1
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Yi L, Kong J, Xiong Y, Yi S, Gan T, Huang C, Duan Y, Zhu X. Genome mining of Streptomyces sp. CB00271 as a natural high-producer of β-rubromycin and the resulting discovery of β-rubromycin acid. Biotechnol Bioeng 2021; 118:2243-2254. [PMID: 33629382 DOI: 10.1002/bit.27732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/06/2022]
Abstract
β-rubromycin (β-RUB) (1) is an efficient inhibitor of human telomerase possessing a unique spiroketal moiety as a potential pharmacophore and regarded as a promising anticancer drug lead. But the development of (β-RUB) (1) has long been hampered by its low titer and very poor water solubility. By adopting a genome mining strategy, an FAD-dependent monooxygenase RubN involving with the formation of the spiro system was applied as the probe and Streptomyces sp. CB00271 was screened out from our strain collection as an alternative natural high producer of β-RUB (1). After a series of fermentation optimizations, CB00271 could produce 124.8 ± 3.4 mg/L β-RUB (1), which was the highest titer up to now. Moreover, the enhanced production of β-RUB (1) in fermentation broth also led to the discovery of a new congener β-RUB acid (7), which was structurally elucidated as the acid form of β-RUB (1). Comparing to β-RUB (1), the substituted carboxyl group endowed β-RUB acid (7) much better solubility in serum and resulted in its higher activity towards tumor cells. Our work set up a solid base for the pilot-scale production of β-RUB (1) and its congeners to facilitate their future development as promising anticancer drug leads, and also provide an alternative and practical strategy for the exploitation of other important microbial natural products.
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Affiliation(s)
- Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Jieqian Kong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Yi Xiong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Sirui Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Ting Gan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Chengshuang Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China
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2
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Wang ZF, Li MH, Chu IT, Winnerdy FR, Phan AT, Chang TC. Cytosine epigenetic modification modulates the formation of an unprecedented G4 structure in the WNT1 promoter. Nucleic Acids Res 2020; 48:1120-1130. [PMID: 31912153 PMCID: PMC7026657 DOI: 10.1093/nar/gkz1207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/09/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
Time-resolved imino proton nuclear magnetic resonance spectra of the WT22m sequence d(GGGCCACCGGGCAGTGGGCGGG), derived from the WNT1 promoter region, revealed an intermediate G-quadruplex G4(I) structure during K+-induced conformational transition from an initial hairpin structure to the final G4(II) structure. Moreover, a single-base C-to-T mutation at either position C4 or C7 of WT22m could lock the intermediate G4(I) structure without further conformational change to the final G4(II) structure. Surprisingly, we found that the intermediate G4(I) structure is an atypical G4 structure, which differs from a typical hybrid G4 structure of the final G4(II) structure. Further studies of modified cytosine analogues associated with epigenetic regulation indicated that slight modification on a cytosine could modulate G4 structure. A simplified four-state transition model was introduced to describe such conformational transition and disclose the possible mechanism for G4 structural selection caused by cytosine modification.
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Affiliation(s)
- Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C
| | - Ming-Hao Li
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C
| | - I-Te Chu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Fernaldo R Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh T Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, R.O.C
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3
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Abstract
The genome-wide occurrence of G-quadruplexes and their demonstrated biological activities call for detailed understanding on the stability and transition kinetics of the structures. Although the core structural element in a G-quadruplex is simple and requires only four tandem repeats of Guanine rich sequences, there is rather rich conformational diversity in this structure. Corresponding to this structural diversity, it displays involved transition kinetics within individual G-quadruplexes and complicated interconversion among different G-quadruplex species. Due to the inherently high signal-to-noise ratio in the measurement, single-molecule tools offer a unique capability to investigate the thermodynamic, kinetic, and mechanical properties of G-quadruplexes with dynamic conformations. In this chapter, we describe different single molecule methods such as atomic-force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), optical, magnetic, and magneto-optical tweezers to investigate G-quadruplex structures as well as their interactions with small-molecule ligands.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | | | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
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4
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Rackwitz J, Bald I. Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology. Chemistry 2018; 24:4680-4688. [PMID: 29359819 DOI: 10.1002/chem.201705889] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 12/19/2022]
Abstract
During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG)2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A)2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT)2 to 5'-(GGG ATT)4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K+ ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy.
