51
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Gerrard SR, Hardiman C, Shelbourne M, Nandhakumar I, Nordén B, Brown T. A new modular approach to nanoassembly: stable and addressable DNA nanoconstructs via orthogonal click chemistries. ACS NANO 2012; 6:9221-9228. [PMID: 22989197 DOI: 10.1021/nn3035759] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures.
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Affiliation(s)
- Simon R Gerrard
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ. UK
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52
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53
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Larsen AF, Nielsen MC, Ulven T. Tetrasubstituted Phenanthrolines as Highly Potent, Water-Soluble, and Selective G-Quadruplex Ligands. Chemistry 2012; 18:10892-902. [DOI: 10.1002/chem.201200081] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/29/2012] [Indexed: 11/11/2022]
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54
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Ong CW, Liu MC, Lee KD, Chang KW, Yang YT, Tung HW, Fox KR. Synthesis of bisquinoline–pyrrole oligoamide as G-quadruplex binding ligand. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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55
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Gray RD, Chaires JB. Isothermal folding of G-quadruplexes. Methods 2012; 57:47-55. [PMID: 22525787 PMCID: PMC3407330 DOI: 10.1016/j.ymeth.2012.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/06/2012] [Accepted: 04/07/2012] [Indexed: 11/26/2022] Open
Abstract
Thermodynamic studies of G-quadruplex stability are an essential complement to structures obtained by NMR or X-ray crystallography. An understanding of the energetics of quadruplex folding provides a necessary foundation for the physical interpretation of quadruplex formation and reactivity. While thermal denaturation methods are most commonly used to evaluate quadruplex stability, it is also possible to study folding using isothermal titration methods. G-quadruplex folding is tightly coupled to specific cation binding. We describe here protocols for monitoring the cation-driven quadruplex folding transition using circular dichroism or absorbance, and for determination of the distribution of free and bound cation using a fluorescence indicator. Together these approaches provide insight into quadruplex folding at constant temperature, and characterize the linkage between cation binding and folding.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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56
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Rusling DA, Nandhakumar IS, Brown T, Fox KR. Triplex-directed recognition of a DNA nanostructure assembled by crossover strand exchange. ACS NANO 2012; 6:3604-3613. [PMID: 22443318 DOI: 10.1021/nn300718z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA has been widely exploited for the self-assembly of nanosized objects and arrays that offer the potential to act as scaffolds for the spatial positioning of molecular components with nanometer precision. Methods that allow the targeting of components to specific locations within these structures are therefore highly sought after. Here we report that the triplex approach to DNA recognition, which relies on the specific binding of an oligonucleotide within the major groove of double-helical DNA, can be exploited to recognize specific loci within a DNA double-crossover tile and array, a nanostructure assembled by crossover strand exchange. The oligonucleotide can be targeted to both crossover and non-crossover strands and, surprisingly, across the region spanning the crossover junction itself. Moreover, by attaching biotin to the end of the oligonucleotide, we show that streptavidin molecules can be recruited to precise locations within a DX array, with an average spacing of 31.9 (±1.3) nm. This is a promising approach that could be exploited to introduce other components compatible with oligonucleotide synthesis into the wide variety of DNA nanostructures assembled by crossover strand exchange, such as those generated by DNA origami.
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Affiliation(s)
- David A Rusling
- Centre for Biological Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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57
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Renčiuk D, Zhou J, Beaurepaire L, Guédin A, Bourdoncle A, Mergny JL. A FRET-based screening assay for nucleic acid ligands. Methods 2012; 57:122-8. [PMID: 22465278 DOI: 10.1016/j.ymeth.2012.03.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/12/2012] [Accepted: 03/17/2012] [Indexed: 11/28/2022] Open
Abstract
Some of the most serious diseases are characterized by the presence of a specific secondary structure within DNA or RNA, often in the promoter or the coding region of the responsible gene, that enhances or disrupts expression of the protein. Structural elements that impact cellular function may also be formed in other genomic regions such as telomeres. Compounds that interact with such structural elements may be useful in diagnosis or treatment of patients. In this report, we present a FRET melting assay that allows testing of libraries of compounds against four different nucleic acid structures. Compounds are tested to determine whether they stabilize preformed secondary structures (i.e., whether they cause an increase in melting temperature (T(m))). This property is described by the ΔT(m) parameter, which is the difference between the T(m) of the compound-stabilized structure and the T(m) of the unbound structure. Model oligonucleotides are labeled with FAM as a fluorescent donor and TAMRA as an acceptor. The intensity of FAM fluorescence is recorded as a function of temperature. Melting temperatures are determined by the FRET method in 96-well plates; this assay could easily be converted into 384-well format.
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Affiliation(s)
- Daniel Renčiuk
- INSERM, U869, ARNA Laboratory, European Institute of Chemistry and Biology, 2 rue Robert Escarpit, F-33600 Pessac, France.
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58
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Zhou S, Acquaah-Harrison G, Jack KD, Bergmeier SC, Hines JV. Ligand-induced changes in T box antiterminator RNA stability. Chem Biol Drug Des 2011; 79:202-8. [PMID: 22117759 DOI: 10.1111/j.1747-0285.2011.01274.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
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Affiliation(s)
- Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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59
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Dash J, Das RN, Hegde N, Pantoş GD, Shirude PS, Balasubramanian S. Synthesis of bis-indole carboxamides as G-quadruplex stabilizing and inducing ligands. Chemistry 2011; 18:554-64. [PMID: 22161991 DOI: 10.1002/chem.201102556] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Indexed: 11/11/2022]
Abstract
The design and synthesis of a series of bis-indole carboxamides with varying amine containing side chains as G-quadruplex DNA stabilising small molecules are reported. Their interactions with quadruplexes have been evaluated by means of Förster resonance energy transfer (FRET) melting analysis, UV/Vis spectroscopy, circular dichroism spectroscopy and molecular modelling studies. FRET analysis indicates that these ligands exhibit significant selectivity for quadruplex over duplex DNA, and the position of the carboxamide side chains is of paramount importance in G-quadruplex stabilisation. UV/Vis titration studies reveal that bis-indole ligands bind tightly to quadruplexes and show a three- to fivefold preference for c-kit2 over h-telo quadruplex DNA. CD studies revealed that bis-indole carboxamide with a central pyridine ring induces the formation of a single, antiparallel, conformation of the h-telo quadruplex in the presence and absence of added salt. The chirality of h-telo quadruplex was transferred to the achiral ligand (induced CD) and the formation of a preferred atropisomer was observed.
