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PubMed2005

Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium.

The circular dichroism, CD, spectra of the telomere repeats of vertebrates, d(TTAGGG), indicate that parallel type quadruplex structures or disordered single-stranded structures are formed in low salt. Anti-parallel quadruplex structures are favored in the presence of high concentrations, 140 mM, of sodium. External loop, also known as propeller, parallel type structures are favored in the presence of high concentrations, 100 mM, of potassium in the presence of either 5 or 140 mM sodium. The cation dependence of the CD spectra of the vertebrate telomere repeat DNAs is distinctly different from that of the telomere repeats of Tetrahymena and Oxytricha as well as that of the thrombin binding aptamer. These results indicate that the external loop structures may be present in vertebrate telomeres under the conditions of high potassium and low sodium concentration found in nuclei.

Animals↗
PubMed2005

8-methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures.

This paper concerns the Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) structural studies of the quadruple helix arrangements adopted by three tailored oligodeoxyribonucleotide analogues, namely d(TG(Me)GGT), d(TGG(Me)GT) and d(TGGG(Me)T), where dG(Me) represents a 8-methyl-2'-deoxyguanosine residue. The results of this study clearly demonstrate that the effects of the incorporation of dG(Me) instead of a dG residue are strongly dependant upon the positioning of a single base replacement along the sequence. As such, d(TG(Me)GGT), d(TGG(Me)GT) have been found to form 4-fold symmetric quadruplexes with all strands parallel and equivalent to each other, each more stable than their natural counterpart. NMR experiments clearly indicate that [d(TG(Me)GGT)]4 possesses a G(Me)-tetrad with all dG(Me) residues in a syn-glycosidic conformation while an anti-arrangement is apparent for the four dG(Me) of [d(TGG(Me)GT)]4. As the two complexes show a quite different CD behaviour, a possible relationship between the presence of residues adopting syn-glycosidic conformations and CD profiles is briefly discussed. As far as d(TGGG(Me)T) is concerned, NMR data indicate that at 25 degrees C it exists primarily as a single-strand conformation in equilibrium with minor amounts of a quadruplex structure.

Circular Dichroism↗
PubMed2006

Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405-16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93-102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.

Computer Simulation↗
PubMed2005

Kinetics and thermodynamics of G-quadruplexes.

The melting of tetramolecular DNA or RNA quadruplexes is kinetically irreversible. However, rather than being a hindrance, this kinetic inertia allows us to study association and dissociation processes independently. General rules have been extended to longer DNA motifs or sequences containing modified bases such as 8-oxo or 7-deaza guanine. Results were compared with the canonical TG4T and TG5T tetramers: we demonstrate huge differences (up to 10(5)-fold) in the association constants of these quadruplexes depending on primary sequence.

DNA↗
PubMed2005

Pharmacodynamics of the G-quadruplex-stabilizing telomerase inhibitor 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium methosulfate (RHPS4) in vitro: activity in human tumor cells correlates with telomere length and can be enhanced, or antagonized, with cytotoxic agents.

Telomeric integrity is required to maintain the replicative ability of cancer cells and is a target for the G-quadruplex-stabilizing drug 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium methosulfate (RHPS4). We report a senescent-like growth arrest in MCF-7 breast cancer cells, within 14 to 17 days, and a reduction in telomere length (from 5.2 kilobases (kb) to 4.7 and 4.3 kb after 17 days of treatment at 0.5 and 1 microM, respectively). These effects occurred at noncytotoxic drug concentrations (doses < 1 microM over a 14-day exposure) compatible with long-term drug dosing. The telomere length of cancer cells influences their sensitivity to growth inhibition by RHPS4: mutant (mt) human telomerase reverse transcriptase (hTERT)-expressing MCF-7 cells [short telomere restriction fragment (TRF) length, 1.9 kb; IC50, 0.2 microM] were 10 times more sensitive to RHPS4 compared with wild-type (wt) hTERT-expressing, vector-transfected control cells (longer TRF-length 5.2 kb; IC50 2 microM) in the 5 day SRB assay. This relationship was corroborated in a panel of 36 human tumor xenografts grown in vitro showing a positive correlation between telomere length and growth inhibitory potency of RHPS4 (15-day clonogenic assay, r = 0.75). These observations are consistent with loss of the protective capping status of telomeres mediated by RHPS4 G-quadruplex-stabilization, thus leading to greater susceptibility of cells with shorter telomeres. In combination studies, paclitaxel (Taxol), doxorubicin (Adriamycin), and the experimental therapeutic agent 17-(allylamino)-17-demethoxygeldanamycin, which inhibits the 90-kDa heat shock protein, conferred enhanced sensitivity in RHPS4 treated MCF-7 cells, whereas the DNA-interactive temozolomide and cisplatin antagonized the action of RHPS4. Our results support the combined use of certain classes of cytotoxic anticancer agents with RHPS4 to enhance potential clinical benefit.

