Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 133
Filter
1.
Chembiochem ; 21(11): 1656-1663, 2020 06 02.
Article in English | MEDLINE | ID: mdl-31943589

ABSTRACT

We present the rapid biophysical characterization of six previously reported putative G-quadruplex-forming RNAs from the 5'-untranslated region (5'-UTR) of silvestrol-sensitive transcripts for investigation of their secondary structures. By NMR and CD spectroscopic analysis, we found that only a single sequence-[AGG]2 [CGG]2 C-folds into a single well-defined G-quadruplex structure. Sequences with longer poly-G strands form unspecific aggregates, whereas CGG-repeat-containing sequences exhibit a temperature-dependent equilibrium between a hairpin and a G-quadruplex structure. The applied experimental strategy is fast and provides robust readout for G-quadruplex-forming capacities of RNA oligomers.


Subject(s)
G-Quadruplexes , Poly G/genetics , RNA, Messenger/genetics , RNA, Untranslated/genetics , ADAM10 Protein/genetics , ADAM10 Protein/metabolism , Amyloid Precursor Protein Secretases/genetics , Amyloid Precursor Protein Secretases/metabolism , E1A-Associated p300 Protein/genetics , E1A-Associated p300 Protein/metabolism , Genome, Human , Histone Deacetylases/genetics , Histone Deacetylases/metabolism , Humans , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Poly G/chemistry , Poly G/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , RNA Folding/drug effects , RNA, Messenger/chemistry , RNA, Messenger/metabolism , RNA, Untranslated/chemistry , RNA, Untranslated/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , Transforming Growth Factor beta1/genetics , Transforming Growth Factor beta1/metabolism , Triterpenes/pharmacology
2.
Nucleic Acids Res ; 43(13): 6439-49, 2015 Jul 27.
Article in English | MEDLINE | ID: mdl-26038313

ABSTRACT

Lysosomes can degrade various biological macromolecules, including nucleic acids, proteins and lipids. Recently, we identified novel nucleic acid-degradation systems termed RNautophagy/DNautophagy (abbreviated as RDA), in which RNA and DNA are directly taken up by lysosomes in an ATP-dependent manner and degraded. We also found that a lysosomal membrane protein, LAMP2C, the cytoplasmic region of which binds to RNA and DNA, functions, at least in part, as an RNA/DNA receptor in the process of RDA. However, it has been unclear whether RDA possesses selectivity for RNA/DNA substrates and the RNA/DNA sequences that are recognized by LAMP2C have not been determined. In the present study, we found that the cytosolic region of LAMP2C binds to poly-G/dG, but not to poly-A/dA, poly-C/dC, poly-dT or poly-U. Consistent with this binding activity, poly-G/dG was transported into isolated lysosomes via RDA, while poly-A/dA, poly-C/dC, poly-dT and poly-U were not. GGGGGG or d(GGGG) sequences are essential for the interaction between poly-G/dG and LAMP2C. In addition to poly-G/dG, G/dG-rich sequences, such as a repeated GGGGCC sequence, interacted with the cytosolic region of LAMP2C. Our findings indicate that RDA does possess selectivity for RNA/DNA substrates and that at least some consecutive G/dG sequence(s) can mediate RDA.


Subject(s)
Autophagy , DNA/metabolism , Lysosomal-Associated Membrane Protein 2/metabolism , RNA/metabolism , Animals , DNA/chemistry , DNA Methylation , Lysosomes/metabolism , Mice , Poly G/metabolism , RNA/chemistry
3.
J Fluoresc ; 25(4): 1013-21, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26076929

ABSTRACT

Binding of a novel cationic porphyrin-imidazophenazine conjugate, TMPyP(3+)-ImPzn, to four-stranded poly(G) was investigated in aqueous solutions of neutral pH under near physiological ionic conditions using absorption, polarized fluorescent spectroscopy and fluorescence titration techniques. In absence of the polymer the conjugate folds into stable internal heterodimer with stacking between the porphyrin and phenazine chromophores. Binding of TMPyP(3+)-ImPzn to poly(G) is realized by two competing ways. At low polymer-to-dye ratio (P/D < 6) outside electrostatic binding of the cationic porphyrin moieties of the conjugate to anionic polynucleotide backbone with their self-stacking is predominant. It is accompanied by heterodimer dissociation and distancing of phenazine moieties from the polymer. This binding mode is characterized by strong quenching of the conjugate fluorescence. Increase of P/D results in the disintegration of the porphyrin stacks and redistribution of the bound conjugate molecules along the polymer chain. At P/D > 10 another binding mode becomes dominant, embedding of TMPyP(3+)-ImPzn heterodimers into poly(G) groove as a whole is occurred.


