Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences.

ABSTRACT: The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.

SUBMITTER: Ishutkina MV

PROVIDER: S-EPMC6174987 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Establishing the robustness of short-tandem-repeat statistics for forensic applications.

Project description:Before the introduction of a four-locus multiplex short-tandem-repeat (STR) system into casework, an extensive series of tests were carried out to determine robust procedures for assessing the evidential value of a match between crime and suspect samples. Twelve databases were analyzed from the three main ethnic groups encountered in casework in the United Kingdom: Caucasians, Afro-Caribbeans, and Asians from the Indian subcontinent. Independence tests resulted in a number of significant results, and the impact that these might have on forensic casework was investigated. It is demonstrated that previously published methods provide a simple procedure for correcting allele frequencies--and that this leads to conservative casework estimates of evidential value.

| S-EPMC1914534 | biostudies-other

Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates.

Project description:Fluorescence detection and imaging are vital technologies in the life sciences and clinical diagnostics. The key to obtaining high-resolution images and sensitive detection is to use fluorescent molecules or particles that absorb and emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template and fluorogenic intercalating dyes. Because dyes can intercalate up to every other base pair, high densities of fluorophores are assembled yet the DNA template keeps them far enough away from each other to prevent self-quenching. The efficiency with which these noncovalent assemblies absorb light is more than 10-fold greater than that of the individual dye molecules. Förster resonance energy transfer from the intercalated dyes to covalently attached acceptor dyes is very efficient, allowing for wavelength shifting of the emission spectrum. Simple biotinylation of the DNA template allows for labeling of streptavidin-coated synthetic microspheres and mouse T-cells.

| S-EPMC2532517 | biostudies-literature

Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements.

Project description:We present DNA sequences flanking cloned hypervariable human minisatellites. In addition to providing confirmatory evidence that minisatellites cluster with other tandem repeats, these flanking sequences contain a high frequency of interspersed repetitive elements. These elements include a retroviral LTR-like sequence, from which one of the minisatellites appears to have expanded, and a recently described short interspersed repeat. We present our own findings concerning this element, in particular that those examples studied do not show significant evolutionary conservation, despite suggestions that the element may have a cis-acting function.

| S-EPMC318084 | biostudies-other

Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing.

Project description:Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington's disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington's disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.

| S-EPMC9719798 | biostudies-literature

Halibut mitochondrial genomes contain extensive heteroplasmic tandem repeat arrays involved in DNA recombination.

Project description:BACKGROUND: Halibuts are commercially important flatfish species confined to the North Pacific and North Atlantic Oceans. We have determined the complete mitochondrial genome sequences of four specimens each of Atlantic halibut (Hippoglossus hippoglossus), Pacific halibut (Hippoglossus stenolepis) and Greenland halibut (Reinhardtius hippoglossoides), and assessed the nucleotide variability within and between species. RESULTS: About 100 variable positions were identified within the four specimens in each halibut species, with the control regions as the most variable parts of the genomes (10 times that of the mitochondrial ribosomal DNA). Due to tandem repeat arrays, the control regions have unusually large sizes compared to most vertebrate mtDNAs. The arrays are highly heteroplasmic in size and consist mainly of different variants of a 61-bp motif. Halibut mitochondrial genomes lacking arrays were also detected. CONCLUSION: The complexity, distribution, and biological role of the heteroplasmic tandem repeat arrays in halibut mitochondrial control regions are discussed. We conclude that the most plausible explanation for array maintenance includes both the slipped-strand mispairing and DNA recombination mechanisms.

| S-EPMC2248175 | biostudies-literature

Development and Validation of a Novel Five-Dye Short Tandem Repeat Panel for Forensic Identification of 11 Species.

