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PubMedDate not supplied

The diimide drug PIPER has a cytotoxic dose-dependent effect in vitro and inhibits telomere elongation in HELA cells.

It is known that, in vitro, PIPER (N,N'-bis [2-(1-piperidino)ethyl]-3,4,9,10-tetracarboxylic diimide) induces the formation of the Hoogsteen quadruplex structure in telomere DNA, thus inhibiting the polymerisation of telomeric repeats. Since the action of PIPER in vivo has been scarcely investigated, this study was addressed to gain some insight into the effects of this drug on cultured HeLa cells. Vital staining with erythrosine, performed on cells exposed to different PIPER concentrations (from 1 to 50 microM), showed that the drug exerts a dose-dependent cytotoxic effect, clearly evident after a short-term (24 h) treatment. This early cytotoxic effect of PIPER on cultured HeLa cells was confirmed by a spectrophotometric/colorimetric method employing methylthiazoletetrazolium (Mossmann assay). Hematoxylin/eosin staining of cells treated with PIPER for 24 h showed a nuclear condensation and a cytoplasmic vacuolisation, very pronounced at higher drug concentrations. These pictures suggest that PIPER-induced cell death might be of the apoptotic type. Finally, the anti-telomerase activity of PIPER was monitored by TRAP assay, performed on HeLa cell nuclear extracts treated with increasing drug concentrations. It was found that some inhibition of telomerase is apparent even at low concentrations, while at the highest concentration the enzyme is completely inhibited. These results indicate that the cytotoxic power of PIPER is possibly related to its antitelomeric effect.

Dose-Response Relationship, Drug↗
PubMed1995

Posttranscriptional regulation of insulin-like growth factor II mRNA.

The insulin-like growth factor II (IGF-II) gene generates multiple mature transcripts with different 5' untranslated regions (5'UTR) but identical coding regions and 3'UTRs. We have analysed the translational regulation and decay of the transcripts. Human IGF-II mRNAs provide a provocative example of translational discrimination in which only the minor 4.8 kb mRNA is actively engaged in protein synthesis while the major 6.0 kb mRNA is present in a 100S RNP particle. The 6.0 kb mRNA exhibits a structured 5'UTR of 1170 nucleotides that function as a cis-acting translational attenuator. IGF-II transcripts are processed by endonucleolytic cleavage 1209 and 2183 nucleotides downstream from the translation termination codons in the rat and human, respectively. The cleavage site is situated in a highly conserved and structured domain that exhibits two large hairpins and an intramolecular guanosine quadruplex. The structural elements may provide binding sites for trans-acting factors and ensure that the cleavage site is not sequestered in stable RNA structures. Since expression of IGF-II is initiated from minimal promoters and finished by constitutive secretion from the cell, regulatory events governing IGF-II production are likely to be implemented between the transcriptional and the posttranslational level. The combined effect of translational discrimination and endonucleolysis may therefore play an important role in the regulation of IGF-II expression.

Animals↗
PubMed1996

The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases.

Arc1p was found in a screen for components that interact genetically with Los1p, a nuclear pore-associated yeast protein involved in tRNA biogenesis. Arc1p is associated with two proteins which were identified as methionyl-tRNA and glutamyl-tRNA synthetase (MetRS and GluRS) by a new mass spectrometry method. ARC1 gene disruption leads to slow growth and reduced MetRS activity, and synthetically lethal arc1- mutants are complemented by the genes for MetRS and GluRS. Recombinant Arc1p binds in vitro to purified monomeric yeast MetRS, but not to an N-terminal truncated form, and strongly increases its apparent affinity for tRNAMet. Furthermore, Arc1p, which is allelic to the quadruplex nucleic acid binding protein G4p1, exhibits specific binding to tRNA as determined by gel retardation and UV-cross-linking. Arc1p is, therefore, a yeast protein with dual specificity: it associates with tRNA and aminoacyl-tRNA synthetases. This functional interaction may be required for efficient aminoacylation in vivo.