Subject(s)
Morpholines/chemistry , Phenazines/chemistry , Poly G/chemistry , Polymers/chemistry , Porphyrins/chemistry , Spectrometry, Fluorescence/methods , Binding Sites , Circular Dichroism , Fluorescence , Morpholines/metabolism , Phenazines/metabolism , Poly G/metabolism , Polymers/metabolism , Porphyrins/metabolism
4.
Nucleic Acids Res ; 40(2): 837-46, 2012 Jan.
Article in English | MEDLINE | ID: mdl-21965533

ABSTRACT

Deadenylation is the first and rate-limiting step during turnover of mRNAs in eukaryotes. In the yeast, Saccharomyces cerevisiae, two distinct 3'-5' exonucleases, Pop2p and Ccr4p, have been identified within the Ccr4-NOT deadenylase complex, belonging to the DEDD and Exonuclease-Endonuclease-Phosphatase (EEP) families, respectively. Ngl3p has been identified as a new member of the EEP family of exonucleases based on sequence homology, but its activity and biological roles are presently unknown. Here, we show using in vitro deadenylation assays on defined RNA species mimicking poly-A containing mRNAs that yeast Ngl3p is a functional 3'-5' exonuclease most active at slightly acidic conditions. We further show that the enzyme depends on divalent metal ions for activity and possesses specificity towards poly-A RNA similar to what has been observed for cellular deadenylases. The results suggest that Ngl3p is naturally involved in processing of poly-adenylated RNA and provide insights into the mechanistic variations observed among the redundant set of EEP enzymes found in yeast and higher eukaryotes.


Subject(s)
Exoribonucleases/metabolism , Poly A/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Exoribonucleases/genetics , Gene Deletion , Nucleic Acid Conformation , Poly G/metabolism , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Ribonucleases/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae Proteins/genetics , Substrate Specificity
5.
Curr Opin Immunol ; 20(4): 396-400, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18656540

ABSTRACT

The prevailing paradigm ascribes activation of Toll-like receptor 9 (TLR9) to the detection of CpG-motifs within pathogen derived DNA. However, new work ties natural phospho-diester (PD) DNA recognition by TLR9 to the detection of the DNA sugar backbone 2' deoxyribose. PD 2' deoxyribose homopolymers lacking DNA bases (abasic) are shown to act as TLR9 agonist while abasic phospho-thioate (PS) 2' deoxyribose functions as TLR9 antagonist. Alignment of bases to PD 2' deoxyribose enhanced its TLR9 agonistic function, while only CpG-motifs introduced to inhibitory PS 2' deoxyribose converted the antagonistic activity into powerful agonistic function. These new data thus restrict the CpG-motif dependency of TLR9 activation to the promising group of immunopharmacons that are based on PS modified synthetic DNA. They also show that natural PD DNA drives TLR9 activation sequence-independently as is the case for ds RNA recognizing TLR3 and ss RNA recognizing TLR7 and TLR8. Thus evolutionary pressure might have exiled nucleic acid recognizing TLRs such as TLR9 to endosomes in order to avoid activation by host (self) derived nucleic acids.


Subject(s)
DNA/immunology , Dendritic Cells/immunology , Deoxyribose/immunology , Endosomes/immunology , Oligodeoxyribonucleotides/immunology , Toll-Like Receptor 9/immunology , Animals , DNA/chemistry , DNA/metabolism , Dendritic Cells/metabolism , Deoxyribose/metabolism , Endosomes/metabolism , Humans , Interferon-alpha/immunology , Interferon-alpha/metabolism , Ligands , Oligodeoxyribonucleotides/metabolism , Poly G/immunology , Poly G/metabolism , Toll-Like Receptor 9/metabolism
6.
ACS Appl Bio Mater ; 4(1): 451-461, 2021 01 18.
Article in English | MEDLINE | ID: mdl-35014296