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Affiliation(s)
- Jyotirmayee Dash
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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60
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Zagotto G, Ricci A, Vasquez E, Sandoli A, Benedetti S, Palumbo M, Sissi C. Tuning G-Quadruplex vs Double-Stranded DNA Recognition in Regioisomeric Lysyl-Peptidyl-Anthraquinone Conjugates. Bioconjug Chem 2011; 22:2126-35. [DOI: 10.1021/bc200389w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Antonio Ricci
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Elena Vasquez
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Andrea Sandoli
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Silvia Benedetti
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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61
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Guittat L, Alberti P, Gomez D, De Cian A, Pennarun G, Lemarteleur T, Belmokhtar C, Paterski R, Morjani H, Trentesaux C, Mandine E, Boussin F, Mailliet P, Lacroix L, Riou JF, Mergny JL. Targeting human telomerase for cancer therapeutics. Cytotechnology 2011; 45:75-90. [PMID: 19003245 DOI: 10.1007/s10616-004-5127-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 09/21/2004] [Indexed: 01/28/2023] Open
Abstract
The enzyme telomerase is involved in the replication of telomeres, specialized structures that cap and protect the ends of chromosomes. Its activity is required for maintenance of telomeres and for unlimited lifespan, a hallmark of cancer cells. Telomerase is overexpressed in the vast majority of human cancer cells and therefore represents an attractive target for therapy. Several approaches have been developed to inhibit this enzyme through the targeting of its RNA or catalytic components as well as its DNA substrate, the single-stranded 3'-telomeric overhang. Telomerase inhibitors are chemically diverse and include modified oligonucleotides as well as small diffusable molecules, both natural and synthetic. This review presents an update of recent investigations pertaining to these agents and discusses their biological properties in the context of the initial paradigm that the exposure of cancer cells to these agents should lead to progressive telomere shortening followed by a delayed growth arrest response.
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Affiliation(s)
- Lionel Guittat
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle USM503, INSERM U 565, CNRS UMR 5153, 43, rue Cuvier, 75231, Paris cedex 05, France
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62
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Chiou CC, Chen SW, Luo JD, Chien YT. Monitoring triplex DNA formation with fluorescence resonance energy transfer between a fluorophore-labeled probe and intercalating dyes. Anal Biochem 2011; 416:1-7. [PMID: 21609711 DOI: 10.1016/j.ab.2011.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) are sequence-dependent DNA binders that may be useful for DNA targeting and detection. A sensitive and convenient method to monitor triplex formation by a TFO and its target DNA duplex is required for the application of TFO probes. Here we describe a novel design by which triplex formation can be monitored homogeneously without prelabeling the target duplex. The design uses a TFO probe tagged with a fluorophore that undergoes fluorescence resonance energy transfer with fluorescent dyes that intercalate into the target duplex. Through color compensation analysis, the specific emission of the TFO probe reveals the status of the triple helices. We used this method to show that triple helix formation with TFOs is magnesium dependent. We also demonstrated that the TFO probe can be used for detection of sequence variation in melting analysis and for DNA quantitation in real-time polymerase chain reaction.
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Affiliation(s)
- Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 333, Taiwan.
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63
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Dash J, Waller ZAE, Pantoş GD, Balasubramanian S. Synthesis and binding studies of novel diethynyl-pyridine amides with genomic promoter DNA G-quadruplexes. Chemistry 2011; 17:4571-81. [PMID: 21387430 DOI: 10.1002/chem.201003157] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Indexed: 12/19/2022]
Abstract
Herein, we report the design, synthesis and biophysical evaluation of novel 1,2,3-triazole-linked diethynyl-pyridine amides and trisubstituted diethynyl-pyridine amides as promising G-quadruplex binding ligands. We have used a Cu(I)-catalysed azide-alkyne cycloaddition click reaction to prepare the 1,2,3-triazole-linked diethynyl-pyridine amides. The G-quadruplex DNA binding properties of the ligands have been examined by using a Förster resonance energy transfer (FRET) melting assay and surface plasmon resonance (SPR) experiments. The investigated compounds are conformationally flexible, having free rotation around the triple bond, and exhibit enhanced G-quadruplex binding stabilisation and specificity between intramolecular promoter G-quadruplex DNA motifs compared to the first generation of diaryl-ethynyl amides (J. Am. Chem. Soc. 2008, 130, 15950-15956). The ligands show versatility in molecular recognition and promising G-quadruplex discrimination with 2-50-fold selectivity exhibited between different intramolecular promoter G-quadruplexes. Circular dichroism (CD) spectroscopic analysis suggested that at higher concentration these ligands disrupt the c-kit2 G-quadruplex structure. The studies validate the design concept of the 1,3-diethynyl-pyridine-based scaffold and demonstrate that these ligands exhibit not only significant selectivity over duplex DNA but also variation in G-quadruplex interaction properties based on small chemical changes in the scaffold, leading to unprecedented differential recognition of different DNA G-quadruplex sequences.