Acridines↗
PubMed2026

Alternative quadruplex real-time PCR reactions for detection and discrimination of Streptococcus pneumoniae serotypes within serogroup 6.

UNLABELLED: Streptococcus pneumoniae causes significant morbidity and mortality worldwide, and serotyping is important to assess the burden of disease that is vaccine preventable. For serotyping, the Centers for Disease Control and Prevention (CDC) use a series of 12 real-time multiplex PCRs (rmPCRs) performed in quadruplex reactions; however, rmPCR reaction 5 (rmPCR-5) for serotypes 6A, 6B, 6C, and 6D often failed at low DNA concentrations. This study investigated the cause of rmPCR-5 failure and provided alternative rmPCRs to resolve this issue. Quadruplex rmPCR target sequences were compared to S. pneumoniae reference genomes. Reactions rmPCR-5 [6ABCD, 6AB, 6BD, and 6CD] and rm-PCR-11 [37, 10F, 11BC, and 18CFBA] were compared to alternative reactions rmPCR-A1 [6ABCD, 10F, 11BC, and 18CFBA] and rmPCR-A2 [37, 6AB, 6BD, and 6CD]. All rmPCRs were tested using 10-fold serial dilutions of DNA from representative serotypes, and analytical specificity was assessed using DNA from other S. pneumoniae serotypes or various streptococci and Gram-positive cocci. Failure of rmPCR-5 was associated with overlapping 6ABCD and 6BD targets. Separation of these targets in the alternative rmPCRs-A1 and rmPCR-A2 allowed sensitive and specific detection and discrimination of serotypes 6A, 6B, 6C, and 6D, without impacting the detection of serotypes 10F, 11BC, 18CFBA, and 37. This study highlights the importance of rigorous author and peer-review to avoid manuscript errors and unintended consequences. By explaining what caused rmPCR-5 failure and proposing alternative reactions rmPCRs-A1 and rmPCR-A2, this study demonstrates the value of scientific collaboration to ensure molecular assays best serve the scientific community. IMPORTANCE: Streptococcus pneumoniae is a bacterium that can cause life-threatening infections like pneumonia and meningitis, leading to millions of deaths worldwide each year. A key feature enabling S. pneumoniae to cause disease is its sugar coating, allowing it to avoid the immune system. These surface sugars are the target of S. pneumoniae vaccines. However, vaccines only protect against some sugars and understanding which ones are on the surface of S. pneumoniae is called "serotyping." The Centers for Disease Control and Prevention (CDC) have protocols that allow us to predict S. pneumoniae serotypes by looking at its DNA. We found errors in the CDC protocols and provided a simple solution to fix them. Ultimately, having accurate serotyping protocols allows us to know how much disease is preventable by vaccine, allows us to monitor how well vaccine are working, and helps develop new vaccines if needed.

Streptococcus pneumoniae↗
PubMed2005

The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function.

Interference with telomerase and telomere maintenance is emerging as an attractive target for anticancer therapies. Ligand-induced stabilization of G-quadruplex formation by the telomeric DNA single-stranded 3' overhang inhibits telomerase from catalyzing telomeric DNA synthesis and from capping telomeric ends. We report here the effects of a 3,6,9-trisubstituted acridine compound, BRACO-19, on telomerase function in vitro and in vivo. The biological activity of BRACO-19 was evaluated in the human uterus carcinoma cell line UXF1138L, which has very short telomeres (2.7 kb). In vitro, nuclear human telomerase reverse transcriptase (hTERT) expression was drastically decreased after 24 hours, induction of cellular senescence and complete cessation of growth was seen after 15 days, paralleled by telomere shortening of ca. 0.4 kb. In vivo, BRACO-19 was highly active as a single agent against early-stage (68 mm(3)) tumors in a s.c. growing xenograft model established from UXF1138L cells, if given chronically at 2 mg per kg per day i.p. BRACO-19 produced growth inhibition of 96% compared with controls accompanied by partial regressions (P < 0.018). Immunostaining of xenograft tissues showed that this response was paralleled by loss of nuclear hTERT protein expression and an increase in atypical mitoses indicative of telomere dysfunction. Cytoplasmic hTERT expression and its colocalization with ubiquitin was observed suggesting that hTERT is bound to ubiquitin and targeted for enhanced degradation upon BRACO-19 treatment. This is in accord with a model of induced displacement of telomerase from the telomere. The in vitro and in vivo data presented here is consistent with the G-quadruplex binding ligand BRACO-19 producing an anticancer effect by inhibiting the capping and catalytic functions of telomerase.

