Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthesis of Macrocyclic Hexaoxazole (6OTD) Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties.

ABSTRACT: Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD) dimers, whose core structure stabilizes telomeric G-quadruplexes (G4). Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium cation. The guanidine functionalized dimer displays a potent stabilizing ability of the G4 structure, as determined by using a FRET melting assay (DeltaT(m) = 14 degrees C).

SUBMITTER: Iida K

PROVIDER: S-EPMC2911606 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Synthesis of Macrocyclic Hexaoxazole (6OTD) Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties.

Iida Keisuke K Tera Masayuki M Hirokawa Takatsugu T Shin-Ya Kazuo K Nagasawa Kazuo K

Journal of nucleic acids 20100524

Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD) dimers, whose core structure stabilizes telomeric G-quadruplexes (G4). Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium ca ...[more]

PMID: 20700415

Similar Datasets

Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains.

Project description:G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore "sequence-dependent" selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4.

| S-EPMC6358838 | biostudies-literature

Access to functionalized steroid side chains via modified Julia olefination.

Project description:Various functionalized steroidal side chains were conveniently accessed by a modified Julia olefination strategy using a common sulfone donor and an appropriate ?-branched aldehyde acceptor. For the coupling of these hindered classes of reaction partners (and in contrast to typically observed trends), the benzothiazolyl(BT)-sulfone anion gave superior outcomes compared to the phenyltetrazolyl(PT)-sulfone anion.

| S-EPMC3045753 | biostudies-literature

Biological Properties of Oleanolic Acid Derivatives Bearing Functionalized Side Chains at C-3.

Project description:Triterpene acids are a class of pentacyclic natural carboxylic compounds endowed with a variety of biological activities including antitumor, antimicrobial, and hepatoprotective effects. In this work, several oleanolic acid derivatives were synthesized by structurally modifying them on the C-3 position. All synthesized derivatives were evaluated for possible antibacterial and antiviral activity, and among all the epimers, 6 and 7 demonstrated the best biological activities. Zone-of-inhibition analyses were conducted against two strains, E. coli as a Gram-negative and S. aureus as a Gram-positive model. Subsequently, experiments were performed using the microdilution method to determine the minimum inhibitory concentration (MIC). The results showed that only the derivative with reduced hydrogen bonding ability on ring A possesses remarkable activity toward E. coli. The conversion from acid to methyl ester implies a loss of activity, probably due to a reduced affinity with the bacterial membrane. Before the antiviral activity, the cytotoxicity of triterpenes was evaluated through a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Samples 6 and 7 showed less than 50% cytotoxicity at 0.625 and 1 mg/mL, respectively. The antiviral activity against SARS-CoV-2 and PV-1 did not indicate that triterpene acids had any inhibitory capacity in the sub-toxic concentration range.

| S-EPMC11312724 | biostudies-literature

Stable polyglutamine dimers can contain ?-hairpins with interdigitated side chains-but not ?-helices, ?-nanotubes, ?-pseudohelices, or steric zippers.

Project description:A common thread connecting nine fatal neurodegenerative protein aggregation diseases is an abnormally expanded polyglutamine tract found in the respective proteins. Although the structure of this tract in the large mature aggregates is increasingly well described, its structure in the small early aggregates remains largely unknown. As experimental evidence suggests that the most toxic species along the aggregation pathway are the small early ones, developing strategies to alleviate disease pathology calls for understanding the structure of polyglutamine peptides in the early stages of aggregation. Here, we present a criterion, grounded in available experimental data, that allows for using kinetic stability of dimers to assess whether a given polyglutamine conformer can be on the aggregation path. We then demonstrate that this criterion can be assessed using present-day molecular dynamics simulations. We find that although the ?-helical conformer of polyglutamine is very stable, dimers of ?-helices lack the kinetic stability necessary to support further oligomerization. Dimers of steric zipper, ?-nanotube, and ?-pseudohelix conformers are also too short-lived to initiate aggregation. The ?-hairpin-containing conformers, instead, invariably form very stable dimers when their side chains are interdigitated. Combining these findings with the implications of recent solid-state NMR data on mature fibrils, we propose a possible pathway for the initial stages of polyglutamine aggregation, in which ?-hairpin-containing conformers act as templates for fibril formation.

| S-EPMC4008795 | biostudies-other

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding.

Project description:Telomeres are specific nucleoprotein structures that are located at the ends of linear eukaryotic chromosomes and play crucial roles in genomic stability. Telomere DNA consists of simple repeats of a short G-rich sequence: TTAGGG in mammals and TTTAGGG in most plants. In recent years, the mammalian telomeric G-rich repeats have been shown to form G-quadruplex (G4) structures, which are crucial for modulating telomere functions. Surprisingly, even though plant telomeres are essential for plant growth, development, and environmental adaptions, only few reports exist on plant telomeric G4 DNA (pTG4). Here, using bulk and single-molecule assays, including CD spectroscopy, and single-molecule FRET approaches, we comprehensively characterized the structure and dynamics of a typical plant telomeric sequence, d[GGG(TTTAGGG)3]. We found that this sequence can fold into mixed G4s in potassium, including parallel and antiparallel structures. We also directly detected intermediate dynamic transitions, including G-hairpin, parallel G-triplex, and antiparallel G-triplex structures. Moreover, we observed that pTG4 is unfolded by the AtRecQ2 helicase but not by AtRecQ3. The results of our work shed light on our understanding about the existence, topological structures, stability, intermediates, unwinding, and functions of pTG4.

| S-EPMC7170514 | biostudies-literature

Dispersion Interactions and the Stability of Amine Dimers.

