151
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Bhattacharjee AJ, Ahluwalia K, Taylor S, Jin O, Nicoludis JM, Buscaglia R, Brad Chaires J, Kornfilt DJP, Marquardt DGS, Yatsunyk LA. Induction of G-quadruplex DNA structure by Zn(II) 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin. Biochimie 2011; 93:1297-309. [PMID: 21679743 DOI: 10.1016/j.biochi.2011.05.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/31/2011] [Indexed: 01/07/2023]
Abstract
G-quadruplexes (GQ) are formed by the association of guanine-rich stretches of DNA. Certain small molecules can influence kinetics and thermodynamics of this association. Understanding the mechanism of ligand-assisted GQ folding is necessary for the design of more efficient cancer therapeutics. The oligonucleotide d(TAGGG)(2) forms parallel bimolecular GQ in the presence of ≥66 mM K(+); GQs are not formed under Na(+), Li(+) or low K(+) conditions. The thermodynamic parameters for GQ folding at 60 μM oligonucleotide and 100 mM KCl are ΔH = -35 ± 2 kcal mol(-1) and ΔG(310) = -1.4 kcal mol(-1). Quadruplex [d(TAGGG)(2)](2) binds 2-3 K(+) ions with K(d) of 0.5 ± 0.2 mM. Our work addresses the question of whether metal free 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) and its Zn(II), Cu(II), and Pt(II) derivatives are capable of facilitating GQ folding of d(TAGGG)(2) from single stranded, or binding to preformed GQ, using UV-vis and circular dichroism (CD) spectroscopies. ZnTMPyP4 is unique among other porphyrins in its ability to induce GQ structure of d(TAGGG)(2), which also requires at least a low amount of potassium. ZnTMPyP4 binds with 2:1 stoichiometry possibly in an end-stacking mode with a ~10(6) M(-1) binding constant, determined through UV-vis and ITC titrations. This process is entropically driven and has ΔG(298) of -8.0 kcal mol(-1). TMPyP4 binds with 3:1 stoichiometry and K(a) of ~10(6) M(-1). ZnTMPyP4 and TMPyP4 are efficient stabilizers of [d(TAGGG)(2)](2) displaying ΔT(1/2) of 13.5 and 13.8 °C, respectively, at 1:2 GQ to porphyrin ratio; CuTMPyP4 shows a much weaker effect (ΔT(1/2) = 4.7 °C) and PtTMPyP4 is weakly destabilizing (ΔT(1/2) = -2.9 °C). The selectivity of ZnTMPyP4 for GQ versus dsDNA is comparable to that of TMPyP4. The ability of ZnTMPyP4 to bind and stabilize GQ, to induce GQ formation, and speed up its folding may suggest an important biological activity for this molecule.
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Affiliation(s)
- Amlan J Bhattacharjee
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA 19081, USA
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152
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Zhao C, Geng J, Feng L, Ren J, Qu X. Chiral Metallo-Supramolecular Complexes Selectively Induce Human Telomeric G-Quadruplex Formation under Salt-Deficient Conditions. Chemistry 2011; 17:8209-15. [DOI: 10.1002/chem.201100272] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Indexed: 12/11/2022]
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153
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Interaction of berberine, palmatine, coralyne, and sanguinarine to quadruplex DNA: A comparative spectroscopic and calorimetric study. Biochim Biophys Acta Gen Subj 2011; 1810:485-96. [DOI: 10.1016/j.bbagen.2011.01.011] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/21/2011] [Accepted: 01/24/2011] [Indexed: 12/11/2022]
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154
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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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155
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Wu WB, Chen SH, Hou JQ, Tan JH, Ou TM, Huang SL, Li D, Gu LQ, Huang ZS. Disubstituted 2-phenyl-benzopyranopyrimidine derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Org Biomol Chem 2011; 9:2975-86. [DOI: 10.1039/c0ob00921k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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156
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Wang JT, Li Y, Tan JH, Ji LN, Mao ZW. Platinum(ii)-triarylpyridines complexes with electropositive pendants as efficient G-quadruplex binders. Dalton Trans 2011; 40:564-6. [DOI: 10.1039/c0dt01161d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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157
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Tera M, Iida K, Shin-ya K, Nagasawa K. Development of Macrocyclic Polyoxazoles and Evaluation of Their G-Quadruplex Stabilizing Activities. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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158