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Affiliation(s)
- Jenny Rackwitz
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
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5
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Lee W, Matsika S. Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures. Phys Chem Chem Phys 2018; 19:3325-3336. [PMID: 28091673 DOI: 10.1039/c6cp05604k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the most commonly formed photochemical products when nucleic acids interact with UV radiation. In duplex DNA, the relative inflexible structure allows for only the cis, syn CPD isomer to be formed. G-quadruplex structures, however, have loops that are more flexible and allow for different orientations of the bases to interact. As a result, the highly unusual formation of an anti CPD has been observed in these structures. Due to the close proximity between two opposing loops containing the TTA sequence in two G-quadruplex structures (called "form-3" and "basket"), a high yield of anti CPD formation was expected in these structures. However, while significant yields of anti CPDs are observed in form-3, the anti CPD is hardly observed in the basket structure. To account for this inconsistency, we examine the process of anti CPD formation in form-3 and basket structures using simulations at the atomistic level. Here, we consider the conformational effect using MD simulations, which show whether the formation of the anti CPD is structurally feasible. Quantum mechanical/molecular mechanical (QM/MM) calculations of excited states are also used to consider the electronic effect by an adjacent guanine base which can quench the formation of the anti CPD through charge transfer (CT). Our results are in qualitative agreement with the experimental results, predicting a significant yield of the anti CPD in the form-3 structure and a negligible yield in the basket structure, while they also predict the formation of the cis, syn CPD between two opposing loops in form-3. Most importantly, our simulation results show that the yields of the anti CPD in the G-quadruplex are affected significantly by both conformational and electronic effects.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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6
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Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
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Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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7
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Davis KJ, Assadawi NMO, Pham SQT, Birrento ML, Richardson C, Beck JL, Willis AC, Ralph SF. Effect of structure variations on the quadruplex DNA binding ability of nickel Schiff base complexes. Dalton Trans 2018; 47:13573-13591. [DOI: 10.1039/c8dt02727g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The synthesis of two new series of nickel complexes is described, along with their ability to bind to duplex and quadruplex DNA structures.
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Affiliation(s)
| | | | | | | | | | | | - Anthony C. Willis
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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8
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Yadav K, Meka PNR, Sadhu S, Guggilapu SD, Kovvuri J, Kamal A, Srinivas R, Devayani P, Babu BN, Nagesh N. Telomerase Inhibition and Human Telomeric G-Quadruplex DNA Stabilization by a β-Carboline-Benzimidazole Derivative at Low Concentrations. Biochemistry 2017; 56:4392-4404. [PMID: 28737386 DOI: 10.1021/acs.biochem.7b00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Guanine rich regions in DNA, which can form highly stable secondary structures, namely, G-quadruplex or G4 DNA structures, affect DNA replication and transcription. Molecules that stabilize G4 DNA have become important in recent years. In this study, G4 DNA stabilization, inhibition of telomerase, and anticancer activity of synthetic β-carboline-benzimidazole derivatives (5a, 5d, 5h, and 5r) were studied. Among them, derivatives containing a 4-methoxyphenyl ring at C1 and a 6-methoxy-substituted benzimidazole at C3 (5a) were found to stabilize telomeric G-quadruplex DNA efficiently. The stoichiometry and interaction of a synthetic, β-carboline-benzimidazole derivative, namely, 3-(6-methoxy-1H-benzo[d]imidazol-2-yl)-1-(4-methoxyphenyl)-9H-pyrido[3,4-b]indole (5a), with human intermolecular G-quadruplex DNA at low concentrations were examined using electrospray ionization mass spectrometry. Spectroscopy techniques indicate that 5a may intercalate between the two stacks of G-quadruplex DNA. This model is supported by docking studies. When cancer cells are treated with 5a, the cell cycle arrest occurs at the sub-G1 phase. In addition, an apoptosis assay and fluorescence microscopy studies using cancer cells indicate that 5a can induce apoptosis. Results of biochemical assays such as the polymerase chain reaction stop assay and telomerase activity assay indicate that 5a has the potential to stabilize G-quadruplex DNA, and thereby, it may interfere with in vitro DNA synthesis and decrease telomerase activity. The results of this study reveal that the β-carboline-benzimidazole derivative (5a) is efficient in G-quadruplex DNA stabilization over double-stranded DNA, inhibits telomerase activity, and induces apoptosis in cancer cells.
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Affiliation(s)
- Kranthikumar Yadav
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Penchala Narasimha Rao Meka
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Sudeshna Sadhu
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Sravanthi Devi Guggilapu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Jeshma Kovvuri
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Ahmed Kamal
- Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Ragampeta Srinivas
- Analytical Chemistry and Mass Spectrometry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500007, India
| | - Panuganti Devayani
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
| | - Bathini Nagendra Babu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) , Hyderabad 500037, India
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology , Hyderabad 500007, India
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9
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Matsumoto S, Iida K, Murata A, Denawa M, Hagiwara M, Nakatani K. Synthetic ligand promotes gene expression by affecting GC sequence in promoter. Bioorg Med Chem Lett 2017; 27:3391-3394. [PMID: 28610980 DOI: 10.1016/j.bmcl.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/18/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.