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Affiliation(s)
- Jyotirmayee Dash
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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64
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You Y, Tataurov AV, Owczarzy R. Measuring thermodynamic details of DNA hybridization using fluorescence. Biopolymers 2011; 95:472-86. [PMID: 21384337 PMCID: PMC3082624 DOI: 10.1002/bip.21615] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/31/2011] [Accepted: 02/21/2011] [Indexed: 11/11/2022]
Abstract
Modern real-time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high-throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides in such a way that changes of fluorescence intensity with temperature indicated progression of denaturation. When fluorescence melting data were compared with traditional ultraviolet optical experiments, commonly used dye/quencher combinations, like fluorescein and tetramethylrhodamine, showed substantial discrepancies. We have therefore screened 22 commercially available fluorophores and quenchers for their ability to reliably report annealing and melting transitions. Dependence of fluorescence on temperature and pH was also investigated. The optimal performance was observed using Texas Red or ROX dyes with Iowa Black RQ or Black Hole quenchers. These labels did not alter two-state nature of duplex melting process and provided accurate melting temperatures, free energies, enthalpies, and entropies. We also suggest a new strategy for determination of DNA duplex thermodynamics where concentration of a dye-labeled strand is kept constant and its complementary strand modified with a quencher is added at increasing excess. These methodological improvements will help build predictive models of nucleic acid hybridization. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 472–486, 2011.
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Affiliation(s)
- Yong You
- Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, IA, USA
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65
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Wang H, Li J, Wang Y, Jin J, Yang R, Wang K, Tan W. Combination of DNA ligase reaction and gold nanoparticle-quenched fluorescent oligonucleotides: a simple and efficient approach for fluorescent assaying of single-nucleotide polymorphisms. Anal Chem 2011; 82:7684-90. [PMID: 20726510 DOI: 10.1021/ac101503t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new fluorescent sensing approach for detection of single-nucleotide polymorphisms (SNPs) is proposed based on the ligase reaction and gold nanoparticle (AuNPs)-quenched fluorescent oligonucleotides. The design exploits the strong fluorescence quenching of AuNPs for organic dyes and the difference in noncovalent interactions of the nanoparticles with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), where ssDNA can be adsorbed onto the surface of AuNPs while dsDNA cannot be. In the assay, two half primer DNA probes, one being labeled with a dye and the other being phosphorylated, were first incubated with a target DNA template. In the presence of DNA ligase, the two captured ssDNAs are linked for the perfectly matched DNA target to form a stable duplex, but the duplex could not be formed by the single-base mismatched DNA template. After addition of AuNPs, the fluorescence of dye-tagged DNA probe will be efficiently quenched unless the perfectly matched DNA target is present. To demonstrate the feasibility of this design, the performance of SNP detection using two different DNA ligases, T4 DNA ligase and Escherichia coli DNA ligase, were investigated. In the case of T4 DNA ligase, the signal enhancement of the dye-tagged DNA for perfectly matched DNA target is 4.6-fold higher than that for the single-base mismatched DNA. While in the presence of E. coli DNA ligase, the value raises to be 30.2, suggesting excellent capability for SNP discrimination.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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66
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Holt PA, Buscaglia R, Trent JO, Chaires JB. A Discovery Funnel for Nucleic Acid Binding Drug Candidates. Drug Dev Res 2010; 72:178-186. [PMID: 21566705 DOI: 10.1002/ddr.20414] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Computational approaches are becoming increasingly popular for the discovery of drug candidates against a target of interest. Proteins have historically been the primary targets of many virtual screening efforts. While in silico screens targeting proteins has proven successful, other classes of targets, in particular DNA, remain largely unexplored using virtual screening methods. With the realization of the functional importance of many non-cannonical DNA structures such as G-quadruplexes, increased efforts are underway to discover new small molecules that can bind selectively to DNA structures. Here, we describe efforts to build an integrated in silico and in vitro platform for discovering compounds that may bind to a chosen DNA target. Millions of compounds are initially screened in silico for selective binding to a particular structure and ranked to identify several hundred best hits. An important element of our strategy is the inclusion of an array of possible competing structures in the in silico screen. The best hundred or so hits are validated experimentally for binding to the actual target structure by a high-throughput 96-well thermal denaturation assay to yield the top ten candidates. Finally, these most promising candidates are thoroughly characterized for binding to their DNA target by rigorous biophysical methods, including isothermal titration calorimetry, differential scanning calorimetry, spectroscopy and competition dialysis.This platform was validated using quadruplex DNA as a target and a newly discovered quadruplex binding compound with possible anti-cancer activity was discovered. Some considerations when embarking on virtual screening and in silico experiments are also discussed.
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Affiliation(s)
- Patrick A Holt
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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67
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Seela F, Jiang D, Budow S. Triplexes with 8-Aza-2'-deoxyisoguanosine replacing protonated dC: probing third strand stability with a fluorescent nucleobase targeting duplex DNA. Chembiochem 2010; 11:1443-50. [PMID: 20544775 DOI: 10.1002/cbic.201000162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The fluorescent 8-aza-2'-deoxyisoguanosine (4) as well as the parent 2'-deoxyisoguanosine (1) were used as protonated dCH(+) surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH(+) are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4. Third-strand binding of oligonucleotides with 4, opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third-strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third-strand binding more flexibility.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster Germany
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68
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Bejugam M, Gunaratnam M, Müller S, Sanders DA, Sewitz S, Fletcher JA, Neidle S, Balasubramanian S. Targeting the c-Kit Promoter G-quadruplexes with 6-Substituted Indenoisoquinolines. ACS Med Chem Lett 2010; 1:306-10. [PMID: 24900212 DOI: 10.1021/ml100062z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 06/24/2010] [Indexed: 11/30/2022] Open
Abstract
Herein, we demonstrate the design, synthesis, biophysical properties, and preliminary biological evaluation of 6-substituted indenoisoquinolines as a new class of G-quadruplex stabilizing small molecule ligands. We have synthesized 6-substituted indenoisoquinolines 1a-e in two steps from commercially available starting materials with excellent yields. The G-quadruplex stabilization potential of indenoisoquinolines 1a-e was evaluated by fluorescence resonance energy transfer-melting analysis, which showed that indenoisoquinolines show a high level of stabilization of various G-quadruplex DNA structures. Indenoisoquinolines demonstrated potent inhibition of cell growth in the GIST882 patient-derived gastrointestinal stromal tumor cell line, accompanied by inhibition of both c-Kit transcription and KIT oncoprotein levels.