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Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40:2719-40. [DOI: 10.1039/c0cs00134a] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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159
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Doi T, Shibata K, Yoshida M, Takagi M, Tera M, Nagasawa K, Shin-ya K, Takahashi T. (S)-Stereoisomer of telomestatin as a potent G-quadruplex binder and telomerase inhibitor. Org Biomol Chem 2011; 9:387-93. [DOI: 10.1039/c0ob00513d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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160
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Chen JLY, Sperry J, Ip NY, Brimble MA. Natural products targeting telomere maintenance. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00241k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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161
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Hou JQ, Tan JH, Wang XX, Chen SB, Huang SY, Yan JW, Chen SH, Ou TM, Luo HB, Li D, Gu LQ, Huang ZS. Impact of planarity of unfused aromatic molecules on G-quadruplex binding: Learning from isaindigotone derivatives. Org Biomol Chem 2011; 9:6422-36. [DOI: 10.1039/c1ob05884c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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162
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Manet I, Manoli F, Zambelli B, Andreano G, Masi A, Cellai L, Monti S. Affinity of the anthracycline antitumor drugs Doxorubicin and Sabarubicin for human telomeric G-quadruplex structures. Phys Chem Chem Phys 2010; 13:540-51. [PMID: 21052579 DOI: 10.1039/c0cp00898b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Combining various techniques in solution we proved that Doxorubicin, also called Adriamycin, and Sabarubicin, also known as MEN 10755, bind to the human telomeric sequence, 5'-d[GGG(TTAGGG)(3)]-3' (21-mer), assuming a G-quadruplex structure in the presence of K(+). Complexes of drugs with the 21-mer in 1 : 1 and 2 : 1 stoichiometry coexist in solution. Association constants were obtained from titration experiments and confirmed by isothermal titration calorimetry. The fluorescence of the drugs was quenched upon complexation. UV circular dichroism (CD) spectra of the complexes were characterized by the G-quadruplex signal and indicated that drug binding influences the equilibrium between quadruplex conformations. The visible CD spectra were exclusively due to the drug and show differences in the complexation modes of the two drugs. Spectroscopic and thermodynamic parameters of the 1 : 1 complexes point to drug stacking with the G-quadruplex top or bottom tetrad. Thermodynamic data suggests that the binding of the second drug molecule in the 2 : 1 complex may occur in a groove. Complexation caused a small increase in the thermal stability of the G-quadruplex main conformation, shifting T(m) from 62 to 67 °C.
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Affiliation(s)
- Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Piero Gobetti 101, I-40129 Bologna, Italy.
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163
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Tetrasubstituted naphthalene diimide ligands with selectivity for telomeric G-quadruplexes and cancer cells. Bioorg Med Chem Lett 2010; 20:6459-63. [DOI: 10.1016/j.bmcl.2010.09.066] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/10/2010] [Accepted: 09/13/2010] [Indexed: 01/22/2023]
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164
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Xu H, Gao S, Yang Q, Pan D, Wang L, Fan C. Amplified fluorescent recognition of g-quadruplex folding with a cationic conjugated polymer and DNA intercalator. ACS APPLIED MATERIALS & INTERFACES 2010; 2:3211-3216. [PMID: 21028820 DOI: 10.1021/am1006854] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The single stranded DNA (ssDNA) with G-rich sequence can fold into G-quadruplex via intramolecular hydrogen-bonding interaction in the presence of ligand. This structure conversion can be specifically detected by a fluorescence method based on different interaction between SYBR Green I (SG) and various DNA structures. SG is proved to intercalate into G-quadruplex and results in high fluorescence intensity, which can be further amplified by 6-fold through fluorescence resonance energy transfer (FRET) from a water-soluble cationic conjugated polymer (CCP) to SG due to the high affinity of positively charged CCP to negatively charged rigid G-quadruplex, whereas it is not performed for ssDNA in the absence of K(+). As a result, the ssDNA/SG/CCP complex can be used to detect potassium ions with improved selectivity in a label-free and cost-effective manner.