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Affiliation(s)
- Saki Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Masatoshi Hagiwara
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan; Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan.
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10
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Zhang L, Zhang K, Rauf S, Dong D, Liu Y, Li J. Single-Molecule Analysis of Human Telomere Sequence Interactions with G-quadruplex Ligand. Anal Chem 2016; 88:4533-40. [DOI: 10.1021/acs.analchem.6b00555] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ling Zhang
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Sana Rauf
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Duo Dong
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Yang Liu
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
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11
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Wang ZF, Li MH, Chen WW, Hsu STD, Chang TC. A novel transition pathway of ligand-induced topological conversion from hybrid forms to parallel forms of human telomeric G-quadruplexes. Nucleic Acids Res 2016; 44:3958-68. [PMID: 26975658 PMCID: PMC4856992 DOI: 10.1093/nar/gkw145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/01/2016] [Indexed: 11/17/2022] Open
Abstract
The folding topology of DNA G-quadruplexes (G4s) depends not only on their nucleotide sequences but also on environmental factors and/or ligand binding. Here, a G4 ligand, 3,6-bis(1-methyl-4-vinylpyridium iodide)-9-(1-(1-methyl-piperidinium iodide)-3,6,9-trioxaundecane) carbazole (BMVC-8C3O), can induce topological conversion of non-parallel to parallel forms in human telomeric DNA G4s. Nuclear magnetic resonance (NMR) spectroscopy with hydrogen-deuterium exchange (HDX) reveals the presence of persistent imino proton signals corresponding to the central G-quartet during topological conversion of Tel23 and Tel25 G4s from hybrid to parallel forms, implying that the transition pathway mainly involves local rearrangements. In contrast, rapid HDX was observed during the transition of 22-CTA G4 from an anti-parallel form to a parallel form, resulting in complete disappearance of all the imino proton signals, suggesting the involvement of substantial unfolding events associated with the topological transition. Site-specific imino proton NMR assignments of Tel23 G4 enable determination of the interconversion rates of individual guanine bases and detection of the presence of intermediate states. Since the rate of ligand binding is much higher than the rate of ligand-induced topological conversion, a three-state kinetic model was evoked to establish the associated energy diagram for the topological conversion of Tel23 G4 induced by BMVC-8C3O.
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Affiliation(s)
- Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Republic of China
| | - Ming-Hao Li
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Republic of China
| | - Wei-Wen Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Republic of China Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 106, Taiwan, Republic of China Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, Republic of China Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Republic of China
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12
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Liu Y, Cheng D, Ge M, Lin W. The Truncated Human Telomeric Sequence forms a Hybrid-Type Intramolecular Mixed Parallel/antiparallel G-quadruplex Structure in K(+) Solution. Chem Biol Drug Des 2016; 88:122-8. [PMID: 26867976 DOI: 10.1111/cbdd.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/03/2015] [Accepted: 01/16/2016] [Indexed: 12/24/2022]
Abstract
In 80-90% tumor cells, telomerase becomes active and stabilizes the length of telomeres. The formation and stabilization of G-quadruplexes formed from human telomeric sequences have been proved able to inhibit the activity of telomerase, thus human telomeric G-quadruplex structure has become a potential target for the development of cancer therapy. Hence, structure of G-quadruplex formed in K(+) solution has been an attractive hotspot for further studies. However, the exact structure of human telomeric G-quadruplex in K(+) is extremely controversial, this study provides information for the understanding of different G-quadruplexes. Here, we report that 22nt and 24nt human telomeric sequences form unimolecular hybrid-type mixed parallel/antiparallel G-quadruplex in K(+) solution elucidated utilizing Circular Dichroism, Differential Scanning Calorimetry, and gel electrophoresis. Moreover, individual configuration of these two sequences was speculated in this study. The detailed structure information of the G-quadruplex formed under physiologically relevant condition is necessary for structure-based rational drug design.
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Affiliation(s)
- Yuxia Liu
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
| | - Dengfeng Cheng
- Department of Nuclear Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institute of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Min Ge
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
| | - Weizhen Lin
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
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13
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Birrento ML, Bryan TM, Samosorn S, Beck JL. ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1165-1173. [PMID: 25906017 DOI: 10.1007/s13361-015-1121-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine (1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of (1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand (1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.