ABSTRACT

Cost-effective, fast, and reliable DNA sequencing can be enabled by advances in nanopore-based methods, such as the use of atomically thin graphene membranes. However, strong interaction of DNA bases with graphene leads to undesirable effects such as sticking of DNA strands to the membrane surface. While surface functionalization is one way to counter this problem, here, we present another solution based on a heterostructure nanopore system, consisting of a monolayer of graphene and hexagonal boron nitride (hBN) each. Molecular dynamics studies of DNA translocation through this heterostructure nanopore revealed a surprising and crucial influence of the heterostructure layer order in controlling the base specific signal variability. Specifically, the heterostructure with graphene on top of hBN had nearly 3-10× lower signal variability than the one with hBN on top of graphene. Simulations point to the role of differential underside sticking of DNA bases as a possible reason for the observed influence of the layer order. Our studies can guide the development of experimental systems to study and exploit DNA translocation through two-dimensional heterostructure nanopores for single molecule sequencing and sensing applications.


Subject(s)
Boron Compounds/chemistry , DNA/metabolism , Graphite/chemistry , Nanopores , Base Pairing , DNA/chemistry , Poly A/chemistry , Poly A/metabolism , Poly C/chemistry , Poly C/metabolism , Poly G/chemistry , Poly G/metabolism , Poly T/chemistry , Poly T/metabolism
7.
J Photochem Photobiol B ; 204: 111804, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32007677

ABSTRACT

The ubiquitous influence of double stranded RNAs in biological events makes them imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situations wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of this study is to delve into the interactive pattern of two small molecule phenothiazinium dyes, methylene blue and new methylene blue, with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic and molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules was evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding patterns of the dye molecules within the RNA duplexes. The novelty of the present work lies towards a new contribution of the phenothiazinium dyes in dysfunctioning double stranded RNAs, advancing our knowledge to their potential use as RNA targeted small molecules.


Subject(s)
Methylene Blue/analogs & derivatives , Methylene Blue/chemistry , RNA, Double-Stranded/chemistry , Binding Sites , Coloring Agents/chemistry , Methylene Blue/metabolism , Microscopy, Atomic Force , Molecular Docking Simulation , Nucleic Acid Conformation , Phenothiazines/chemistry , Poly C/chemistry , Poly C/metabolism , Poly G/chemistry , Poly G/metabolism , RNA, Double-Stranded/metabolism , Spectrometry, Fluorescence , Spectrophotometry , Viscosity
8.
Science ; 193(4253): 592-5, 1976 Aug 13.
Article in English | MEDLINE | ID: mdl-959820

ABSTRACT

Evidence has been obtained that a specific isomer of a diol epoxide derivative of benzo(a)pyrene, (+/-)-7 beta,8alpha-dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene, is an intermediate in the binding of benzo(a)pyrene to RNA in cultured bovine bronchial mucosa. An adduct is formed between position 10 of this derivative and the 2-amino group of guanine.


Subject(s)
Benzopyrenes/metabolism , DNA/metabolism , RNA/metabolism , Animals , Binding Sites , Bronchi , Cattle , Chemical Phenomena , Chemistry , Ethers, Cyclic , Models, Structural , Mucous Membrane , Poly G/metabolism , Structure-Activity Relationship
9.
Biochim Biophys Acta ; 1770(12): 1636-50, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17942232

ABSTRACT

A key step in the rational design of new RNA binding small molecules necessitates a complete elucidation of the molecular aspects of the binding of existing molecules to RNA structures. This work focuses towards the understanding of the interaction of a DNA intercalator, quinacrine and a minor groove binder 4',6-diamidino-2-phenylindole (DAPI) with the right handed Watson-Crick base paired A-form and the left-handed Hoogsteen base paired H(L)-form of poly(rC).poly(rG) evaluated by multifaceted spectroscopic and viscometric techniques. The energetics of their interaction has also been elucidated by isothermal titration calorimetry. Results of this study converge to suggest that (i) quinacrine intercalates to both A-form and H(L)-form of poly(rC).poly(rG); (ii) DAPI shows both intercalative and groove-binding modes to the A-form of the RNA but binds by intercalative mode to the H(L)-form. Isothermal calorimetric patterns of quinacrine binding to both the forms of RNA and of DAPI binding to the H(L)-form are indicative of single binding while the binding of DAPI to the A-form reveals two kinds of binding. The binding of both the drugs to both conformations of RNA is exothermic; while the binding of quinacrine to both conformations and DAPI to the A-form (first site) is entropy driven, the binding of DAPI to the second site of A-form and H(L)-conformation is enthalpy driven. Temperature dependence of the binding enthalpy revealed that the RNA-ligand interaction reactions are accompanied by small heat capacity changes that are nonetheless significant. We conclude that the binding affinity characteristics and energetics of interaction of these DNA binding molecules to the RNA conformations are significantly different and may serve as data for the development of effective structure selective RNA-based antiviral drugs.