Acylation↗
PubMed1997

The effects of fingermark enhancement light sources on subsequent PCR-STR DNA analysis of fresh bloodstains.

This paper describes a study designed to investigate the effects of light sources used to enhance fingermarks on the subsequent polymerase chain reaction (PCR)-short tandem repeat (STR) analysis of bloodstains. Dried bloodstains on glass were exposed for up to 30 min to five different light sources: Argon ion laser, Polilight UV, Polilight green, Superlite, and shortwave UV. The bloodstains were subsequently analyzed using a quadruplex PCR system. It was found that treating the bloodstains with four of the five light sources had no appreciable effect on the results obtained from subsequent PCR analysis. However, exposure of the bloodstains to shortwave UV light for more than 30 s precluded the acquisition of results from PCR testing. Therefore, under casework conditions, it would be preferable to avoid exposing bloodstains, on which PCR typing is to be performed, to shortwave UV.

Argon↗
PubMed1997

A pentaplex automated fluorescent typing system for forensic identification and French Caucasian population data.

The polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci has already proven to be a method of choice for large scale typing of DNA samples in which the conventional restriction fragment length polymorphism (RFLP) technique is ineffective. A quadruplex PCR including HUMvWFA31A, HUMF13A01, HUMTH01, and HUMFESFPS STR loci is used successfully for routine forensic applications in our laboratory. However, the need to increase the discrimination power of the PCR systems used prompted us to develop a second system of a pentaplex PCR for the analysis of 4 additional STR loci (HUMD8S1179, HUMD18S51, HUMD21S11, and HUMFIBRA) and the sex determination by amplification of a segment of the X-Y homologous Amelogenin gene. Allele and phenotype frequencies for these 4 STR systems were obtained by multiplex amplification, from approximately 200 randomly selected and unrelated French Caucasian individuals. Statistical calculations for these phenotype distributions met expectations for Hardy-Weinberg equilibrium. Furthermore, the French allelic frequencies of D18S51, D21S11, and HUMFIBRA loci were compared with the data obtained by the Forensic Science Service (UK) for the British Caucasian population and proved to be similar.

Alleles↗
PubMed1997

Interlaboratory evaluation of short tandem repeat triplex CTT.

An interlaboratory comparison of typing results for Short Tandem Repeats (STRs) at the GenBank loci HUMCSF1PO, HUMTPOX, HUMTH01, and HUMVWFA31 using the "CTT triplex" and "CTTv quadruplex" has been evaluated. These STRs all have a nominal four basepair (bp) repeat. Seven different samples were distributed to 41 laboratories. The 34 laboratories that returned results used a wide variety of analytical systems. Comparable results were obtained for all samples at all loci when results were reported as an allelic name. Raw sizing results obtained from internal-lane sizing standards differed by nearly five bp at some loci. Many different factors contribute to this observed sizing variability, including choice of sizing standards and matrix composition. Although sizing results can be made more comparable by locus-specific offsets or calibration to a comprehensive set of alleles at each locus, samples typed to the allelic name can now be validly compared regardless of analytical method. Interlaboratory comparison of raw allelic size remains problematic.

Algorithms↗
PubMed1997

[Detection of DNA single-copy sequences of prehistoric teeth. Site milieu as a factor for preservation of DNA].

DNA-extracts from prehistoric roots of teeth were analyzed by PCR to investigate microsatellite-systems. At the same time the x/y-chromosome specific system Amel A/B was investigated. The samples were collected from different burial conditions of similar age. Factors leading to limited DNA-degradation are given. For the first time reproducible Quadruplex-amplification on single-copy loci of prehistoric tissue was obtained in samples from the Lichtenstein-Cave, Kr. Osterode/Harz. Positive results are explained by low temperature in the burial site. In addition the results show that desiccation allows DNA-preservation but cannot protect the DNA from damage due to microbial origin. Microorganisms can destroy DNA-structures completely.