Acridines↗
PubMed2006

The G-quadruplex ligand telomestatin inhibits POT1 binding to telomeric sequences in vitro and induces GFP-POT1 dissociation from telomeres in human cells.

Telomestatin is a potent G-quadruplex ligand that specifically interacts with the 3' telomeric overhang, leading to its degradation and that induces a delayed senescence and apoptosis of cancer cells. Protection of Telomere 1 (POT1) was recently identified as a specific single-stranded telomere-binding protein involved in telomere capping and T-loop maintenance. We showed here that a telomestatin treatment inhibits POT1 binding to the telomeric overhang in vitro. The treatment of human EcR293 cells by telomestatin induces a dramatic and rapid delocalization of POT1 from its normal telomere sites but does not affect the telomere localization of the double-stranded telomere-binding protein TRF2. Thus, we propose that G-quadruplex stabilization at telomeric G-overhang inactivates POT1 telomeric function, generating a telomere dysfunction in which chromosome ends are no longer properly protected.

Cell Line↗
PubMed2003

Telomerase inhibition and cell growth arrest by G-quadruplex interactive agent in multiple myeloma.

OBJECTIVE: The aim of this study was to test the efficacy of telomerase inhibitor (TMPyP4 [tetra(N-methyl-4-pyridyl)-porphyrin chloride]; a G-quadruplex-intercalating porphyrin) as a potential therapeutic agent for multiple myeloma. MATERIALS AND METHODS: We studied telomere length, telomerase activity, and effect of telomerase inhibition in multiple myeloma cells. Several myeloma cell lines were analyzed for telomerase activity, telomere length, and gene expression. Three myeloma cell lines (U266, ARH77, and ARD) were treated with TMPyP4 for 3-4 weeks. Viable cell number was assessed by trypan blue exclusion, and nature of cell death was determined by annexin labeling and/or DNA fragmentation. In situ oligo ligation technique was used to identify specific DNase I-type DNA cleavage. RESULTS: We report high telomerase activity and shortened telomeres in myeloma cells compared to normal B cells. We have also observed inhibition of telomerase activity, reduction in telomere length, and decline of myeloma cell growth, as measured by trypan blue dye exclusion, following exposure to TMPyP4. Exposure to porphyrin reduced telomerase activity of U266, ARH77, and ARD myeloma cells by 98%, 92%, and 99%, respectively. Exposure to porphyrin had no effect on viability for the first 14 days, followed by death of 75-90% of cells over the next 2 weeks. The nature of cell death was apoptotic, as determined by annexin and DNA nick labeling. Majority of cells showed DNA fragmentation specific to caspase-3-activated DNase I. CONCLUSIONS: These results demonstrate anti-proliferative activity of G-quadruplex-intercalating agents, and suggest telomerase as an important therapeutic target for myeloma therapy.

Antineoplastic Agents↗
PubMed1999

Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells.

A series of cationic porphyrins has been identified as G-quadruplex interactive agents (QIAs) that stabilize telomeric G-quadruplex DNA and thereby inhibit human telomerase; 50% inhibition of telomerase activity was achieved in HeLa cell-free extract at porphyrin concentrations in the range < or = 50 microM. Cytotoxicity of the porphyrins in vitro was assessed in normal human cells (fibroblast and breast) and human tumor cells representing models selected for high telomerase activity and short telomeres (breast carcinoma, prostate, and lymphoma). In general, the cytotoxicity (EC50, effective concentration for 50% inhibition of cell proliferation) against normal and tumor cells was > 50 microM. The porphyrins were readily absorbed into tumor cell nuclei in culture. Inhibition of telomerase activity in MCF7 cells by subcytotoxic concentrations of TMPyP4 showed time and concentration dependence at 1-100 microM TMPyP4 over 15 days in culture (10 population doubling times). The inhibition of telomerase activity was paralleled by a cell growth arrest in G2-M. These results suggest that relevant biological effects of porphyrins can be achieved at concentrations that do not have general cytotoxic effects on cells. Moreover, the data support the concept that a rational, structure-based approach is possible to design novel telomere-interactive agents with application to a selective and specific anticancer therapy.

Antineoplastic Agents↗
PubMed2004

Duplex, triplex and quadruplex PCR for the preimplantation genetic diagnosis (PGD) of cystic fibrosis (CF), an exhaustive approach.