Subject(s)
DNA/metabolism , Indoles/pharmacology , Poly C/metabolism , Poly G/metabolism , Quinacrine/pharmacology , RNA/drug effects , Binding Sites , Calorimetry/methods , Indoles/metabolism , Molecular Conformation , Quinacrine/metabolism , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet
10.
Biomaterials ; 29(8): 1099-108, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18022687

ABSTRACT

Aggregates of the self-assembling peptide EAK16II or EAK16IV and oligodeoxynucleotides (ODNs) were prepared, and their stability upon diluting the solution was investigated by UV-vis spectroscopy. The aggregates prepared at pH 4 and pH 7 did not dissociate after the solution was diluted 5- and 10-fold. The resistance against Escherichia coli exonuclease I of the ODN located in the EAK-ODN aggregates was studied by fluorescence resonance energy transfer (FRET) after the ODN had aggregated with EAK16II or EAK16IV at pH 4 or pH 7. The effect that the peptide sequence, peptide concentration, pH, and centrifugation had on protecting the aggregated ODN against nuclease degradation was investigated. Significant nuclease resistance was obtained after the EAK-ODN aggregates had been prepared at pH 4, with an EAK16IV concentration greater than a threshold value, and ensuring that the solution was not centrifuged immediately after sample preparation. Centrifuging the EAK16IV-ODN solution immediately after sample preparation resulted in the loss of this nuclease protection. However, if the solution of EAK-ODN aggregates was centrifuged 24 h after sample preparation, the nuclease protection afforded by the EAK16IV-ODN aggregates to the ODN was maintained even after being subject to a 10-fold dilution and up to 4 rounds of centrifugation over 4 days.


Subject(s)
Deoxyribonucleases/chemistry , Oligodeoxyribonucleotides/chemistry , Oligopeptides/chemistry , Escherichia coli/enzymology , Exodeoxyribonucleases/chemistry , Fluorescence Resonance Energy Transfer , Hydrogen-Ion Concentration , Oligodeoxyribonucleotides/metabolism , Oligopeptides/metabolism , Poly C/chemistry , Poly C/metabolism , Poly G/chemistry , Poly G/metabolism , Protein Binding , Spectrophotometry, Ultraviolet
11.
J Biomol Struct Dyn ; 26(1): 99-114, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18533731

ABSTRACT

It was found recently that Hoechst 33258, a dsDNA fluorescent dye used in cytological studies, is an efficient inhibitor of the interaction of TATA-box-binding protein with DNA, DNA topoisomerase I, and DNA helicases. In addition it proved to be a radioprotector. Biological activity of Hoechst 33258 may be associated with dsDNA complexes of not only monomeric, but also dimeric type. In this work, the Hoechst 33258 interaction with poly(dG-dC).poly(dG-dC) was studied using UV-vis and fluorescent spectroscopy, circular and flow-type linear dichroism. It was found that Hoechst 33258 formed with poly(dG-dC).poly(dG-dC) complexes of three types, namely, monomeric, dimeric, and, apparently, tetrameric, and their spectral properties were studied. Complexes of monomeric and dimeric types competed with distamycin A, a minor groove ligand, for binding to poly(dG-dC).poly(dG-dC). We proposed that Hoechst 33258 both monomers and dimers form complexes of the external type with poly(dG-dC).poly(dG-dC) from the side of the minor groove.