Burial↗
PubMed1998

Enhancement of PCR amplification yield and specificity using AmpliTaq Gold DNA polymerase.

Inadequate yields of PCR product and the generation of nonspecific PCR products can complicate genotyping studies, particularly when the DNA template is of inferior quality and/or has a low-copy number. In this study, the ability of AmpliTaq Gold DNA Polymerase to enhance the specificity and yield of amplification was evaluated in a quadruplex short tandem repeat (STR) system in which a nonspecific PCR product and poor yield had been previously observed with AmpliTaq DNA Polymerase usage. Because AmpliTaq Gold is inactive until heated during the PCR before thermal cycling, effects similar to those achieved with "hot-start" PCR were attained in a fast, simple and practical fashion. A significant enhancement in yield at the four STR loci and improved balance of alleles resulted with the use of AmpliTaq Gold. Furthermore, a non-specific PCR product, the result of mispriming, was effectively eliminated. The consistency of quality results was improved, thereby promoting successful typing of suboptimal DNA samples and enhancing the accuracy of genotyping. Since PCR product yield is elevated with AmpliTaq Gold usage, and consistent performance and low background are achieved with higher amounts of AmpliTaq Gold compared with AmpliTaq, AmpliTaq Gold can be used to augment measures taken to counteract the effects of some PCR/Taq DNA polymerase inhibitors, such as those found in blood and some forensic specimens. Studies showed that pH affects either the activity or the activation of the polymerase. AmpliTaq Gold was found to be compatible with pH 8.3 buffers, such as GeneAmp PCR Buffer and AmpFlSTR PCR Reaction Mix but not compatible with pH 9.0 buffers, such as GenePrint STR 10 x Buffer (however, conditions for the usage of AmpliTaq Gold with the GenePrint CTTv system are provided). AmpliTaq Gold is useful for the development and optimization of multiplex amplification systems, particularly those in which the primers are not well designed and/or the reaction conditions are not optimal. Finally, because AmpliTaq Gold is initially inactive, preparation of reactions at ambient temperature and automation of the PCR are facilitated. Therefore throughput can be expanded significantly with the use of AmpliTaq Gold DNA Polymerase.

Buffers↗
PubMedDate not supplied

Drug-DNA recognition: energetics and implications for design.

In this article we review thermodynamic studies designed to examine the interaction of low molecular weight ligands or drugs with DNA. Over the past 10 years there has been an increase in the number of rigorous biophysical studies of DNA-drug interactions and considerable insight has been gained into the energetics of these binding reactions. The advent of high-sensitivity calorimetric techniques has meant that the energetics of DNA-drug association reactions can be probed directly and enthalpic and entropic contributions to the binding free energy established. There are two principal consequences arising from this type of work, firstly three-dimensional structures of DNA-drug complexes from X-ray and NMR studies can be put into a thermodynamic context and the energetics responsible for stabilizing the observed structures can be more fully understood. Secondly, any rational approach to structure-based drug design requires a fundamental base of knowledge where structural detail and thermodynamic data on complex formation are intimately linked. Therefore these types of studies allow a set of general guidelines to be established, which can then be used to develop drug design algorithms. In this review we describe recent breakthroughs in duplex DNA-directed drug design and also discuss how similar principles are now being used to target higher-order DNA molecules, for example, triplex (three-stranded) and tetraplex (four-stranded) structures.

Binding Sites↗
PubMed1996

Synapsable DNA.

We describe a simple innovation that allows DNA double helices to stably bind one another at specific sites, with regulatable affinity, under physiological conditions. This type of DNA synapsis requires neither an unraveling of the participating duplexes not heteroduplex formation, and is achieved by the intermolecular dimerization of short blocks of guanine-guanine mismatch base-pairs introduced within standard Watson-Crick duplexes. We propose that in vivo such "sticky" guanine domains, formed transiently in cruciforms, could initiate illegitimate recombination events. In practical terms, this type of synapsis, achievable in vitro by simply mixing the participating duplexes, could provide a novel and general technology for the self-assembly of arrays of important DNA sequences, and serve as a tool for investigating certain protein-DNA interactions in vivo.