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Affiliation(s)
- Mallesham Bejugam
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Mekala Gunaratnam
- Cancer Research UK Biomolecular Structure Group, School of Pharmacy, University of London, 29-39 Brunswick Square, London WC19 1AX, United Kingdom
| | - Sebastian Müller
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Deborah A. Sanders
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Sven Sewitz
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | | | - Stephen Neidle
- Cancer Research UK Biomolecular Structure Group, School of Pharmacy, University of London, 29-39 Brunswick Square, London WC19 1AX, United Kingdom
| | - Shankar Balasubramanian
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, United Kingdom
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
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69
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Lou C, Xiao Q, Brennan L, Light ME, Vergara-Irigaray N, Atkinson EM, Holden-Dye LM, Fox KR, Brown T. Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine. Bioorg Med Chem 2010; 18:6389-97. [PMID: 20674370 DOI: 10.1016/j.bmc.2010.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 07/01/2010] [Accepted: 07/06/2010] [Indexed: 10/19/2022]
Abstract
2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability with their target duplexes as measured by ultraviolet/fluorescence melting and DNase I footprinting. The incorporation of MEPU into TFOs renders them resistant to degradation by serum nucleases.
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Affiliation(s)
- Chenguang Lou
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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70
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Guédin A, Gros J, Alberti P, Mergny JL. How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res 2010; 38:7858-68. [PMID: 20660477 PMCID: PMC2995061 DOI: 10.1093/nar/gkq639] [Citation(s) in RCA: 316] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compared here 80 different sequences containing four tracts of three guanines with loops of variable length (between 1 and 15 bases for unmodified sequences, up to 30 for fluorescently labeled oligonucleotides). All sequences were capable of forming stable quadruplexes, with Tm above physiological temperature in most cases. Unsurprisingly, the melting temperature was systematically lower in sodium than in potassium but the difference between both ionic conditions varied between 1 and >39°C (average difference: 18.3°C). Depending on the sequence context, and especially for G4 sequences involving two very short loops, the third one may be very long without compromising the stability of the quadruplex. A strong inverse correlation between total loop length and Tm was found in K+: each added base leads to a 2°C drop in Tm or ∼0.3 kcal/mol loss in ΔG°. The trend was less clear in Na+, with a longer than expected optimal loop length (up to 5 nt). This study will therefore extend the sequence repertoire of quadruplex-prone sequences, arguing for a modification of the widely used consensus (maximal loop size of 7 bases).
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Affiliation(s)
- Aurore Guédin
- INSERM, U869, European Institute of Chemistry and Biology, Bordeaux 2 University, 2 rue Robert Escarpit, Pessac F-33607, France
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71
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Schneider UV, Mikkelsen ND, Jøhnk N, Okkels LM, Westh H, Lisby G. Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids--TINA. Nucleic Acids Res 2010; 38:4394-403. [PMID: 20338879 PMCID: PMC2910062 DOI: 10.1093/nar/gkq188] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Twisted intercalating nucleic acid (TINA) is a novel intercalator and stabilizer of Hoogsteen type parallel triplex formations (PT). Specific design rules for position of TINA in triplex forming oligonucleotides (TFOs) have not previously been presented. We describe a complete collection of easy and robust design rules based upon more than 2500 melting points (Tm) determined by FRET. To increase the sensitivity of PT, multiple TINAs should be placed with at least 3 nt in-between or preferable one TINA for each half helixturn and/or whole helixturn. We find that ΔTm of base mismatches on PT is remarkably high (between 7.4 and 15.2°C) compared to antiparallel duplexes (between 3.8 and 9.4°C). The specificity of PT by ΔTm increases when shorter TFOs and higher pH are chosen. To increase ΔTms, base mismatches should be placed in the center of the TFO and when feasible, A, C or T to G base mismatches should be avoided. Base mismatches can be neutralized by intercalation of a TINA on each side of the base mismatch and masked by a TINA intercalating direct 3′ (preferable) or 5′ of it. We predict that TINA stabilized PT will improve the sensitivity and specificity of DNA based clinical diagnostic assays.
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Affiliation(s)
- Uffe V Schneider
- QuantiBact Inc, Department of Clinical Microbiology, Hvidovre Hospital, Kettegaards Alle 30, 2650 Hvidovre, Denmark.