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Affiliation(s)
- Monica L Birrento
- School of Chemistry, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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14
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Chen ZF, Qin QP, Qin JL, Liu YC, Huang KB, Li YL, Meng T, Zhang GH, Peng Y, Luo XJ, Liang H. Stabilization of G-quadruplex DNA, inhibition of telomerase activity, and tumor cell apoptosis by organoplatinum(II) complexes with oxoisoaporphine. J Med Chem 2015; 58:2159-79. [PMID: 25650792 DOI: 10.1021/jm5012484] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Two G-quadruplex ligands [Pt(L(a))(DMSO)Cl] (Pt1) and [Pt(L(b))(DMSO)Cl] (Pt2) have been synthesized and fully characterized. The two complexes are more selective for SK-OV-3/DDP tumor cells versus normal cells (HL-7702). It was found that both Pt1 and Pt2 could be a telomerase inhibitor targeting G-quadruplex DNA. This is the first report demonstrating that telomeric, c-myc, and bcl-2 G-quadruplexes and caspase-3/9 preferred to bind with Pt2 rather than Pt1, which also can induce senescence and apoptosis. The different biological behavior of Pt1 and Pt2 may correlate with the presence of a 6-hydroxyl group in L(b). Importantly, Pt1 and Pt2 exhibited higher safety in vivo and more effective inhibitory effects on tumor growth in the HCT-8 and NCI-H460 xenograft mouse model, compared with cisplatin. Taken together, these mechanistic insights indicate that both Pt1 and Pt2 display low toxicity and could be novel anticancer drug candidates.
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Affiliation(s)
- Zhen-Feng Chen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University , Yucai Road 15, Guilin 541004, P. R. China
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15
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Raju G, Srinivas R, Reddy MD, Reddy CR, Nagesh N. Studies on non-covalent interaction of coumarin attached pyrimidine and 1-methyl indole 1,2,3 triazole analogues with intermolecular telomeric G-quadruplex DNA using ESI-MS and spectroscopy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:489-506. [PMID: 24972013 DOI: 10.1080/15257770.2014.891742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the present study, electrospray ionization mass spectrometry (ESI-MS) and spectroscopy have been used to evaluate the non-covalent interaction, stoichiometry, and selectivity of two synthetic coumarin-attached nucleoside and non-nucleoside 1,2,3-triazoles, namely, (1-(5-(hydroxymethyl)-4-(4-((2-oxo-2H-chromen-4-yloxy)methyl)-1H-1,2,3-triazol-1-yl)tetrahydro-furan-2-yl)5-methyl pyrimidine-2,4(1H,3H)-dione (Tr1) and 4-((1-((-1-methyl-1H-indol-2-yl)methyl)-1H-1,2,3-triazol-4-yl)methoxy)-2H-chromen-2-one (Tr2) with two different human telomeric intermolecular G-quadruplex DNA structures formed by d(T2AG3) and d(T2AG3)2 sequences. ESI-MS studies indicate that Tr1 specifically interacts with four-stranded intermolecular parallel quadruplex complex, whereas Tr2 interacts with two hairpin as well as four-stranded intermolecular parallel quadruplex complexes. UV-Visible spectroscopic studies suggest that Tr1 and Tr2 interact with G-quadruplex structure and unwind them. Job plots show that stoichiometry of ligand:quadruplex DNA is 1:1. Circular dichroism (CD) studies of G-quadruplex DNA and Tr1/Tr2 ligands manifest that they unfold DNA on interaction. Fluorescence studies demonstrate that ligand molecules intercalate between the two stacks of quadruplex DNA and non-radiative energy transfer occurs between the excited ligand molecules (donor) and quadruplex DNA (acceptor), resulting in enhancement of fluorescence emission intensity. Thus, these studies suggest that nucleoside and non-nucleoside ligands efficiently interact with d(T2AG3) and d(T2AG3)2 G-quadruplex DNA but the interaction is not alike with all kinds of quadruplex DNA, this is probably due to the variation in the pharmacophores and structure of the ligand molecules.