Project description:Weak, intermolecular interactions in amine dimers were studied by using the combination of a dispersionless density functional and a function that describes the dispersion contribution to the interaction energy. The validity of this method was shown by comparison of structural and energetic properties with data obtained with a conventional density functional and the coupled cluster method. The stability of amine dimers was shown to depend on the size, the shape, and the relative orientation of the alkyl substituents, and it was shown that the stabilization energy for large substituents is dominated by dispersion interactions. In contrast to traditional chemical explanations that attribute stability and condensed matter properties solely to hydrogen bonding and, thus, to the properties of the atoms forming the hydrogen bridge, we show that without dispersion interactions not even the stability and structure of the ammonia dimer can be correctly described. The stability of amine dimers depends crucially on the interaction between the non-polar alkyl groups, which is dominated by dispersion interactions. This interaction is also responsible for the energetic part of the free energy interaction used to describe hydrophobic interactions in liquid alkanes. The entropic part has its origin in the high degeneracy of the interaction energy for complexes of alkane molecules, which exist in a great variety of conformers, having their origin in internal rotations of the alkane chains.

| S-EPMC5542769 | biostudies-literature

Distinct activities of exonuclease 1 and flap endonuclease 1 at telomeric g4 DNA.

Project description:BackgroundExonuclease 1 (EXO1) and Flap endonuclease 1 (FEN1) are members of the RAD2 family of structure-specific nucleases. Genetic analysis has identified roles for EXO1 and FEN1 in replication, recombination, DNA repair and maintenance of telomeres. Telomeres are composed of G-rich repeats that readily form G4 DNA. We recently showed that human EXO1 and FEN1 exhibit distinct activities on G4 DNA substrates representative of intermediates in immunoglobulin class switch recombination.Methodology/principal findingsWe have now compared activities of these enzymes on telomeric substrates bearing G4 DNA, identifying non-overlapping functions that provide mechanistic insight into the distinct telomeric phenotypes caused by their deficiencies. We show that hFEN1 but not hEXO1 cleaves substrates bearing telomeric G4 DNA 5'-flaps, consistent with the requirement for FEN1 in telomeric lagging strand replication. Both hEXO1 and hFEN1 are active on substrates bearing telomeric G4 DNA tails, resembling uncapped telomeres. Notably, hEXO1 but not hFEN1 is active on transcribed telomeric G-loops.Conclusion/significanceOur results suggest that EXO1 may act at transcription-induced telomeric structures to promote telomere recombination while FEN1 has a dominant role in lagging strand replication at telomeres. Both enzymes can create ssDNA at uncapped telomere ends thereby contributing to recombination.

| S-EPMC2811187 | biostudies-literature

Synthesis of functionalized macrocyclic derivatives of trioxabicyclo[3.3.0]nonadiene.

Project description:C(72)-Macrocyclic systems functionalized with nitroaryl and arylamino groups were synthesized from the bisdioxine diacid dichloride 1,3,5,7-tetra-tert-butyl-2,6,9-trioxabicyclo[3.3.1]nona-3,7-diene-4,8-dicarbonyl dichloride (3).

| S-EPMC3388861 | biostudies-other

Amine-Functionalized Spin Crossover Building Blocks.

Project description:Bistable spin crossover complexes such as [Fe{HB(pz)3}2] (pzH = pyrazole) show promise for sensor applications and electrically-controlled data storage units, but exploiting their potential hinges on their integration into a functional environment. We here present a system enabling such covalent post-functionalization steps in both symmetric and asymmetric patterns, based on the amine-functionalized complex [Fe{HB(4-NH2pz)(pz)2}2], obtained by reduction of the nitro analogue. The building block aspects of [Fe{HB(4-NH2pz)(pz)2}2] are showcased by its transformation into amide, imine and azo derivatives, which are structurally and magnetically characterized. All tris(pyrazolyl)borate complexes retain the spin crossover properties of their parent compound, with spin crossover temperatures ranging from 350 to 430 K. The transition parameters are correlated with the electronic properties of the functionalizing group, opening the possibility of fine-tuning the spin crossover properties of the building block as it is integrated in the environment of choice.

| S-EPMC6919924 | biostudies-literature

Sequence-specific binding of Taz1p dimers to fission yeast telomeric DNA.

Project description:The fission yeast (Schizosaccharomyces pombe) taz1 gene encodes a telomere-associated protein. It contains a single copy of a Myb-like motif termed the telobox that is also found in the human telomere binding proteins TRF1 and TRF2, and Tbf1p, a protein that binds to sequences found within the sub-telomeric regions of budding yeast (Saccharomyces cerevisiae) chromosomes. Taz1p was synthesised in vitro and shown to bind to a fission yeast telomeric DNA fragment in a sequence specific manner that required the telobox motif. Like the mammalian TRF proteins, Taz1p bound to DNA as a preformed homodimer. The isolated Myb-like domain was also capable of sequence specific DNA binding, although with less specificity than the full-length dimer. Surprisingly, a protein extract produced from a taz1- fission yeast strain still contained the major telomere binding activity (complex I) we have characterised previously, suggesting that there could be other abundant telomere binding proteins in fission yeast. One candidate, SpX, was also synthesised in vitro, but despite the presence of two telobox domains, no sequence specific binding to telomeric DNA was detected.

| S-EPMC102532 | 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