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72
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Avila Figueroa A, Delaney S. Mechanistic studies of hairpin to duplex conversion for trinucleotide repeat sequences. J Biol Chem 2010; 285:14648-57. [PMID: 20228068 DOI: 10.1074/jbc.m109.061853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The expansion of a trinucleotide repeat sequence, such as CAG/CTG, has been pinpointed as the molecular basis for a number of neurodegenerative disorders. It has been proposed that as part of the expansion process, these repetitive sequences adopt non-B conformations such as hairpins. However, the prevalence of these hairpins and their contributions to the DNA expansion have not been well defined. In this work, we utilized a molecular beacon strategy to examine the stability of the (CAG)(10) hairpin and also its behavior in the presence of the complementary (CTG)(10) hairpin. We find that the two hairpins represent kinetically trapped species that can coexist but irreversibly convert to duplex upon thermal induction. Furthermore, as monitored by fluorescence and optical analysis, modifications to the base composition of either the loop or stem region have a profound effect on the ability of the trinucleotide repeat hairpins to convert to duplex. Additionally, the rate of duplex formation is also reduced with these loop and stem-modified hairpins. These results demonstrate that the trinucleotide repeat hairpins can convert to duplex via two independent mechanisms as follows: the loop-loop interactions found in kissing hairpins or the stem-stem interactions of a cruciform.
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73
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Elfeky S, Flower S, Masumoto N, D'Hooge F, Labarthe L, Chen W, Len C, James T, Fossey J. Diol Appended Quenchers for Fluorescein Boronic Acid. Chem Asian J 2010; 5:581-8. [DOI: 10.1002/asia.200900386] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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74
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Schneider UV, Severinsen JK, Géci I, Okkels LM, Jøhnk N, Mikkelsen ND, Klinge T, Pedersen EB, Westh H, Lisby G. A novel FRET pair for detection of parallel DNA triplexes by the LightCycler. BMC Biotechnol 2010; 10:4. [PMID: 20102641 PMCID: PMC2823659 DOI: 10.1186/1472-6750-10-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melting temperature of DNA structures can be determined on the LightCycler using quenching of FAM. This method is very suitable for pH independent melting point (Tm) determination performed at basic or neutral pH, as a high throughput alternative to UV absorbance measurements. At acidic pH quenching of FAM is not very suitable, since the fluorescence of FAM is strongly pH dependent and drops with acidic pH.Hoogsteen based parallel triplex helix formation requires protonation of cytosines in the triplex forming strand. Therefore, nucleic acid triplexes show strong pH dependence and are stable only at acidic pH. This led us to establish a new pH independent fluorophore based measuring system on the LightCycler for thermal stability studies of parallel triplexes. RESULTS A novel LightCycler FRET pair labelled with ATTO495 and ATTO647N was established for parallel triplex detection with antiparallel duplex as a control for the general applicability of these fluorophores for Tm determination. The ATTO fluorophores were pH stable from pH 4.5 to 7.5. Melting of triplex and duplex structures were accompanied by a large decrease in fluorescence intensity leading to well defined Tm and high reproducibility. Validation of Tm showed low intra- and inter-assay coefficient of variation; 0.11% and 0.14% for parallel triplex and 0.19% and 0.12% for antiparallel duplex. Measurements of Tm and fluorescence intensity over time and multiple runs showed great time and light stability of the ATTO fluorophores. The variance on Tm determinations was significant lower on the LightCycler platform compared to UV absorbance measurements, which enable discrimination of DNA structures with very similar Tm. Labelling of DNA probes with ATTO fluorophore increased Tm of antiparallel duplexes significantly, but not Tm of parallel triplexes. CONCLUSIONS We have established a novel pH independent FRET pair with high fluorescence signals on the LightCycler platform for both antiparallel duplex and parallel triplex formation. The method has been thoroughly validated, and is characterized by an excellent accuracy and reproducibility. This FRET pair is especially suitable for DeltaTm and Tm determinations of pH dependent parallel triplex formation.
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Affiliation(s)
- Uffe V Schneider
- QuantiBact Inc, Department of Clinical Microbiology, Hvidovre Hospital, Kettegaards Alle 30, 2650 Hvidovre, Denmark.
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75
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Abstract
A simple thermal melting experiment may be used to demonstrate the stabilization of a given structure by a ligand (usually a small molecule, sometimes a peptide). Preparation of the sample is straightforward, and the experiment itself requires an inexpensive apparatus. Furthermore, reasonably low amounts of sample are required. A qualitative analysis of the data is simple: An increase in the melting temperature (T(m)) indicates preferential binding to the folded form as compared to the unfolded form. However, it is perilous to derive an affinity constant from an increase in T(m) as other factors play a role.
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Affiliation(s)
- Aurore Guédin
- Equipe Santé, Laboratoire Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle USM 503, INSERM UR 565, CNRS UMR 5153, Paris, France
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76
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Gerrard SR, Edrees MM, Bouamaied I, Fox KR, Brown T. CG base pair recognition within DNA triple helices by modified N-methylpyrrolo-dC nucleosides. Org Biomol Chem 2010; 8:5087-96. [DOI: 10.1039/c0ob00119h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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Rusling DA, Rachwal PA, Brown T, Fox KR. The stability of triplex DNA is affected by the stability of the underlying duplex. Biophys Chem 2009; 145:105-10. [PMID: 19819611 DOI: 10.1016/j.bpc.2009.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/16/2009] [Accepted: 09/16/2009] [Indexed: 11/16/2022]
Abstract
We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C(+).GC and T.AT triplets) at pH 5.0 the T(m) is more than 10 degrees C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at either end. A similar effect is seen with triplex-forming oligonucleotides that contain stabilising analogues, for which the T(m) is higher for an intramolecular than an intermolecular duplex target. These results suggest that the use of simple intermolecular duplex targets may underestimate the triplex stabilisation that is produced by some nucleotide analogues.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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78
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Triple-helix DNA structural studies using a Love wave acoustic biosensor. Biosens Bioelectron 2009; 25:702-7. [PMID: 19748772 DOI: 10.1016/j.bios.2009.08.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 08/06/2009] [Accepted: 08/07/2009] [Indexed: 11/22/2022]
Abstract
The development of sensors for detecting the conformation of surface-attached molecules is an emerging field with significance in the pharmaceutical industry and in drug design. In this work, triplex-forming oligos (TFOs), a separate class of non-natural DNA bending agents that can affect the mechanical properties of DNA through the formation of triple-helical structures of specific conformation and/or flexibility, are used as a model system in combination with an acoustic biosensor to determine molecular geometrical features. In practice, the degree of bending of a specific DNA target caused by a particular TFO was evaluated by measuring the ratio of acoustic energy change over phase change observed during the binding of pre-formed triplex DNA molecules to the device surface. The DNA bending angle derived via acoustic measurements is in excellent agreement with previously reported values using molecular biology techniques. The reported acoustic technique appears quite appealing for the biophysical study of DNA molecules providing rapid qualitative and quantitative information, at the same time holding promise to be developed as a high-throughput method for the evaluation of DNA conformational changes.