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Affiliation(s)
- G Raju
- a National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology , Hyderabad , India
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16
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Nagesh N, Raju G, Srinivas R, Ramesh P, Reddy MD, Reddy CR. A dihydroindolizino indole derivative selectively stabilizes G-quadruplex DNA and down-regulates c-MYC expression in human cancer cells. Biochim Biophys Acta Gen Subj 2015; 1850:129-40. [DOI: 10.1016/j.bbagen.2014.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/03/2014] [Accepted: 10/07/2014] [Indexed: 12/30/2022]
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Salem AA, El Haty IA, Abdou IM, Mu Y. Interaction of human telomeric G-quadruplex DNA with thymoquinone: a possible mechanism for thymoquinone anticancer effect. Biochim Biophys Acta Gen Subj 2014; 1850:329-42. [PMID: 25450185 DOI: 10.1016/j.bbagen.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND Thymoquinone (TQ) has been documented to possess chemo-preventive and chemotherapeutic antitumor effects. Studies reported that TQ inhibits the growth of cancer cells in animal models, culture and xenografted tumors. Molecular mechanisms underlying these anticancer effects were attributed to inductions of cell cycle arrest, apoptosis, oxidative damage of cellular macromolecules, blockade of tumor angiogenesis and inhibitions in migration, invasion and metastasis of cancer cells. On the other hand, human telomere DNA plays a role in regulating genes' transcriptions. It folds up into G-quadruplex structures that inhibit telomerase enzyme over-expressed in cancerous cells. Molecules that selectively stabilize G-quadruplex are potential anticancer agents. Therefore, this work aimed to explore the interaction of TQ with G-quadruplex DNA as a possible underlying mechanism for the anticancer effect of TQ. METHODS Interactions of TQ with telomeric G-quadruplex (5'-AGGG(TTAGGG)3-3') and duplex DNAs were studied using UV-vis, fluorescence, circular dichroism, liquid and solid NMR (1H and 13C), melting temperature and docking simulation. RESULTS Changes in UV-vis, CD, fluorescence, 1H NMR and 13C NMR, spectra as well as melting temperatures and docking simulations provided evidences for TQ's interactions with G-quadruplex. TQ was found to interact with G-quadruplex on two binding sites adjacent to the TTA loop with binding constants 1.80×10(5) and 1.12×10(7) M(-1). Melting temperatures indicated that TQ stabilized G-quadruplex by 5.6 °C and destabilized ct-DNA by 5.1 °C. Selectivity experiment indicated that TQ is preferentially binding to G-quadruplex over duplex with selectivity coefficients of 2.80-3.33×10(-3). Results suggested an intercalation binding mode based on π-π stacking. CONCLUSION Our results propose that TQ can possibly act as a G-quadruplex DNA stabilizer and subsequently contribute to the inhibition of telomerase enzyme and cancer's proliferation. GENERAL SIGNIFICANCE Our results represent a change in the paradigms reported for structural features of G-quadruplex's stabilizers and anticancer mechanisms of TQ.
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Affiliation(s)
- Alaa A Salem
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Ismail A El Haty
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Ibrahim M Abdou
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Yuguang Mu
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Singapore
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Recognition of chelerythrine to human telomeric DNA and RNA G-quadruplexes. Sci Rep 2014; 4:6767. [PMID: 25341562 PMCID: PMC4208030 DOI: 10.1038/srep06767] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/29/2014] [Indexed: 01/25/2023] Open
Abstract
A study on binding of antitumor chelerythrine to human telomeric DNA/RNA G-quadruplexes was performed by using DNA polymerase stop assay, UV-melting, ESI-TOF-MS, UV-Vis absorption spectrophotometry and fluorescent triazole orange displacement assay. Chelerythrine selectively binds to and stabilizes the K(+)-form hybrid-type human telomeric DNA G-quadruplex of biological significance, compared with the Na(+)-form antiparallel-type DNA G-quadruplex. ESI-TOF-MS study showed that chelerythrine possesses a binding strength for DNA G-quadruplex comparable to that of TMPyP4 tetrachloride. Both 1:1 and 2:1 stoichiometries were observed for chelerythrine's binding with DNA and RNA G-quadruplexes. The binding strength of chelerythrine with RNA G-quadruplex is stronger than that with DNA G-quadruplex. Fluorescent triazole orange displacement assay revealed that chelerythrine interacts with human telomeric RNA/DNA G-quadruplexes by the mode of end- stacking. The relative binding strength of chelerythrine for human telomeric RNA and DNA G-quadruplexes obtained from ESI-TOF-MS experiments are respectively 6.0- and 2.5-fold tighter than that with human telomeric double-stranded hairpin DNA. The binding selectivity of chelerythrine for the biologically significant K(+)-form human telomeric DNA G-quadruplex over the Na(+)-form analogue, and binding specificity for human telomeric RNA G-quadruplex established it as a promising candidate in the structure-based design and development of G-quadruplex specific ligands.