Subject(s)
Bisbenzimidazole/metabolism , DNA Topoisomerases, Type I/metabolism , Fluorescent Dyes/metabolism , Poly C/metabolism , Poly G/metabolism , Polynucleotides/metabolism , Circular Dichroism , Dimerization , Models, Molecular , Nucleic Acid Conformation , Poly C/chemistry , Poly G/chemistry , Polydeoxyribonucleotides , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet
12.
Mol Cell Biol ; 18(3): 1498-505, 1998 Mar.
Article in English | MEDLINE | ID: mdl-9488466

ABSTRACT

The alpha- and beta-tubulin mRNAs of Chlamydomonas reinhardtii exhibit different half-lives under different conditions: when expressed constitutively, they degrade with half-lives of about 1 h, whereas when induced by deflagellation, they degrade with half-lives of only 10 to 15 min. To investigate the decay pathway(s) used under these two conditions, an alpha1-tubulin gene construct which included an insert of 30 guanidylate residues within the 3' untranslated region was introduced into cells. This transgene was efficiently expressed in stably transformed cells, and the mRNA exhibited constitutive and postinduction half-lives like those of the alpha1-tubulin mRNA. Northern blot analysis revealed the occurrence of a 3' RNA fragment derived from the poly(G)-containing alpha1-tubulin transcripts. The 3' fragment was shown to accumulate as full-length mRNA disappeared in actinomycin D-treated cells, indicating a precursor-product relationship. Insertion of a second poly(G) tract upstream of the first resulted in accumulation of only a longer 3' fragment, suggesting that the decay intermediate is generated by 5'-to-3' exonucleolytic digestion. A translational requirement for generation of the 3' fragment was demonstrated by experiments in which cells were deflagellated in the presence of cycloheximide. Analysis of fragment poly(A) length revealed that the fragments were, at most, oligoadenylated in nondeflagellated cells but had a long poly(A) tail in deflagellated cells. These findings suggest that the oligoadenylated fragment is a decay intermediate in a deadenylation-dependent, constitutive degradation pathway and that the requirement for deadenylation is bypassed in deflagellated cells. This represents the first example in which a single transcript has been shown to be targeted to different decay pathways under different cellular conditions.


Subject(s)
Chlamydomonas reinhardtii/metabolism , Poly A/metabolism , RNA, Messenger/metabolism , RNA, Plant/metabolism , Tubulin/genetics , Animals , Cycloheximide/pharmacology , Flagella , Oligodeoxyribonucleotides/metabolism , Poly G/metabolism , Protein Synthesis Inhibitors/pharmacology
13.
Mol Cell Biol ; 19(5): 3829-41, 1999 May.
Article in English | MEDLINE | ID: mdl-10207106

ABSTRACT

In the fission yeast Schizosaccharomyces pombe the nrd1(+) gene encoding an RNA binding protein negatively regulates the onset of differentiation. Its biological role is to block differentiation by repressing a subset of the Ste11-regulated genes essential for conjugation and meiosis until the cells reach a critical level of nutrient starvation. By using the phenotypic suppression of the S. pombe temperature-sensitive pat1 mutant that commits lethal haploid meiosis at the restrictive temperature, we have cloned ROD1, a functional homologue of nrd1(+), from rat and human cDNA libraries. Like nrd1(+), ROD1 encodes a protein with four repeats of typical RNA binding domains, though its amino acid homology to Nrd1 is limited. When expressed in the fission yeast, ROD1 behaves in a way that is functionally similar to nrd1(+), being able to repress Ste11-regulated genes and to inhibit conjugation upon overexpression. ROD1 is predominantly expressed in hematopoietic cells or organs of adult and embryonic rat. Like nrd1(+) for fission yeast differentiation, overexpressed ROD1 effectively blocks both 12-O-tetradecanoyl phorbol-13-acetate-induced megakaryocytic and sodium butyrate-induced erythroid differentiation of the K562 human leukemia cells without affecting their proliferative ability. These results suggest a role for ROD1 in differentiation control in mammalian cells. We discuss the possibility that a differentiation control system found in the fission yeast might well be conserved in more complex organisms, including mammals.


Subject(s)
Cell Differentiation/genetics , RNA-Binding Proteins/genetics , Schizosaccharomyces pombe Proteins , Amino Acid Sequence , Animals , Base Sequence , Butyrates/pharmacology , Cloning, Molecular , Flow Cytometry , Fungal Proteins/chemistry , Fungal Proteins/genetics , Gene Expression Regulation/genetics , Humans , Molecular Sequence Data , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Poly G/metabolism , Poly U/metabolism , Polypyrimidine Tract-Binding Protein , RNA-Binding Proteins/chemistry , Rats , Ribonucleoproteins/chemistry , Schizosaccharomyces/genetics , Sequence Homology, Amino Acid , Tetradecanoylphorbol Acetate/pharmacology , Transcription Factors/genetics , Tumor Cells, Cultured
14.
J Inorg Biochem ; 101(8): 1129-32, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17560654

ABSTRACT

The Al(III)-salophen complex 1 exhibited strong spectroscopic changes specifically upon addition of polyG and GpG, while double stranded DNA and RNA, and single stranded polyA, polyU and polyC induced negligible spectral changes of 1. Titrations with mono-nucleotides yielded no spectroscopic changes, revealing that there must be at least two consecutive guanines in single stranded oligonucleotide structure for a measurable spectroscopic change of 1. Preliminary results show that 1 has moderate antiproliferative effect on a number of human tumour cell lines.