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79
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Smargiasso N, Gabelica V, Damblon C, Rosu F, De Pauw E, Teulade-Fichou MP, Rowe JA, Claessens A. Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes. BMC Genomics 2009; 10:362. [PMID: 19660104 PMCID: PMC2736202 DOI: 10.1186/1471-2164-10-362] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 08/06/2009] [Indexed: 11/24/2022] Open
Abstract
Background Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS) in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro. Results We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes). The var gene family encodes PfEMP1, the parasite's major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q) to form stable G-quadruplex structures in vitro was confirmed using 1H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q. Conclusion This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family.
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Affiliation(s)
- Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, University of Liege, Liege, Belgium.
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80
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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81
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Rusling DA, Peng G, Srinivasan N, Fox KR, Brown T. DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine. Nucleic Acids Res 2009; 37:1288-96. [PMID: 19139069 PMCID: PMC2651792 DOI: 10.1093/nar/gkn1060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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82
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
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83
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Dash J, Shirude PS, Hsu STD, Balasubramanian S. Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes. J Am Chem Soc 2008; 130:15950-6. [PMID: 18980309 PMCID: PMC2746964 DOI: 10.1021/ja8046552] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report bis-phenylethynyl amide derivatives as a potent G-quadruplex binding small molecule scaffold. The amide derivatives were efficiently prepared in 3 steps by employing Sonogashira coupling, ester hydrolysis and a chemoselective amide coupling. Ligand-quadruplex recognition has been evaluated using a fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism (CD) and (1)H nuclear magnetic resonance (NMR) spectroscopy. While most of the G-quadruplex ligands reported so far comprise a planar, aromatic core designed to stack on the terminal tetrads of a G-quadruplex, these compounds are neither polycyclic, nor macrocyclic and have free rotation around the triple bond enabling conformational flexibility. Such molecules show very good binding affinity, excellent quadruplex:duplex selectivity and also promising discrimination between intramolecular promoter quadruplexes. Our results indicate that the recognition of the c-kit2 quadruplex by these ligands is achieved through groove binding, which favors the formation of a parallel conformation.
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Affiliation(s)
- Jyotirmayee Dash
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Pravin S. Shirude
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Shang-Te Danny Hsu
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Shankar Balasubramanian
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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84
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Zagotto G, Sissi C, Lucatello L, Pivetta C, Cadamuro SA, Fox KR, Neidle S, Palumbo M. Aminoacyl−Anthraquinone Conjugates as Telomerase Inhibitors: Synthesis, Biophysical and Biological Evaluation. J Med Chem 2008; 51:5566-74. [DOI: 10.1021/jm800160v] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Lorena Lucatello
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Claudia Pivetta
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Sergio A. Cadamuro
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Keith R. Fox
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Stephen Neidle
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom, CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
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85
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Dash J, Shirude PS, Balasubramanian S. G-quadruplex recognition by bis-indole carboxamides. Chem Commun (Camb) 2008:3055-7. [PMID: 18688346 PMCID: PMC2746961 DOI: 10.1039/b806042h] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Herein we report the de novo design and synthesis of a geometrically flexible bis-indole carboxamide and a constrained derivative, as a novel class of small molecule scaffold that exhibits high stabilization potential for DNA G-quadruplex sequences associated with the promoters of c-kit2 and c-myc.
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Affiliation(s)
- Jyotirmayee Dash
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
| | - Pravin S. Shirude
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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86
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Zhao Z, Peng G, Michels J, Fox KR, Brown T. Synthesis of anthraquinone oligonucleotides for triplex stabilization. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:921-5. [PMID: 18058509 DOI: 10.1080/15257770701506491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The synthesis of two anthraquinone phosphoramidites is described. In both cases the anthraquinone moiety is attached via a linker to the 5-position of a uracil base, allowing incorporation at any thymidine position in an oligonucleotide sequence. Anthraquinone-modified oligonucleotides have potential applications as triplex stabilizers and fluorescence quenchers.
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Affiliation(s)
- Zhengyun Zhao
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
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87
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Durand A, Brown T. Synthesis and properties of oligonucleotides containing a cholesterol thymidine monomer. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:785-94. [PMID: 18066901 DOI: 10.1080/15257770701501534] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Highly selective base-pair recognition makes DNA a suitable building block for orderly self-assembled structures. For some applications in nanotechnology DNA complexes need to be fixed onto surfaces. To fulfil this requirement on lipid membranes we have synthesised a thymidine monomer modified with a cholesterol moiety. Solution studies show that the melting temperature (Tm) of the duplex, with adjacent cholesterols on each strand, is much higher than that of the unmodified duplex.