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Li YL, Qin QP, Liu YC, Chen ZF, Liang H. A platinum(II) complex of liriodenine from traditional Chinese medicine (TCM): Cell cycle arrest, cell apoptosis induction and telomerase inhibition activity via G-quadruplex DNA stabilization. J Inorg Biochem 2014; 137:12-21. [DOI: 10.1016/j.jinorgbio.2014.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 01/02/2023]
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20
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Xu CX, Shen Y, Hu Q, Zheng YX, Cao Q, Qin PZ, Zhao Y, Ji LN, Mao ZW. Stabilization of human telomeric G-quadruplex and inhibition of telomerase activity by propeller-shaped trinuclear Pt(II) complexes. Chem Asian J 2014; 9:2519-26. [PMID: 24996049 DOI: 10.1002/asia.201402258] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/15/2014] [Indexed: 12/21/2022]
Abstract
Two novel propeller-shaped, trigeminal-ligand-containing, flexible trinuclear Pt(II) complexes, {[Pt(dien)]3(ptp)}(NO3)6 (1) and {[Pt(dpa)]3(ptp)}(NO3)6 (2) (dien: diethylenetriamine; dpa: bis-(2-pyridylmethyl)amine; ptp: 6'-(pyridin-3-yl)-3,2':4',3''-terpyridine), have been designed and synthesized, and their interactions with G-quadruplex (G4) sequences are characterized. A combination of biophysical and biochemical assays reveals that both Pt(II) complexes exhibit higher affinity for human telomeric (hTel) and c-myc promoter G4 sequences than duplex DNA. Complex 1 binds and stabilizes hTel G4 sequence more effectively than complex 2. Both complexes are found to induce and stabilize either antiparallel or parallel conformation of G4 structures. Molecular docking studies indicate that complex 1 binds into the large groove of the antiparallel hTel G4 structure (PDB ID: 143D) and complex 2 stacks onto the exposed G-quartet of the parallel hTel G4 structure (PDB ID: 1KF1). Telomeric repeat amplification protocol assays demonstrate that both complexes are good telomerase inhibitors, with IC50 values of (16.0±0.4) μM and (4.20±0.25) μM for 1 and 2, respectively. Collectively, the results suggest that these propeller-shaped flexible trinuclear Pt(II) complexes are effective and selective G4 binders and good telomerase inhibitors. This work provides valuable information for the interaction between multinuclear metal complexes with G4 DNA.
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Affiliation(s)
- Cui-Xia Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, 510275 (China), Fax: (+86) 20-84112245
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21
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22
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Wang ZF, Li MH, Hsu STD, Chang TC. Structural basis of sodium-potassium exchange of a human telomeric DNA quadruplex without topological conversion. Nucleic Acids Res 2014; 42:4723-33. [PMID: 24476914 PMCID: PMC3985656 DOI: 10.1093/nar/gku083] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Understanding the mechanism of Na(+)/K(+)-dependent spectral conversion of human telomeric G-quadruplex (G4) sequences has been limited not only because of the structural polymorphism but also the lack of sufficient structural information at different stages along the conversion process for one given oligonucleotide. In this work, we have determined the topology of the Na(+) form of Tel23 G4, which is the same hybrid form as the K(+) form of Tel23 G4 despite the distinct spectral patterns in their respective nuclear magnetic resonance (NMR) and circular dichroism spectra. The spectral difference, particularly the well-resolved imino proton NMR signals, allows us to monitor the structural conversion from Na(+) form to K(+) form during Na(+)/K(+) exchange. Time-resolved NMR experiments of hydrogen-deuterium exchange and hybridization clearly exclude involvement of the global unfolding for the fast Na(+)/K(+) spectral conversion. In addition, the K(+) titration monitored by NMR reveals that the Na(+)/K(+) exchange in Tel23 G4 is a two-step process. The addition of K(+) significantly stabilizes the unfolding kinetics of Tel23 G4. These results offer a possible explanation of rapid spectral conversion of Na(+)/K(+) exchange and insight into the mechanism of Na(+)/K(+) structural conversion in human telomeric G4s.
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Affiliation(s)
- Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, Republic of China, Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, Republic of China, Institute of Biophotonics, National Yang-Ming University, Taipei 112, Taiwan, Republic of China, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, Republic of China and Department of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, Republic of China
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23
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Wang J, Chen Y, Ren J, Zhao C, Qu X. G-Quadruplex binding enantiomers show chiral selective interactions with human telomere. Nucleic Acids Res 2014; 42:3792-802. [PMID: 24413564 PMCID: PMC3973297 DOI: 10.1093/nar/gkt1354] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chiral recognition of DNA molecules is important because DNA chiral transition and its different conformations are involved in a series of important life events. Among them, polymorphic human telomere DNA has attracted great interests in recent years because of its important roles in chromosome structural integrity. In this report, we examine the short-term effect of chiral metallo-supramolecular complex enantiomers treatment on tumor cells, and find that a zinc-finger-like alpha helical chiral metallo-supramolecular complex, [Ni2L3]4+-P enantiomer (NiP), can selectively provoke the rapid telomere uncapping, trigger DNA damage responses at telomere and degradation of G-overhang and the delocalization of telomeric protein from telomeres. Further studies indicate that NiP can induce an acute cellular apoptosis and senescence in cancer cells rather than normal cells. These results are further evidenced by the upregulation of p21 and p16 proteins. Moreover, NiP can cause translocation of hTERT from nuclear to cytoplasm through Tyr 707 phosphorylation. While its enantiomer, [Ni2L3]4+-M (NiM), has no such mentioned effects, these results clearly demonstrate the compound’s chiral selectivity in cancer cells. Our work will shed light on design of chiral anticancer drugs targeting G-quadruplex DNA, and developing telomere and telomerase modulation agents.