Project description:Species identification of unknown biological samples is of fundamental importance for forensic applications, especially in crime detection, poaching, and illegal trade of endangered animals as well as meat fraud. In this study, a novel panel was developed to simultaneously identify 10 different animal species (Gallus domesticus, Anas platyrhynchos domesticus, Ovis aries, Sus scrofa domesticus, Bos taurus, Equus caballus, Columba livia domestica, Rattus norvegicus, Mus musculus, and Canis lupus familiaris) and human beings by amplifying 22 short tandem repeat (STR) loci in a multiplex PCR using a set of five fluorescently labeled dyes. This novel 22-STR panel was validated by optimization of PCR conditions as well as species specificity, sensitivity, reproducibility, precision, DNA mixture, and tissue/organ consistency. The results of developmental validation showed that the 22-STR loci achieved high species specificity among 10 animal species and human beings, and the sensitivity of this panel was 0.09 ng. This 22-STR panel identified different meats in mixed samples, and the minimum detected mixture ratio in the current test was 10% (0.1 ng/1 ng). This sensitive, accurate, and specific 22-STR panel can be used for forensic species identification and the detection of meat fraud and adulteration.

| S-EPMC7541953 | biostudies-literature

Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome.

Project description:BackgroundMacrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized.ResultsHere we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain.ConclusionsOur results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.

| S-EPMC3018141 | biostudies-literature

Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs.

Project description:Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such repeats in bacterial vectors, especially with large repeat expansions. Designing constructs for more precise genome engineering projects, such as engineering knock-in mice, proves a greater challenge still, since these unstable repeats require numerous cloning steps in order to introduce homology arms or selection cassettes. Here, we report our efforts to clone a large hexanucleotide repeat in the C9orf72 gene, originating from within a BAC construct, derived from a C9orf72-ALS patient. We provide detailed methods for efficient repeat sizing and growth conditions in bacteria to facilitate repeat retention during growth and sub-culturing. We report that sub-cloning into a linear vector dramatically improves stability, but is dependent on the relative orientation of DNA replication through the repeat, consistent with previous studies. We envisage the findings presented here provide a relatively straightforward route to maintaining large-range microsatellite repeat-expansions, for efficient cloning into vectors.

| S-EPMC8215685 | biostudies-literature

Anisotropic Polyoxometalate Cages Assembled via Layers of Heteroanion Templates.

Project description:The synthesis of anisotropic redox-active polyoxometalates (POMs) that can switch between multiple states is critical for understanding the mechanism of assembly of structures with a high aspect ratio, as well as for their application in electronic devices. However, a synthetic methodology for the controlled growth of such clusters is lacking. Here we describe a strategy, using the heteroanion-directed assembly, to produce a family of 10 multi-layered, anisotropic POM cages templated by redox-active pyramidal heteroanions with the composition [W16Mo2O54(XO3)]n-, [W21Mo3O75/76(XO3)2]m-, and [W26Mo4O93(XO3)3]o- for the double, triple, and quadruple layered clusters, respectively. It was found that the introduction of reduced molybdate is essential for self-assembly and results in mixed-metal (W/Mo) and mixed-valence (WVI/MoV) POM cages, as confirmed by an array of analytical techniques. To probe the archetype in detail, a tetrabutyl ammonium (TBA) salt derivative of a fully oxidized two-layered cage is produced as a model structure to confirm that all the cages are a statistical mixture of isostructures with variable ratios of W/Mo. Finally, it was found that multilayered POM cages exhibit dipolar relaxations due to the presence of the mixed valence WVI/MoV metal centers, demonstrating their potential use for electronic materials.

| S-EPMC6716119 | biostudies-literature

Uniform gold nanorod arrays from polyethylenimine-coated alumina templates.

Project description:Monolithic Au nanorod arrays can be grown by electrodeposition in Au-backed nanoporous alumina templates using polyethylenimine (PEI) as an adhesion layer, with excellent height control between 300 nm and 1.4 microm. The local height distribution can be extremely narrow with relative standard deviations well below 2%. The uniform growth rate appears to be determined by the adsorbed PEI matrix, which controls the growth kinetics of the grains comprising the nanorods. The nanorods can be retained as free-standing 2D arrays after careful removal of the AAO template. Reflectance spectroscopy reveals a collective plasmon mode with a maximum near 1.2 microm, in accord with recent calculations for 2D arrays of closely spaced cylindrical nanoparticles.

| S-EPMC2531144 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data