Subject(s)
Aluminum/chemistry , Poly G/chemistry , Salicylates/chemistry , Aluminum/metabolism , Animals , Binding Sites , Cell Line, Tumor , DNA/metabolism , HeLa Cells , Humans , Magnetic Resonance Spectroscopy , Poly G/metabolism , Salicylates/metabolism , Solubility , Spectrophotometry, Ultraviolet , Static Electricity
15.
Mol Biol Cell ; 10(3): 649-64, 1999 Mar.
Article in English | MEDLINE | ID: mdl-10069809

ABSTRACT

The fundamental process of nucleocytoplasmic transport takes place through the nuclear pore. Peripheral pore structures are presumably poised to interact with transport receptors and their cargo as these receptor complexes first encounter the pore. One such peripheral structure likely to play an important role in nuclear export is the basket structure located on the nuclear side of the pore. At present, Nup153 is the only nucleoporin known to localize to the surface of this basket, suggesting that Nup153 is potentially one of the first pore components an RNA or protein encounters during export. In this study, anti-Nup153 antibodies were used to probe the role of Nup153 in nuclear export in Xenopus oocytes. We found that Nup153 antibodies block three major classes of RNA export, that of snRNA, mRNA, and 5S rRNA. Nup153 antibodies also block the NES protein export pathway, specifically the export of the HIV Rev protein, as well as Rev-dependent RNA export. Not all export was blocked; Nup153 antibodies did not impede the export of tRNA or the recycling of importin beta to the cytoplasm. The specific antibodies used here also did not affect nuclear import, whether mediated by importin alpha/beta or by transportin. Overall, the results indicate that Nup153 is crucial to multiple classes of RNA and protein export, being involved at a vital juncture point in their export pathways. This juncture point appears to be one that is bypassed by tRNA during its export. We asked whether a physical interaction between RNA and Nup153 could be observed, using homoribopolymers as sequence-independent probes for interaction. Nup153, unlike four other nucleoporins including Nup98, associated strongly with poly(G) and significantly with poly(U). Thus, Nup153 is unique among the nucleoporins tested in its ability to interact with RNA and must do so either directly or indirectly through an adaptor protein. These results suggest a unique mechanistic role for Nup153 in the export of multiple cargos.


Subject(s)
Cell Nucleus/metabolism , Nuclear Pore Complex Proteins , Nuclear Proteins/metabolism , Animals , Antibodies/metabolism , Antibodies/pharmacology , Biological Transport/drug effects , Female , Gene Products, rev/metabolism , Karyopherins , Nuclear Proteins/immunology , Oocytes/drug effects , Oocytes/metabolism , Poly G/metabolism , Poly U/metabolism , RNA/metabolism , RNA Precursors/metabolism , RNA, Small Nuclear/metabolism , Xenopus
16.
J Clin Endocrinol Metab ; 91(9): 3515-20, 2006 Sep.
Article in English | MEDLINE | ID: mdl-16804045

ABSTRACT

BACKGROUND: Sufficient androgen receptor (AR) activity is crucial for normal male sexual differentiation. Here we report on two unrelated 46, XY patients suffering from undervirilization and genital malformations. Both patients had a short polyglycine (polyG) repeat of 10 residues and a relatively long polyglutamine (polyQ) repeat of 28 and 30 residues within the transactivation domain of the AR. In addition, they also harbor a rare A645D substitution. OBJECTIVE: We made a set of AR expression plasmid constructs with varying polyQ and polyG tract sizes in context with or without the A645D substitution and analyzed their in vitro transactivation capacity in transfected CHO cells. RESULTS: We found that a short polyG repeat downmodulated AR activity to approximately 60-65% of the wild-type receptor. This effect was aggravated by A645D in context of a long polyQ repeat to less than 50% activity. In contrast, in the context of a short polyQ and a short polyG repeat, the A645D mutation rescues AR activity to almost wild-type levels, demonstrating a contradictory effect of this mutation, depending on the size of the polymorphic repeats. CONCLUSIONS: A combination of a short polyG repeat with a long polyQ repeat and an A645D substitution might contribute to the development of virilization disorders and explain the observed phenotypes of our patients as a form of androgen insensitivity. The whole recreation of AR sequence variations including individual polymorphic repeat sizes could unravel possible interference of mutations and variations on AR activity by in vitro transfection.


