◽

1993 ◽

Vol 135 (3) ◽

pp. 711-718 ◽

Cited By ~ 4

Author(s):

R L Keil ◽

A D McWilliams

Keyword(s):

Saccharomyces Cerevisiae ◽

Mating Type ◽

Copy Number ◽

Tandem Repeats ◽

Chromosomal Location ◽

Specific Factor ◽

Yeast Saccharomyces Cerevisiae ◽

Naturally Occurring ◽

Type Information ◽

Repeated Genes

Abstract The preservation of sequence homogeneity and copy number of tandemly repeated genes may require specific mechanisms or regulation of recombination. We have identified mutations that specifically affect recombination among natural repetitions in the yeast Saccharomyces cerevisiae. The rrm3 mutation stimulates mitotic recombination in the naturally occurring tandem repeats of the rDNA and copper chelatin (CUP1) genes. This mutation does not affect recombination of several other types of repeated genes tested including Ty elements, mating type information and duplications created by transformation. In addition to stimulating exchange among the multiple CUP1 repeats at their natural chromosomal location, rrm3 also increases recombination of a duplication of CUP1 units present at his4. This suggests that the RRM3 gene may encode a sequence-specific factor that contributes to a global suppression of mitotic exchange in sequences that can be maintained as tandem arrays.

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On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

Journal of Biological Chemistry ◽

10.1074/jbc.rev119.007678 ◽

2020 ◽

Vol 295 (13) ◽

pp. 4134-4170 ◽

Cited By ~ 27

Author(s):

Alexandra N. Khristich ◽

Sergei M. Mirkin

Keyword(s):

Molecular Mechanisms ◽

Tandem Repeats ◽

Genome Instability ◽

Current Knowledge ◽

Model Systems ◽

Dna Repeats ◽

Repeat Instability ◽

Repeat Expansions ◽

Induced Mutagenesis ◽

Simple Tandem Repeats

Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?

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Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

BioMed Research International ◽

10.1155/2016/8036450 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Hua Wan ◽

Shan Chang ◽

Jian-ping Hu ◽

Xu-hong Tian ◽

Mei-hua Wang

Keyword(s):

Tandem Repeats ◽

Potential Role ◽

Phosphate Binding ◽

Tal Effectors ◽

Naturally Occurring ◽

C Terminus ◽

Modeled Structure ◽

High Efficient ◽

Dynamics Simulations

TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.

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Characterization of two Segregation distorter revertants: evidence that the tandem duplication is necessary for Sd activity in Drosophila melanogaster.

Genetics ◽

10.1093/genetics/136.1.209 ◽

1994 ◽

Vol 136 (1) ◽

pp. 209-215

Author(s):

M F Palopoli ◽

P Doshi ◽

C I Wu

Keyword(s):

Drosophila Melanogaster ◽

Tandem Duplication ◽

Tandem Repeats ◽

Direct Evidence ◽

Consistent Difference ◽

Naturally Occurring ◽

Segregation Distorter ◽

Topoisomerase 2 ◽

Flanking Regions

Abstract Segregation Distorter (SD) is a naturally occurring system of meiotic drive in Drosophila melanogaster. Males heterozygous for an SD second chromosome and a normal homolog (SD+) transmit predominantly SD-bearing sperm. To accomplish this, the Segregation distorter (Sd) locus induces the dysfunction of those spermatids that receive the SD+ chromosome. Recently, P. A. Powers and B. Ganetzky isolated overlapping DNA clones spanning the region of DNA known to contain the Sd gene and identified a 5-kb tandem duplication that is present on all SD chromosomes examined, but is apparently absent from wild-type chromosomes. Here we report a molecular analysis of two spontaneous revertants from an Australian SD chromosome (SD-Arm28). Both of these revertants have lost the 5-kb tandem duplication along with the ability to distort transmission; the critical observation, however, is that they retain the DNA haplotype in the flanking regions (both proximally and distally) that is characteristic of the original SD-Arm28. We propose unequal sister chromatid exchange between the tandem repeats as the only plausible explanation for loss of a repeat while retaining flanking markers. This provides direct evidence that the tandem duplication is indeed necessary for the Sd phenotype. Further, we examined testes-specific levels of both RNA and protein for the nearby Topoisomerase 2 gene. Neither revealed a consistent difference between SD and SD+ strains. We also measured testes-specific levels of RNA using the tandem duplication itself as probe. Our results suggest that there is strong up-regulation of one or several 2.0-2.3-kb transcripts from the duplicated region in the testes of an SD strain.(ABSTRACT TRUNCATED AT 250 WORDS)

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