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Affiliation(s)
- Adeline Durand
- School of Chemistry, University of Southampton, Highfield, Southampton, UK
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88
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Abstract
Melting curves are commonly used to determine the stability of folded nucleic acid structures and their interaction with ligands. This paper describes how the technique can be applied to study the properties of four-stranded nucleic acid structures that are formed by G-rich oligonucleotides. Changes in the absorbance (at 295nm), circular dichroism (at 260 or 295nm) or fluorescence of appropriately labelled oligonucleotides, can be used to measure the stability and kinetics of folding. This paper focuses on a fluorescence melting technique, and explains how this can be used to determine the T(m) (T((1/2))) of intramolecular quadruplexes and the effects of quadruplex-binding ligands. Quantitative analysis of these melting curves can be used to determine the thermodynamic (DeltaH, DeltaG, and DeltaS) and kinetic (k(1), k(-1)) parameters. The method can also be adapted to investigate the equilibrium between quadruplex and duplex DNA and to explore the selectivity of ligands for one or other structure.
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89
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Zagotto G, Sissi C, Moro S, Dal Ben D, Parkinson GN, Fox KR, Neidle S, Palumbo M. Amide bond direction modulates G-quadruplex recognition and telomerase inhibition by 2,6 and 2,7 bis-substituted anthracenedione derivatives. Bioorg Med Chem 2008; 16:354-61. [DOI: 10.1016/j.bmc.2007.09.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 09/11/2007] [Accepted: 09/19/2007] [Indexed: 10/22/2022]
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90
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Huppert JL. Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chem Soc Rev 2008; 37:1375-84. [DOI: 10.1039/b702491f] [Citation(s) in RCA: 391] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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91
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Bhattacharya P, Sharma S, Gochhait S, Bamezai RNK. Biophysical characterization of double-stranded oligonucleotides using ETBR and isothermal fluorescence spectroscopy: implication for SNP genotyping. ACTA ACUST UNITED AC 2007; 70:1163-73. [PMID: 18177945 DOI: 10.1016/j.jprot.2007.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 07/11/2007] [Accepted: 10/22/2007] [Indexed: 10/22/2022]
Abstract
The UV-absorption, fluorescence and CD spectra of aps 23 bp oligoduplexes were performed for potential diagnostic purpose. These oligonucleotide sequences were mimicked from natural mutations (mitochondrial genome) of human population (unpublished). This work was designed on the basis of hybridization of non-self complementary oligoduplexes (aps) containing no mismatch, one-mismatch and two-mismatches. Since melting temperature is dependent on concentration of the oligoduplex, various concentrations were used in this study protocol. The thermal spectra profiles (UV absorbance and fluorescence) of these oligoduplexes (aps) are different for a particular concentration, and can be implicated for mutations. -dF/dT (or dA/dT) vs T, lnK (or RlnK) vs TM, DeltaG vs TM, DeltaS vs TM and DeltaH vs TM are also variable for those sequences. All these thermodynamic data were calculated from absorbance (at 260 nm) data. On the contrary to the 23 bp oligoduplexes (aps), the PCR products of 97 bp and 256 bp length were genotyped with ETBR (excitation 530 nm, emission 600 nm) fluorimetrically. But our attempts to genotype these PCR sequences with isothermal UV absorbance spectroscopy were unsuccessful. Isothermal UV absorbance spectra has a limitation of sequence length. However, the structural conformation (all B-type) of the oligoduplexes (aps) was determined using CD. The minor discrepancy in CD spectra of these oligoduplexes are not significant for mutational analysis. 97 bp nested PCR product was an amplicon having either GcT or AcC mutation of mitochondria of normal human population, whereas 256 bp PCR product was an amplicon of human BRCA2 gene (NCBI Accession No. AY151039) of chromosome 13 having either A or G mutation at position -26.
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Affiliation(s)
- Pradip Bhattacharya
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
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92
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Rusling DA, Broughton-Head VJ, Tuck A, Khairallah H, Osborne SD, Brown T, Fox KR. Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine. Org Biomol Chem 2007; 6:122-9. [PMID: 18075656 DOI: 10.1039/b713088k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both the number and location of the modifications. BAU-containing oligonucleotides generate triplexes with extremely slow kinetics, as evidenced by 14 degrees C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 degrees C min(-1). The association kinetics were measured by analysis of the hysteresis profiles, temperature-jump relaxation and DNase I footprinting. We find that the slow kinetics are largely due to the decreased rate of dissociation; BAU modification has little effect on the association reaction. The sequence selectivity is also due to the slower dissociation of BAU from AT than other base pairs.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, UK.
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93
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Bejugam M, Sewitz S, Shirude PS, Rodriguez R, Shahid R, Balasubramanian S. Trisubstituted isoalloxazines as a new class of G-quadruplex binding ligands: small molecule regulation of c-kit oncogene expression. J Am Chem Soc 2007; 129:12926-7. [PMID: 17918848 DOI: 10.1021/ja075881p] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mallesham Bejugam
- The University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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94
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Lytton-Jean AKR, Han MS, Mirkin CA. Microarray detection of duplex and triplex DNA binders with DNA-modified gold nanoparticles. Anal Chem 2007; 79:6037-41. [PMID: 17614366 PMCID: PMC2525617 DOI: 10.1021/ac070635h] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarrays. The detection and screening of duplex DNA binders are important because these molecules, in many cases, are potential anticancer agents as well as toxins. Triplex DNA binders are also promising drug candidates. These molecules, in conjunction with triplex-forming oligonucleotides, could potentially be used to achieve control of gene expression by interfering with transcription factors that bind to DNA. Therefore, the ability to screen for these molecules in a high-throughput fashion could dramatically improve the drug screening process. The assay reported here provides excellent discrimination between strong, intermediate, and weak duplex and triplex DNA binders in a high-throughput fashion.