Most of cystic fibrosis (CF) pre-implantation genetic diagnosis (PGD) cases described to date are limited to the detection of DeltaF508. Beside this predominant mutation, over 1000 mutations have been identified, rendering the development of a mutation-based PGD protocol impracticable. This is the reason why we, as well as the others, have developed PGD strategies on the basis of the identification of the pathogenic haplotype instead of the mutation(s). In a previous article, we reported the conditions for the co-amplification of two intragenic polymorphic markers and the F508 locus. Here we describe an improved protocol allowing the additional amplification of two new intragenic markers, intron 1 CA repeat (I1CA) and IVS17bTA. This new protocol should, theoretically, allow us to provide a diagnosis to all couples requiring PGD for CF. Using single lymphoblasts, we have tested four different PCR configurations, including one duplex, two triplexes and one quadruplex PCR. All of them gave results compatible with a clinical application. The number of single lymphoblasts tested in each series varied from 89 to 155. PCR efficiency ranged from 95.4 to 100%. A complete haplotype was achieved for 83.2 to 90.7% of the tested cells, with an allele drop out (ADO) rate comprised between 6.0 and 11.6%. We present here three cases that we performed either with the former test (one case using the triplex PCR combining F508, IVS8CA and IVS17bCA) or with the new one (one case using the triplex combining F508, I1CA and IVS17bTA and one case using a quadruplex test). We obtained two single pregnancies.

Adult↗
PubMed2006

Japanese population data for eight X-STR loci using two new quadruplex systems.

Using two new X-chromosome short tandem repeats (X-STR) multiplex (quadruplex) systems, we investigated Japanese population data (drawn from 401 individuals) for eight X-STR loci (DXS10011, DXS9898, DXS8377, HPRTB, DXS7132, DXS6797, GATA172D05, and DXS6807). Allele typing with the systems was successful for all loci. The combined powers of discrimination of the eight loci in men and women were 0.999997 and 0.9999999996, respectively. We conclude that combined analyses of the eight X-STR loci using these two quadruplex polymerase chain reaction systems represent a powerful tool for Japanese forensic practice.

Female↗
PubMed2004

Structural studies of oligonucleotides containing G-quadruplex motifs using AFM.

G-quadruplex DNAs are cyclic arrays of four guanine bases binding by Hoogsteen hydrogen bonds, found in the telomeric regions of chromosomes and in transcriptional regulatory regions of several important oncogenes. Here, we used high resolution atomic force microscopy (AFM) to observe a specific guanine (G) tetrad mediated complex formation of oligonucleotides containing a G-quadruplex motifs (G-ODN) combined with a palindromic sequence under physiological extracellular conditions. These oligonucleotides have been investigated in correlation to their immunostimulatory effects. We observed structural dependence on ion concentration and G-ODN concentration, where high concentration self-assembled DNA networks were formed.

Adjuvants, Immunologic↗
PubMed2004

Effect of gamma-hydroxypropano deoxyguanosine, the major acrolein-derived adduct, on monomolecular quadruplex structure of telomeric repeat d(TTAGGG)(4).

The three oligodeoxyribonucleotides (ODNs) a-c, having the telomeric repeat d(TTAGGG)(4) sequence and incorporating gamma-hydroxypropano deoxyguanosine at different positions, were synthesized. Gel electrophoresis and CD analyses indicated that the ODNs assume monomolecular quadruplex structures in Na+ and in K+ buffers. The T(m) values, obtained by CD melting experiments, showed that the presence of the acrolein-dG adduct into the ODN b decreases the thermal stability of the monomolecular quadruplex structure in Na+ solution, whereas for a and c no significant effect could be detected in the same experimental conditions. On the contrary, all ODNs a-d show the same behaviour in K+ buffer. These findings are briefly discussed.

Acrolein↗
PubMed2006

Synthesis and G-quadruplex stabilizing properties of a series of oxazole-containing macrocycles.

The synthesis of 24-membered macrocycles containing four, six, and seven oxazole moieties is described. Selected compounds were evaluated for their ability to specifically bind and stabilize G-quadruplex DNA and for cytotoxic activity. An unexpected oxidative cleavage reaction afforded a macrocyclic imide that was also evaluated for G-quadruplex stabilizing and cytotoxic activity.

DNA↗
PubMed2004

Inhibition of DNA synthesis by K+-stabilised G-quadruplex promotes allelic preferential amplification.

PCR preferential amplification consists of the inefficient amplification of one allele in a heterozygous sample. Here, we report the isolation of a GC-rich human minisatellite, MsH43, that undergoes allelic preferential amplification during PCR. This effect requires the existence of a (TGGGGC)(4) motif that is able to form a G-quadruplex in the presence of K(+). This structure interferes with the DNA synthesis of the alleles harbouring this motif during PCR The present results are the first demonstration that the formation of G-quadruplex can be one of the mechanisms involved in some kinds of preferential amplification.

Base Sequence↗