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Affiliation(s)
- Hui Xu
- School of Chemistry and Material Sciences, Ludong University, Yantai 264025, China
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165
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Dutikova YV, Borisova OF, Shchyolkina AK, Lin J, Huang S, Shtil AA, Kaluzhny DN. 5,10,15,20-Tetra-(N-methyl-3-pyridyl)porphyrin destabilizes the antiparallel telomeric quadruplex d(TTAGGG)4. Mol Biol 2010. [DOI: 10.1134/s0026893310050201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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166
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Agarwal T, Roy S, Chakraborty TK, Maiti S. Selective Targeting of G-Quadruplex Using Furan-Based Cyclic Homooligopeptides: Effect on c-MYC Expression. Biochemistry 2010; 49:8388-97. [DOI: 10.1021/bi1005927] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Tani Agarwal
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
| | - Saumya Roy
- Indian Institute of Chemical Technology, CSIR, Hyderabad 500 007, India
| | - Tushar Kanti Chakraborty
- Indian Institute of Chemical Technology, CSIR, Hyderabad 500 007, India
- Central Drug Research Institute, CSIR, Lucknow 226 001, India
| | - Souvik Maiti
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
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167
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Agarwal T, Roy S, Chakraborty TK, Maiti S. Furan based cyclic homo-oligopeptides bind G-quadruplex selectively and repress c-MYC transcription. Bioorg Med Chem Lett 2010; 20:4346-9. [DOI: 10.1016/j.bmcl.2010.06.080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/24/2010] [Accepted: 06/14/2010] [Indexed: 12/01/2022]
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168
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Murat P, Bonnet R, Van der Heyden A, Spinelli N, Labbé P, Monchaud D, Teulade-Fichou MP, Dumy P, Defrancq E. Template-assembled synthetic G-quadruplex (TASQ): a useful system for investigating the interactions of ligands with constrained quadruplex topologies. Chemistry 2010; 16:6106-14. [PMID: 20397247 DOI: 10.1002/chem.200903456] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a pi-stacking binding mode showed a higher binding affinity for intermolecular-like G-quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G-quadruplex DNA over the duplex DNA. A numerical parameter, termed the G-quadruplex binding mode index (G4-BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G-quadruplex 1 against intramolecular G-quadruplex 2. The G-quadruplex binding mode index (G4-BMI) of a ligand is defined as follows: G4-BMI=K(D)(intra)/K(D)(inter), where K(D)(intra) is the dissociation constant for intramolecular G-quadruplex 2 and K(D)(inter) is the dissociation constant for intermolecular G-quadruplex 1. In summary, the present work has demonstrated that the use of parallel-constrained quadruplex topology provides more precise information about the binding modes of ligands.
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Affiliation(s)
- Pierre Murat
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France
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169
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Wang XD, Ou TM, Lu YJ, Li Z, Xu Z, Xi C, Tan JH, Huang SL, An LK, Li D, Gu LQ, Huang ZS. Turning off transcription of the bcl-2 gene by stabilizing the bcl-2 promoter quadruplex with quindoline derivatives. J Med Chem 2010; 53:4390-8. [PMID: 20481493 DOI: 10.1021/jm100445e] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human bcl-2 gene is an apoptosis-related oncogene containing a GC-rich sequence which is located upstream from P1 promoter and has the potential to form G-quadruplex structures. However, the regulatory role of the quadruplex and the effect of its ligands on bcl-2 have not been clarified. Here, we demonstrated that the G-quadruplex structure was disrupted when partial mutation of G --> A was made, resulting in a 2-fold increase in basal transcriptional activity of bcl-2 promoter. Quindoline derivatives, the highly active G-quadruplex ligands developed by our group, could significantly suppress bcl-2 transcriptional activation but had less effect on mutated bcl-2 transcription. These results provided direct evidence that G-quadruplex structure formed in bcl-2 promoter region could function as a transcriptional repressor element, and G-quadruplex specific ligands could regulate the transcription of bcl-2 through stabilization of quadruplex structure. The results further indicated that quindoline derivatives could induce apoptosis of HL-60 tumor cells.