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Affiliation(s)
- Jiasi Wang
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China and Department of Neurosurgery, First Hospital of Jilin University, Changchun, Jilin 130021, China
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24
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Rajendran A, Endo M, Hidaka K, Thao Tran PL, Teulade-Fichou MP, Mergny JL, Sugiyama H. G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame. RSC Adv 2014. [DOI: 10.1039/c3ra45676e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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25
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Funayama R, Nakahara Y, Kado S, Tanaka M, Kimura K. A single-molecule force-spectroscopic study on stabilization of G-quadruplex DNA by a telomerase inhibitor. Analyst 2014; 139:4037-43. [DOI: 10.1039/c4an00439f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stabilization of G-quadruplex DNA by a telomerase inhibitor was semi-quantitatively evaluated by AFM-based SMFS.
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Affiliation(s)
- Ryoto Funayama
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Yoshio Nakahara
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Shinpei Kado
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Mutsuo Tanaka
- National Institute of Advanced Industrial Science and Technology
- Tsukuba, Japan
| | - Keiichi Kimura
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Gorelick RJ, Sugiyama H. HIV-1 nucleocapsid proteins as molecular chaperones for tetramolecular antiparallel G-quadruplex formation. J Am Chem Soc 2013; 135:18575-85. [PMID: 24224650 PMCID: PMC3898174 DOI: 10.1021/ja409085j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Phong Lan Thao Tran
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Robert J. Gorelick
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, P. O. Box B, Frederick, Maryland 21702-1201, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Sugiyama H. Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame. Nucleic Acids Res 2013; 41:8738-47. [PMID: 23863846 PMCID: PMC3794576 DOI: 10.1093/nar/gkt592] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Guanine-rich oligonucleotides often show a strong tendency to form supramolecular architecture, the so-called G-quadruplex structure. Because of the biological significance, it is now considered to be one of the most important conformations of DNA. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G-G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands. In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time. The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan, Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan, CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan and University of Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
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Li H, Bu X, Lu J, Xu C, Wang X, Yang X. Interaction study of ciprofloxacin with human telomeric DNA by spectroscopy and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:227-234. [PMID: 23434548 DOI: 10.1016/j.saa.2013.01.069] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 06/01/2023]
Abstract
The interaction of ciprofloxacin (CIP) with human telomeric DNA was studied in vitro using multi-spectroscopy and molecular modeling methods. The hypochromic effect with a red shift in ultraviolet (UV) absorption indicated the occurrence of the interaction between CIP and DNA. The fluorescence quenching of CIP was observed with the addition of DNA and was proved to be the static quenching. The binding constant was found to be 9.62×10(4) L mol(-1). Electrospray ionization mass spectrometry (ESI-MS) result further confirmed the formation of 1:1 non-covalent complex between DNA and CIP. Combined with the UV melting results, circular dichroism (CD) results confirmed the existence of groove binding mode, as well as conformational changes of DNA. Molecular docking studies illustrated the visual display of the CIP binding to the GC region in the minor groove of DNA. Specific hydrogen bonds and van der Waals forces were demonstrated as main acting forces between CIP and guanine bases of DNA.
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Affiliation(s)
- Huihui Li
- Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, China.
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Meng L, Liu K, Mo S, Mao Y, Yi T. From G-quartets to G-ribbon gel by concentration and sonication control. Org Biomol Chem 2013; 11:1525-32. [DOI: 10.1039/c3ob27204d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sassano MF, Schlesinger AP, Jarstfer MB. Identification of G-Quadruplex Inducers Usinga Simple, Inexpensiveand Rapid High Throughput Assay, and TheirInhibition of Human Telomerase. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2012; 6:20-8. [PMID: 23173022 PMCID: PMC3502892 DOI: 10.2174/1874104501206010020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 11/22/2022]
Abstract
Telomeres are protein and DNA complexes located atchromosome ends. Telomeric DNA is composed of a double stranded region of repetitive DNA followed by single-stranded 3' extension of aG-rich sequence. Single-stranded G-rich sequencescan fold into G-quadruplex structures,and molecules that stabilize G-quadruplexes are known to inhibit the enzyme telomerase and disrupt telomere maintenance. Because telomere maintenance is required for proliferation of cancer cells, G-quadruplex stabilizers have become attractive prospects for anticancer drug discovery.However, telomere-targeting G-quadruplex ligands have yet to enter the clinic owing in part to poor pharmacokinetics and target selectivity. Increasing the pharmacophore diversity of G-quadruplex and specifically telomeric-DNA targeting agents should assist in overcoming these shortcomings. In this work, we report the identification and validation ofligands that bind telomeric DNA and induce G-quadruplex formationusing the NCI Diversity Set I, providing validation of anextremely simple, rapid and high-throughput screen using FRET technology. Hits from the screen were validated by examining telomerase inhibition and G-quadruplex inductionusing CD spectroscopy and DNA polymerase stop assays. We show that two known DNA binding molecules, ellipticine derivativeNSC 176327 (apyridocarbazole) and NSC 305831 (an antiparasitic hetero-cyclediamidine referred to as furamidine and DB75),are selective induceG-quadruplex formation in the human telomeric sequence and bind telomeric DNA quadruplexes in the absence of stabilizing monovalent cations with molar ratios(molecule: DNA)of 4:1and 1.5:1, respectively.