Subject(s)
Androgen-Insensitivity Syndrome/genetics , Microsatellite Repeats/genetics , Point Mutation , Receptors, Androgen/genetics , Androgen-Insensitivity Syndrome/metabolism , Animals , Blotting, Western , CHO Cells , Cricetinae , Genetic Variation , Humans , Infant , Male , Plasmids/genetics , Poly G/genetics , Poly G/metabolism , Receptors, Androgen/metabolism , Transcription, Genetic/genetics , Transfection
17.
Methods Mol Biol ; 335: 311-41, 2006.
Article in English | MEDLINE | ID: mdl-16785636

ABSTRACT

A guanine (G)-quadruplex DNA motif has recently emerged as a biologically important structure that is believed to interfere with telomere maintenance by telomerase. G-quadruplexes exhibit four-stranded structures containing one or more nucleic acid strands with central channel able to accommodate metal cations. Coordination of certain metal cations stabilizes G-quadruplex as with some promising small organic molecules that promote the formation and/or stabilization of G-quadruplex. Among many techniques employed to explore properties of G-quadruplexes, the fluorescence resonance energy transfer (FRET) technique has been recognized as a powerful tool to study G-quadruplex formation. This review summarizes the current developments in the uses of FRET technique for the fundamental structural investigations and its practical applications. Applications include FRET-based selection of efficient quadruplex-binding ligands, design of a nanomolecular machine, and a molecular aptamer beacon for protein recognition. We also describe a technique for detection of potassium ions in aqueous solution with the use of quadruplex-based sensor (potassium-sensing oligonucleotide).


Subject(s)
DNA/chemistry , Fluorescence Resonance Energy Transfer/methods , Guanine/chemistry , Molecular Probe Techniques , Poly G/chemistry , DNA/metabolism , Fluorescent Dyes , G-Quadruplexes , Guanine/metabolism , Molecular Probes , Poly G/metabolism
18.
Nucleic Acids Res ; 31(17): 5054-63, 2003 Sep 01.
Article in English | MEDLINE | ID: mdl-12930956

ABSTRACT

The Schizosaccharomyces pombe Ku70-Ku80 heterodimer is required for telomere length regulation. Lack of pku70+ results in telomere shortening and striking rearrangements of telomere-associated sequences. We found that the rearrangements of telomere-associated sequences in pku80+ mutants are Rhp51 dependent, but not Rad50 dependent. Rhp51 bound to telomere ends when the Ku heterodimer was not present at telomere ends. We also found that the single-stranded G-rich tails increased in S phase in wild-type strains, while deletion of pku70+ increased the single-stranded overhang in both G2 and S phase. Based on these observations, we propose that Rhp51 binds to the G-rich overhang and promotes homologous pairing between two different telomere ends in the absence of Ku heterodimer. Moreover, pku80 rhp51 double mutants showed a significantly reduced telomere hybridization signal. Our results suggest that, although Ku heterodimer sequesters Rhp51 from telomere ends to inhibit homologous recombination activity, Rhp51 plays important roles for the maintenance of telomere ends in the absence of the Ku heterodimer.


Subject(s)
Antigens, Nuclear/genetics , DNA Helicases , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Telomere/genetics , Antigens, Nuclear/chemistry , Antigens, Nuclear/metabolism , DNA, Fungal/genetics , DNA, Fungal/metabolism , DNA-Binding Proteins/chemistry , Dimerization , Fungal Proteins/genetics , Fungal Proteins/metabolism , G2 Phase , Ku Autoantigen , Meiosis/genetics , Mutation , Poly G/genetics , Poly G/metabolism , Protein Binding , Rad51 Recombinase , S Phase , Schizosaccharomyces/genetics , Schizosaccharomyces/physiology , Schizosaccharomyces pombe Proteins/genetics , Spores, Fungal/genetics , Spores, Fungal/growth & development , Telomere/metabolism
19.
Cancer Res ; 43(10): 4799-804, 1983 Oct.
Article in English | MEDLINE | ID: mdl-6683992