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Affiliation(s)
- Xiao-Dong Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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170
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Cationic porphyrin induced a telomeric DNA to g-quadruplex form in water. Bioinorg Chem Appl 2010:294756. [PMID: 18350116 PMCID: PMC2266808 DOI: 10.1155/2008/294756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 10/11/2007] [Accepted: 12/13/2007] [Indexed: 11/28/2022] Open
Abstract
The formation of the DNA G-quadruplex is induced by the addition of a novel porphyrin carrying four cationic tethers. Circular dichroism spectroscopy reveals that the porphyrin binds to Tetrahymena telomeric repeat to form G-quadruplex under stabilizing-cation-deficient and no buffer conditions.
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171
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Iida K, Tera M, Hirokawa T, Shin-Ya K, Nagasawa K. Synthesis of Macrocyclic Hexaoxazole (6OTD) Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties. J Nucleic Acids 2010; 2010. [PMID: 20700415 PMCID: PMC2911606 DOI: 10.4061/2010/217627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 03/01/2010] [Indexed: 12/03/2022] Open
Abstract
Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD) dimers, whose core structure stabilizes telomeric G-quadruplexes (G4). Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium cation. The guanidine functionalized dimer displays a potent stabilizing ability of the G4 structure, as determined by using a FRET melting assay (ΔTm = 14°C).
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Affiliation(s)
- Keisuke Iida
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan
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172
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Monchaud D, Granzhan A, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition. J Nucleic Acids 2010; 2010. [PMID: 20725629 PMCID: PMC2915875 DOI: 10.4061/2010/525862] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/01/2023] Open
Abstract
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
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Affiliation(s)
- David Monchaud
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Batiment 110, 91405 Orsay, France
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173
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Abstract
Thermodynamic and kinetic studies complement high-resolution structures of G-quadruplexes. Such studies are essential for a thorough understanding of the mechanisms that govern quadruplex folding and conformational changes in quadruplexes. This perspective article reviews representative thermodynamic and kinetic studies of the folding of human telomeric quadruplex structures. Published thermodynamic data vary widely and are inconsistent; possible reasons for these inconsistencies are discussed. The key issue of whether such folding reactions are a simple two-state process is examined. A tentative energy balance for the folding of telomeric quadruplexes in Na(+) and K(+) solution, and for the conformational transition between these forms is presented.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, Kentucky, KY 40202, USA.
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174
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A theoretical investigation on the spectroscopic properties and photosensitizing capability of 5, 10, 15, 20-tetraphenylsapphyrin and 5, 10, 15, 20-tetraphenyl-26,28-diheterosapphyrins with two O, S, or Se Atoms. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0735-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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175
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Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG. Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs. Nucleic Acids Res 2010; 37:7570-80. [PMID: 19820116 PMCID: PMC2794188 DOI: 10.1093/nar/gkp840] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Numerous regulatory genes have G-rich regions that can potentially form quadruplex structures, possibly playing a role in transcription regulation. We studied a G-rich sequence in the BCL2 gene 176-bp upstream of the P1 promoter for G-quadruplex formation. Using circular dichroism (CD), thermal denaturation and dimethyl sulfate (DMS) footprinting, we found that a single-stranded oligonucleotide with the sequence of the BCL2 G-rich region forms a potassium-stabilized G-quadruplex. To study G-quadruplex formation in double-stranded DNA, the G-rich sequence of the BCL2 gene was inserted into plasmid DNA. We found that a G-quadruplex did not form in the insert at physiological conditions. To induce G-quadruplex formation, we used short peptide nucleic acids (PNAs) that bind to the complementary C-rich strand. We examined both short duplex-forming PNAs, complementary to the central part of the BCL2 gene, and triplex-forming bis-PNAs, complementary to sequences adjacent to the G-rich BCL2 region. Using a DMS protection assay, we demonstrated G-quadruplex formation within the G-rich sequence from the promoter region of the human BCL2 gene in plasmid DNA. Our results show that molecules binding the complementary C-strand facilitate G-quadruplex formation and introduce a new mode of PNA-mediated sequence-specific targeting.