Base Sequence↗
PubMed2000

Preferential binding of fd gene 5 protein to tetraplex nucleic acid structures.

The gene 5 protein of filamentous bacteriophage fd is a single-stranded DNA-binding protein that binds non-specifically to all single-stranded nucleic acid sequences, but in addition is capable of specific binding to the sequence d(GT(5)G(4)CT(4)C) and the RNA equivalent r(GU(5)G(4)CU(4)C), the latter interaction being important for translational repression. We show that this sequence preference arises from the formation of a tetraplex structure held together by a central block of G-quartets, the structure of which persists in the complex with gene 5 protein. Binding of gene 5 protein to the tetraplex leads to formation of a approximately 170 kDa nucleoprotein complex consisting of four oligonucleotide strands and eight gene 5 protein dimers, with a radius of gyration of 45 A and an overall maximum dimension of 120-130 A. A model of the complex is presented that is consistent with the data obtained. It is proposed that the G-quartet may act as a nucleation site for binding gene 5 protein to adjacent single-stranded regions, suggesting a novel mechanism for translational repression.

Chromatography, Gel↗
PubMed1998

Determination of internuclear angles of DNA using paramagnetic-assisted magnetic alignment.

Paramagnetic ions have been used to assist the magnetic alignment of DNA. The anisotropy of the binding sites is sufficient to give rise to significant alignment of the DNA with the observed proton-carbon dipolar couplings spanning a 70-Hz range. The dipolar couplings have been used to determine the positions of the axial and rhombic alignment axes. The positions of the alignment axes relative to the positions of the binding sites of the paramagnetic europium ions have also been determined.

Anisotropy↗
PubMed2001

The 4N cell cycle delay in Fanconi anemia reflects growth arrest in late S phase.

Fanconi anemia (FA) is a human genetic disorder characterized by hypersensitivity to DNA crosslinking agents. Its cellular phenotypes include increased chromosome breakage and a marked cell-cycle delay with 4N DNA content after introduction of interstrand DNA crosslinks (ICL). To further understand the nature of this delay previously described as a G2/M arrest, we introduced ICL specifically during G2 and monitored the cells for passage into mitosis. Our results showed that, even at the highest doses, postreplication ICL produced neither G2/M arrest nor chromosome breakage in FA-A or FA-C cells. This suggests that, similar to wild-type cells, DNA replication is required to trigger both responses. Therefore, the 4N cell DNA content observed in FA cells after ICL treatment also represents incomplete DNA replication and arrest in late S phase. FA fibroblasts from complementation groups A and C were able to recover from the ICL-induced cell-cycle arrest, but took approximately 3 times longer than controls. These results indicate that the FA pathway is required for the efficient resolution of ICL-induced S-phase arrest.

Cell Line↗
PubMed2026

B-MYB (MYBL2): from cell cycle regulator to an oncogenic player.