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Affiliation(s)
| | | | - Chad A. Mirkin
- *Author to whom correspondence should be addressed. ; Phone: (847) 467-3327; Fax: (847) 467-5123
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95
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Grossmann T, Röglin L, Seitz O. Triplex-basierte “molecular beacons” als modulare Sonden zur DNA-Detektion. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700289] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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96
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Grossmann TN, Röglin L, Seitz O. Triplex Molecular Beacons as Modular Probes for DNA Detection. Angew Chem Int Ed Engl 2007; 46:5223-5. [PMID: 17535003 DOI: 10.1002/anie.200700289] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tom N Grossmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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97
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Brassart B, Gomez D, De Cian A, Paterski R, Montagnac A, Qui KH, Temime-Smaali N, Trentesaux C, Mergny JL, Gueritte F, Riou JF. A new steroid derivative stabilizes g-quadruplexes and induces telomere uncapping in human tumor cells. Mol Pharmacol 2007; 72:631-40. [PMID: 17586599 DOI: 10.1124/mol.107.036574] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human telomeric DNA consists of tandem repeats of the sequence d(TTAGGG) with a 3' single-stranded extension (the G-overhang). The stabilization of G-quadruplexes in the human telomeric sequence by small-molecule ligands inhibits the activity of telomerase and results in telomere uncapping, leading to senescence or apoptosis of tumor cells. Therefore, the search for new and selective G-quadruplex ligands is of considerable interest because a selective ligand might provide a telomere-targeted therapeutic approach to treatment of cancer. We have screened a bank of derivatives from natural and synthetic origin using a temperature fluorescence assay and have identified two related compounds that induce G-quadruplex stabilization: malouetine and steroid FG. These steroid derivatives have nonplanar and nonaromatic structures, different from currently known G-quadruplex ligands. Malouetine is a natural product isolated from the leaves of Malouetia bequaaertiana E. Woodson and is known for its curarizing and DNA-binding properties. Steroid FG, a funtumine derivative substituted with a guanylhydrazone moiety, interacted selectively with the telomeric G-quadruplex in vitro. This derivative induced senescence and telomere shortening of HT1080 tumor cells at submicromolar concentrations, corresponding to the phenotypic inactivation of telomerase activity. In addition, steroid FG induced a rapid degradation of the telomeric G-overhang and the formation of anaphase bridges, characteristics of telomere uncapping. Finally, the expression of protection of telomere 1 (POT1) induced resistance to the growth effect of steroid FG. These results indicate that these steroid ligands represent a new class of telomere-targeted agents with potential as antitumor drugs.
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Affiliation(s)
- Bertrand Brassart
- Laboratoire d'Onco-Pharmacologie, JE 2428, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, F-51096 Reims, France
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98
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Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR. Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 2007; 35:4214-22. [PMID: 17576685 PMCID: PMC1919480 DOI: 10.1093/nar/gkm316] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G3 tracts separated by either single T or T4 loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T4, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T4 the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T4 loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.
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Affiliation(s)
- Phillip A. Rachwal
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - I. Stuart Findlow
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Joern M. Werner
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK and School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- *To whom correspondence should be addressed. +44 23 8059 4374+44 23 8059 4459
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99
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Negri A, Marco E, García-Hernández V, Domingo A, Llamas-Saiz AL, Porto-Sandá S, Riguera R, Laine W, David-Cordonnier MH, Bailly C, García-Fernández LF, Vaquero JJ, Gago F. Antitumor Activity, X-ray Crystal Structure, and DNA Binding Properties of Thiocoraline A, a Natural Bisintercalating Thiodepsipeptide. J Med Chem 2007; 50:3322-33. [PMID: 17571868 DOI: 10.1021/jm070381s] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine natural product thiocoraline A displayed approximately equal cytotoxic activity at nanomolar concentrations in a panel of 12 human cancer cell lines. X-ray diffraction analyses of orthorhombic crystals of this DNA-binding drug revealed arrays of docked pairs of staple-shaped molecules in which one pendent hydroxyquinoline chromophore from each cysteine-rich molecule appears intercalated between the two chromophores of a facing molecule. This arrangement is in contrast to the proposed mode of binding to DNA that shows the two drug chromophores clamping two stacked base pairs, in agreement with the nearest-neighbor exclusion principle. Proof of DNA sequence recognition was obtained from both classical DNase I footprinting experiments and determination of the melting temperatures of several custom-designed fluorescently labeled oligonucleotides. A rationale for the DNA-binding behavior was gained when models of thiocoraline clamping a central step embedded in several octanucleotides were built and studied by means of unrestrained molecular dynamics simulations in aqueous solution.
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Affiliation(s)
- Ana Negri
- Departamento de Farmacología, Universidad de AlcalA, E-28871 Madrid, Spain
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100
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Casals J, Debéthune L, Alvarez K, Risitano A, Fox KR, Grandas A, Pedroso E. Directing quadruplex-stabilizing drugs to the telomere: synthesis and properties of acridine-oligonucleotide conjugates. Bioconjug Chem 2007; 17:1351-9. [PMID: 16984147 DOI: 10.1021/bc060194t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Conjugates containing quadruplex-stabilizing acridines linked to oligonucleotides that are complementary to the G-rich human telomere sequence were synthesized. Acylation of 3,6-diaminoacridine followed by two Michael reactions provided derivatives suitable for conjugation, which were coupled to resin-linked amine-modified oligonucleotides by activating the carboxyl group with pentafluorophenyl 4-nitrobenzenesulfonate. After deprotection with aqueous ammonia at room temperature, conjugates incorporating different acridines, linkers, and oligonucleotide sequences were obtained. These were tested for their ability to stabilize intramolecular DNA quadruplexes that are based on the human telomeric repeat sequence (GGGTTA)(n).
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Affiliation(s)
- Joan Casals
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
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