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Affiliation(s)
- Mykola I. Onyshchenko
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timur I. Gaynutdinov
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ethan A. Englund
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel H. Appella
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D. Neumann
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor G. Panyutin
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
- *To whom correspondence should be addressed. Tel: +1 301 496 8308; Fax: +1 301 480 9712;
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176
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Du Y, Zhang D, Chen W, Zhang M, Zhou Y, Zhou X. Cationic N-confused porphyrin derivative as a better molecule scaffold for G-quadruplex recognition. Bioorg Med Chem 2010; 18:1111-6. [DOI: 10.1016/j.bmc.2009.12.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 12/15/2009] [Accepted: 12/16/2009] [Indexed: 01/12/2023]
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177
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Shi S, Geng X, Zhao J, Yao T, Wang C, Yang D, Zheng L, Ji L. Interaction of [Ru(bpy)2(dppz)]2+ with human telomeric DNA: preferential binding to G-quadruplexes over i-motif. Biochimie 2010; 92:370-7. [PMID: 20096325 DOI: 10.1016/j.biochi.2010.01.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 01/07/2010] [Indexed: 10/19/2022]
Abstract
Inspired by the enormous importance attributed to the structure and function of human telomeric DNA, we focus our attention on the interaction of [Ru(bpy)(2)(dppz)](2+) with the guanine-rich single-strand oligomer 5'-AGGGTTAGGGTTAGGGTTAGGG-3' (22AG) and the complementary cytosine-rich strand (22CT). In Na(+) buffer, 22AG may adopt an antiparallel basket quadruplex, whereas, it favours a mixed parallel/antiparallel structure in K(+) buffer. 22CT may self-associate at acidic pH into an i-motif. In this paper, the interaction between [Ru(bpy)(2)(dppz)](2+) and each unusual DNA was evaluated. It was interesting that [Ru(bpy)(2)(dppz)](2+) could promote the human telomeric repeat 22AG to fold into intramolecular antiparallel G-quadruplex without any other cations. What's more, [Ru(bpy)(2)(dppz)](2+) was found to have a strong preference for binding to G-quadruplexes that were induced through either Na(+) or K(+), while weak binding to i-motif was observed. The results also indicated that [Ru(bpy)(2)(dppz)](2+) could serve as a prominent molecular "light switch" for both G-quadruplexes, revealing a potential application of the title complex in luminescent signaling of G-quadruplex DNA.
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Affiliation(s)
- Shuo Shi
- Department of Chemistry, Tongji University, Shanghai, PR China.
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178
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Chen C, Zhao C, Yang X, Ren J, Qu X. Enzymatic manipulation of DNA-modified gold nanoparticles for screening G-quadruplex ligands and evaluating selectivities. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:389-393. [PMID: 20217725 DOI: 10.1002/adma.200901924] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Cuie Chen
- Key Laboratory of Rare Earth Chemistry and Physics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P R China
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179
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Ma H, Zhang M, Zhang D, Huang R, Zhao Y, Yang H, Liu Y, Weng X, Zhou Y, Deng M, Xu L, Zhou X. Pyridyl-Substituted Corrole Isomers: Synthesis and their Regulation to G-quadruplex Structures. Chem Asian J 2010; 5:114-22. [DOI: 10.1002/asia.200900270] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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180
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Nagasawa K, Majima S, Tera M, Iida K, Shin-ya K. Design and Synthesis of Telomestatin Derivatives Containing Methyl Oxazole and Their G-Quadruplex Stabilizing Activities. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)85] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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181
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Song G, Ren J. Recognition and regulation of unique nucleic acid structures by small molecules. Chem Commun (Camb) 2010; 46:7283-94. [DOI: 10.1039/c0cc01312a] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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182
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Wang JT, Zheng XH, Xia Q, Mao ZW, Ji LN, Wang K. 1,10-Phenanthroline platinum(ii) complex: a simple molecule for efficient G-quadruplex stabilization. Dalton Trans 2010; 39:7214-6. [DOI: 10.1039/c0dt00211a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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183
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Abstract
G-quartets are square planar arrangements of four guanine bases, which can form extraordinarily stable stacks when present in nucleic acid sequences. Such G-quadruplex structures were long regarded as an in vitro phenomenon, but the widespread presence of suitable sequences in genomes and the identification of proteins that stabilize, modify, or resolve these nucleic acid structures have provided circumstantial evidence for their physiological relevance. The therapeutic potential of small molecules that can stabilize or disrupt G-quadruplex structures has invigorated the field in recent years. Here we review some of the key observations that support biological functions for G-quadruplex DNA as well as the techniques and tools that have enabled researchers to probe these structures and their interactions with proteins and small molecules.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute and the University of Sydney, Sydney, Australia