B-MYB (MYBL2) is a transcription factor of the MYB family that plays critical roles in cell cycle progression, proliferation, and survival. Through the DREAM-MMB-FOXM1 network, B-MYB coordinates the expression of genes required for mitosis and cytokinesis (G2/M genes), while genes required for DNA replication during S phase are regulated by E2F-DP complexes. Initially identified as a regulator of normal cell cycle processes, B-MYB has emerged as a key oncogenic driver across multiple cancer types. This review addresses the physiological roles of B-MYB, the mechanisms underlying its oncogenic activation, and its contributions to tumorigenesis and clinical relevance as a prognostic biomarker and potential therapeutic target. Aberrant activation of B-MYB, driven by gene amplification, transcriptional upregulation, or post-translational modification, is reported as a recurrent feature of aggressive cancers. The consequences of B-MYB overexpression, including uncontrolled proliferation, genomic instability, apoptosis evasion, epithelial-to-mesenchymal transition, therapy resistance and metabolic reprogramming, further underscore B-MYB as a central oncogenic driver. Clinically, B-MYB overexpression correlates with poor prognosis, advanced disease and chemoresistance across multiple malignancies. Thus, we aim to emphasise the biological roles of B-MYB in physiological and cancer mechanisms, alongside the growing evidence establishing it as both a biomarker of disease and a potential therapeutic target. While previous reviews have addressed isolated aspects of B-MYB biology, this review provides a comprehensive and updated integration of recent mechanistic advances (A-MYB/B-MYB functional redundancy and YAP/TAZ-TEAD crosstalk) and the therapeutic potential of non-canonical DNA structures at the B-MYB promoter. We further review current trends and methodologies for targeting B-MYB and outline new perspectives for future therapeutic research.

Humans↗
PubMed2006

The thrombin binding aptamer GGTTGGTGTGGTTGG forms a bimolecular guanine tetraplex.

In the literature, the thrombin binding aptamer GGTTGGTGTGGTTGG is generally taken as a prototype of an intramolecular guanine tetraplex of DNA. Our results, however, show that this notion is not true in aqueous solutions. This conclusion is based on a dependence of the CD spectra on aptamer concentration, migration of the aptamer in polyacrylamide gels, and the Ferguson analysis of the gel migration data. The presented data document that the aptamer forms a bimolecular tetraplex. We furthermore show that only an extension of the aptamer by a sequence containing further guanines, or an elongation of loop regions, causes that its tetraplex folding is intramolecular.

Aptamers, Nucleotide↗
PubMed2005

Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy.

A series of G-rich oligonucleotides able to form tetraplexes has been studied by FTIR spectroscopy. Characteristic markers of the formation of guanine tetrads are given. Moreover, we propose a new marker discriminating between parallel and antiparallel tetraplexes: the position of the C6O6 guanine carbonyl stretching vibration. In intermolecular parallel tetrameric structures formed by four separate strands this absorption is observed at 1693 cm-1 while for antiparallel tetrameric structures, either intramolecular or formed by dimerization of hairpins, this vibrational mode is observed at 1682 cm-1. These shifts to higher wavenumbers, when compared to the position of a free guanine C6O6 carbonyl stretching vibration observed at 1666 cm-1(Deltanu=27 cm-1 for parallel tetraplexes and Deltanu=16 cm-1 for antiparallel tetraplexes) reflect different strand orientations in the structures. This marker has been used to evidence the possibility of an antiparallel-parallel tetraplex reorganization for Oxytricha nova d(G4T4G4) and d((G4T4)3G4) and human d(G3T2AG3) telomeric sequences induced by Na+/K+ or Na+/Ca2+ ion exchange. Formation of the guanine tetrads, characterization of the phosphate geometries and of the sugar conformations have also been obtained by FTIR for the different tetraplexes.

Animals↗
PubMed2000

NB-506, an indolocarbazole topoisomerase I inhibitor, binds preferentially to triplex DNA.

A novel competition dialysis method was used to study the structural selectivity of the nucleic acid binding of NB-506, a promising indolocarbazole anticancer agent. A pronounced preference for NB-506 binding to the DNA triplex poly [dA]:(poly[dT])(2) was observed among potential binding to 12 different nucleic acid structures and sequences. Structures included in the assay ranged from single-stranded DNA, through a variety of right-handed DNA duplexes, to multistranded triplex and tetraplex forms. RNA and left-handed Z DNA were also included in the assay. The preferential binding to triplex was confirmed by UV melting experiments. The novel and unexpected structural selectivity shown by NB-506 may arise from a complementary shape between its extended aromatic ring system and the planar triplex stack.

Animals↗