ABSTRACT

Cisplatin has been shown to create interstrand DNA crosslinks by several methods. These experiments were performed to determine if cisplatin coordinates cross-links between deoxyguanylic and deoxycytidylic acids. After incubation at pH 7.2 with cisplatin at various platinum/base nucleotide ratios, ri, for 3 days at 20 degrees, polydeoxyguanylic acid . polydeoxycytidylic acid [poly(dG) . poly(dC)] was centrifuged in alkaline cesium sulfate for 3 days at 35,000 rpm. Untreated samples resulted in a low-density deoxycytidylic acid peak and a high-density deoxyguanylic acid peak, as identified by the ultraviolet absorption spectrum. The density gradient profiles of cisplatin-treated poly(dG). poly(dC) had an additional hybrid-density peak the area of which increased with the dose (ri) as the areas under the polydeoxycytidylic acid [poly(dC)] and polydeoxyguanylic acid [poly(dG)] peaks diminished. With increasing ri, the densities of both the poly(dG) and hybrid peaks increased while that of the poly(dC) peak remained unchanged. Similarly, the amount of bound platinum in the poly(dG) and hybrid-density peaks increased with ri, while no platinum could be detected in the poly(dC) peak. Therefore, cisplatin appears to react first with the deoxyguanylic acid strand, followed by a second reaction with the deoxycytidylic acid strand to form the interstrand cross-links that are necessary for the formation of the hybrid-density bands. Based upon the intercept of the percent cross-linked poly(dG) . poly(dC) versus ri curve with the abscissa, the minimum amount of cisplatin or the threshold amount of cisplatin required to observe cross-links was ri = 0.017. When multiplied by the molecular weight of the poly(dG) . poly(dC) used, this was equivalent to 1 cross-link per 15 molecules of bound platinum. However, based upon the amount of bound drug, the frequency of cross-links per platinum reaction was calculated to range from one of 50 to 67 reactions. Due to limitations in the sensitivity of the platinum assay and to a progressively lower recovery of the cross-linked material at lower ri values, it was not possible to calculate the cross-linking efficiency based upon the amount of bound drug for ri values equal to or less than 0.025. The monofunctional analogue, [diethylenetriaminechloroplatinum] chloride, did not cause a hybrid peak to form. These studies demonstrate that cisplatin coordinates interstrand cross-links between poly(dG) and poly(dC).


Subject(s)
Cisplatin/pharmacology , Poly C/metabolism , Poly G/metabolism , Polydeoxyribonucleotides/metabolism , Polyribonucleotides/metabolism , Centrifugation, Density Gradient
20.
Cancer Res ; 40(12): 4704-8, 1980 Dec.
Article in English | MEDLINE | ID: mdl-7002295

ABSTRACT

A series of hydroxamic acids (aceto-, propiono-, benzo-, and p-nitrobenzo-) and seven derivatives of these were examined for biological activity using Salmonella typhimurium. Acylation to yield O-acetyl and O-benzoyl derivatives markedly enhanced toxic properties and was necessary for mutagenic activity for all but p-nitrobenzohydroxamic acid. The dose necessary to produce a minimum significant mutagenic response varied from 21 microM for O-benzoyl benzohydroxamate to 430 microM for O-acetyl acetohydroxamate. These two compounds were also tested with human lymphoblasts to which they were toxic at 100 microM but not mutagenic. O-Acetyl benzohydroxamate, a mutagen, was prepared wih a 14C label in the carbonyl carbon atom of the benzoyl group and was shown to form an adduct in vitro with DNA and polyguanylic acid. The level of binding was 1 mol of 14C per 5 X 10(4) mol of DNA phosphate and 1 mol of 14C per 10(5) mol of polyguanylic acid phosphate.


Subject(s)
Hydroxamic Acids , Mutagens , Cells, Cultured , Chemical Phenomena , Chemistry , DNA/metabolism , Humans , Hydroxamic Acids/metabolism , Lymphocytes/drug effects , Poly G/metabolism , Salmonella typhimurium/drug effects , Structure-Activity Relationship
SELECTION OF CITATIONS
SEARCH DETAIL