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184
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Shi S, Zhao J, Geng X, Yao T, Huang H, Liu T, Zheng L, Li Z, Yang D, Ji L. Molecular “light switch” for G-quadruplexes and i-motif of human telomeric DNA: [Ru(phen)2(dppz)]2+. Dalton Trans 2010; 39:2490-3. [DOI: 10.1039/b916094a] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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185
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Balkwill GD, Derecka K, Garner TP, Hodgman C, Flint APF, Searle MS. Repression of translation of human estrogen receptor alpha by G-quadruplex formation. Biochemistry 2009; 48:11487-95. [PMID: 19860473 DOI: 10.1021/bi901420k] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tissue-specific expression of the human estrogen receptor alpha gene (ESR1) is achieved through multiple promoter sequences resulting in various mRNA transcripts encoding a common protein but differing in their 5'-untranslated region (5'-UTR). Many cancers are estrogen-sensitive with neoplastic growth stimulated through the estrogen receptor, a transcription factor that regulates developmental genes. We demonstrate that the human ESR1 gene is rich in potential quadruplex-forming sequences with 3 of 20 identified within exonic regions. In particular, we show using CD, UV, and NMR spectroscopy that a stable DNA G-quadruplex motif is formed within the exon C gene sequence. This motif, which PCR shows is transcribed in normal and neoplastic endometrium and in MCF-7 cells, forms a stable RNA quadruplex demonstrable by CD and UV analysis. Cloning the exon C G-quadruplex sequence upstream of a luciferase reporter gene caused a 6-fold reduction of enzymatic activity compared to a mutant sequence. We conclude that the exon C G-quadruplex motif is present in the 5'-UTR of the mRNA transcript, where it modulates the efficiency of translation.
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Affiliation(s)
- Graham D Balkwill
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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186
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Gaynutdinov TI, Brown P, Neumann RD, Panyutin IG. Duplex formation at the 5' end affects the quadruplex conformation of the human telomeric repeat overhang in sodium but not in potassium. Biochemistry 2009; 48:11169-77. [PMID: 19856972 DOI: 10.1021/bi901063g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human telomeres contain numerous copies of the (TTAGGG)(n).(AATCCC)(n) repeated sequence with multiple TTAGGG repeats in 3' single-stranded overhangs. Single-stranded oligonucleotides consisting of four TTAGGG repeats can fold into various intramolecular quadruplex structures stabilized by quartets of guanines. The quadruplex structures are believed to play a role in telomere functions and considered as targets for anticancer drug design. In an effort to create a more realistic model of telomeric DNA, we designed oligonucleotides containing a duplex region at the 5' end and four telomeric repeats in the 3' overhang. We applied CD spectroscopy and (125)I radioprobing to determine the conformation of the quadruplexes formed in the 3' overhangs. We found that in the presence of NaCl the conformation of the quadruplex changes with formation of the 5' duplex and depends on the position of the interface between the duplex and the 3' telomeric sequence. When the duplex region extended to the first T of the first TTAGGG repeat, both CD and radioprobing data are consistent with the parallel propeller conformation of the overhang. In the presence of KCl, formation of the duplex at the 5' end of DNA molecules did not change the fold of the quadruplex in the overhang which was interpreted as a mixture of two isomers of 3+1 conformation regardless of the duplex-overhang interface position. Our results demonstrate that the interface between the duplex and single-stranded overhang can affect the conformation of the telomeric quadruplex.
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Affiliation(s)
- Timur I Gaynutdinov
- Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892-1180, USA
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187
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Chen M, Song G, Wang C, Hu D, Ren J, Qu X. Small-molecule selectively recognizes human telomeric G-quadruplex DNA and regulates its conformational switch. Biophys J 2009; 97:2014-23. [PMID: 19804733 DOI: 10.1016/j.bpj.2009.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/30/2009] [Accepted: 07/13/2009] [Indexed: 01/08/2023] Open
Abstract
Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na(+) or K(+) solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions. These results may stimulate the design of new quadruplex binders that would be capable of discriminating different G-quadruplex structures as well as controlling biological phenomena, functional molecules, and nanomaterials.
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Affiliation(s)
- Mingli Chen
- State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
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188
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Abstract
Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies.
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Affiliation(s)
- Anh Tuân Phan
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore.
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189
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Arora A, Kumar N, Agarwal T, Maiti S. Retraction: Human telomeric G-quadruplex: targeting with small molecules. FEBS J 2009; 277:1345. [DOI: 10.1111/j.1742-4658.2009.07461.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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190
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Huang J, Wang M, Zhou Y, Weng X, Shuai L, Zhou X, Zhang D. Visual observation of G-quadruplex DNA with the label-free fluorescent probe silole with aggregation-induced emission. Bioorg Med Chem 2009; 17:7743-8. [DOI: 10.1016/j.bmc.2009.09.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/18/2009] [Accepted: 09/19/2009] [Indexed: 11/26/2022]
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191
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Affiliation(s)
- Shinzi Ogasawara
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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192
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Nakayama S, Sintim HO. Colorimetric split G-quadruplex probes for nucleic acid sensing: improving reconstituted DNAzyme's catalytic efficiency via probe remodeling. J Am Chem Soc 2009; 131:10320-33. [PMID: 19621970 DOI: 10.1021/ja902951b] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Split G-rich DNA probes can assemble into active peroxidase-mimicking DNAzymes in the presence of bioanalytes such as DNA, thereby providing a simple and cheap means to detect analytes in biological samples. A comprehensive study designed to reveal the salient probe architectural features and reaction conditions that facilitate facile reconstitution into enzymatically proficient enzymes unveiled these important findings: (a) The loops that connect the G3-tracts in a G-quadruplex structure can be replaced with a stem-loop or loop-stem-loop motif without destabilizing the resulting quadruplex structure; endowing the split G-rich probes with regions of limited complementarity leads to more proficient reconstituted enzymes. (b) The addition of hemin to antiparallel G-quadruplex DNAzymes lead to a blue shift in the CD spectra of the G-quadruplex DNAzymes. (c) The architectures of the DNA motifs that lie adjacent to the G-quadruplex structure influence both the stability and the enzymatic proficiency of the reconstituted enzymes. (d) The nature of the monovalent cation that is present in excess is a key determinant of the turnover number of the G-quadruplex DNAzyme; decomposition of G-quadruplex DNAzymes is slower in buffers that contain ammonium ions than those that contain sodium or potassium ions. These findings are important for the design of bioassays that use peroxidase-mimicking G-quadruplexes as detection labels.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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193
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The 3D structures of G-Quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase. J Mol Model 2009; 16:645-57. [DOI: 10.1007/s00894-009-0592-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Accepted: 09/10/2009] [Indexed: 10/20/2022]
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194
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Zhang D, Deng M, Xu L, Zhou Y, Yuwen J, Zhou X. The sensitive and selective optical detection of mercury(II) ions by using a phosphorothioate DNAzyme strategy. Chemistry 2009; 15:8117-20. [PMID: 19637166 DOI: 10.1002/chem.200901268] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, China
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195
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Gray RD, Li J, Chaires JB. Energetics and kinetics of a conformational switch in G-quadruplex DNA. J Phys Chem B 2009; 113:2676-83. [PMID: 19708205 DOI: 10.1021/jp809578f] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Circular dichroism and differential scanning calorimetry were used to determine the energetics of the conformational switch of the human telomere quadruplex formed by the sequence d[AGGG(TTAGGG)3] between the sodium basket form and the potassium hybrid form. The energy barrier separating the two conformations was found to be modest, only 1.4-2.4 kcal mol(-1). The kinetics of exchange of bound K+ for Na+ cations and the concomitant conformational switch was assessed by measuring time-dependent changes in the circular dichroism spectrum accompanying the cation exchange reaction. The time course of these changes was found to consist of three distinct kinetic processes: a rapid phase that was complete in less than 5 ms followed by two slower phases with relaxation times of 40-50 s and 600-800 s at 25 degrees C and pH 7.0. We interpret these kinetics in terms of a model in which the bound Na+ cations are rapidly replaced by K+ followed by relatively slow structural rearrangements to generate the final K(+)-bound product(s). Circular dichroism studies showed that addition of the porphyrin TmPyP4 promoted conversion of the basket to the hybrid form. The kinetics of the TmPyP4-induced conformational change were the same as those observed for the cation exchange reaction.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 529 South Jackson Street, Louisville, Kentucky 40202, USA
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196
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Zhang XF, Xiang JF, Tian MY, Yang QF, Sun HX, Yang S, Tang YL. Formation of an intramolecular G-quadruplex of human telomere induced by poly(L-lysine) under salt-deficient conditions. J Phys Chem B 2009; 113:7662-7. [PMID: 19408914 DOI: 10.1021/jp811183a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A single-stranded G-tract human telomere DNA sequence is able to fold into intramolecular G-quadruplex structures which may be important for a number of biological processes and disease-related mechanisms. Poly(L-lysine) (PLL) polymer is linear polypeptides with lysine as the repeat unit and has been employed as a gene carrier in achieving targeted delivery of DNA to cancer cells. To explore the influence of PLL on the conformation of Hum24 DNA, we have investigated the interaction of PLL with Hum24 by biophysical methods, mainly CD, ESI-MS, and polyacrylamide gel electrophoresis for the first time. The CD data have shown that PLL can induce single-stranded Hum24 to form an intramolecular parallel G-quadruplex structure, further confirmed by ESI-MS analysis and gel electrophoresis results. The formation of an intramolecular G-quadruplex is strongly dependent on the Hum24/PLL molar ratios and the length of both the polypeptides and oligonucleotide. Such phenomena may be interpreted by electrostatically attracting negative-charged Hum24 by positive-charged PLL which facilitates the close contact between the guanines and formation of hydrogen bonding, thus leading the final shape of a G-quadruplex structure.
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Affiliation(s)
- Xiu-feng Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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197
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Iida K, Tera M, Hirokawa T, Shin-ya K, Nagasawa K. G-quadruplex recognition by macrocyclic hexaoxazole (6OTD) dimer: greater selectivity than monomer. Chem Commun (Camb) 2009:6481-3. [PMID: 19841816 DOI: 10.1039/b910242f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Macrocyclic hexaoxazole (6OTD) dimers were designed as candidates for potent G-quadruplex binders and synthesized.
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Affiliation(s)
- Keisuke Iida
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan
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198
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Human telomeric G-quadruplex formed from duplex under near physiological conditions: Spectroscopic evidence and kinetics. Biochimie 2009; 91:1104-11. [DOI: 10.1016/j.biochi.2009.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022]
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199
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Renciuk D, Kejnovská I, Skoláková P, Bednárová K, Motlová J, Vorlícková M. Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions. Nucleic Acids Res 2009; 37:6625-34. [PMID: 19717545 PMCID: PMC2770667 DOI: 10.1093/nar/gkp701] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The arrangement of the human telomeric quadruplex in physiologically relevant conditions has not yet been unambiguously determined. Our spectroscopic results suggest that the core quadruplex sequence G3(TTAG3)3 forms an antiparallel quadruplex of the same basket type in solution containing either K+ or Na+ ions. Analogous sequences extended by flanking nucleotides form a mixture of the antiparallel and hybrid (3 + 1) quadruplexes in K+-containing solutions. We, however, show that long telomeric DNA behaves in the same way as the basic G3(TTAG3)3 motif. Both G3(TTAG3)3 and long telomeric DNA are also able to adopt the (3 + 1) quadruplex structure: Molecular crowding conditions, simulated here by ethanol, induced a slow transition of the K+-stabilized quadruplex into the hybrid quadruplex structure and then into a parallel quadruplex arrangement at increased temperatures. Most importantly, we demonstrate that the same transitions can be induced even in aqueous, K+-containing solution by increasing the DNA concentration. This is why distinct quadruplex structures were detected for AG3(TTAG3)3 by X-ray, nuclear magnetic resonance and circular dichrosim spectroscopy: Depending on DNA concentration, the human telomeric DNA can adopt the antiparallel quadruplex, the (3 + 1) structure, or the parallel quadruplex in physiologically relevant concentrations of K+ ions.
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200
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