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Affiliation(s)
- Maria Florencia Sassano
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Paul A, Maji B, Misra SK, Jain AK, Muniyappa K, Bhattacharya S. Stabilization and structural alteration of the G-quadruplex DNA made from the human telomeric repeat mediated by Tröger's base based novel benzimidazole derivatives. J Med Chem 2012; 55:7460-71. [PMID: 22827615 DOI: 10.1021/jm300442r] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Tröger's base skeleton with the G-quadruplex DNA (G4DNA). These Tröger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.
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Affiliation(s)
- Ananya Paul
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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Raju G, Srinivas R, Santhosh Reddy V, Idris MM, Kamal A, Nagesh N. Interaction of pyrrolobenzodiazepine (PBD) ligands with parallel intermolecular G-quadruplex complex using spectroscopy and ESI-MS. PLoS One 2012; 7:e35920. [PMID: 22558271 PMCID: PMC3338766 DOI: 10.1371/journal.pone.0035920] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 03/25/2012] [Indexed: 11/18/2022] Open
Abstract
Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5'GGGGTTGGGG3') designated as d(T(2)G(8)), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T(2)G(8)) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T(2)G(8))(2) and d(T(2)G(8))(4) forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T(2)G(8)) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex.
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Affiliation(s)
- Gajjela Raju
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad, India
| | - Ragampeta Srinivas
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad, India
| | - Vangala Santhosh Reddy
- Division of Organic Chemistry, Indian Institute of Chemical Technology, Hyderabad, India
| | | | - Ahmed Kamal
- Division of Organic Chemistry, Indian Institute of Chemical Technology, Hyderabad, India
| | - Narayana Nagesh
- Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail:
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Dohno C, Kohyama I, Hong C, Nakatani K. Naphthyridine tetramer with a pre-organized structure for 1:1 binding to a CGG/CGG sequence. Nucleic Acids Res 2011; 40:2771-81. [PMID: 22127864 PMCID: PMC3315301 DOI: 10.1093/nar/gkr1148] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A naphthyridine carbamate dimer (NCD) is a synthetic ligand for DNA containing a CGG/CGG sequence. Although NCD can bind selectively and tightly to a CGG/CGG sequence, the highly cooperative 2:1 binding mode has hampered precise analysis of the binding. We describe herein the synthesis of a series of naphthyridine tetramers consisting of two NCD molecules connected with various linkers to seek a ligand that binds to a CGG/CGG sequence exclusively with a 1:1 stoichiometry. Among the tested ligands, NCTB and Z-NCTS, which have linker moieties with restricted conformational flexibility [biphenyl and (Z)-stilbene linker, respectively], gave the exclusive formation of a 1:1 ligand–CGG/CGG complex. The (Z)-stilbene linker in Z-NCTS was designed to have pre-organized conformation appropriate for the binding and, in fact, resulted in the highest binding affinity. Thermodynamic parameters obtained by isothermal titration calorimetry indicated that the stronger binding of Z-NCTS was attributed to its lower entropic cost. The present study provides not only a novel 1:1 binding ligand, but also valuable feedback for subsequent molecular design of DNA and RNA binding ligands.
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Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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Lin S, Li S, Chen Z, He X, Zhang Y, Xu X, Xu M, Yuan G. Formation, recognition and bioactivities of a novel G-quadruplex in the STAT3 gene. Bioorg Med Chem Lett 2011; 21:5987-91. [DOI: 10.1016/j.bmcl.2011.07.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/14/2011] [Accepted: 07/14/2011] [Indexed: 01/04/2023]
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A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Nat Chem 2011; 3:782-7. [PMID: 21941250 DOI: 10.1038/nchem.1126] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 07/25/2011] [Indexed: 01/20/2023]
Abstract
Ligands that stabilize the formation of telomeric DNA G-quadruplexes have potential as cancer treatments, because the G-quadruplex structure cannot be extended by telomerase, an enzyme over-expressed in many cancer cells. Understanding the kinetic, thermodynamic and mechanical properties of small-molecule binding to these structures is therefore important, but classical ensemble assays are unable to measure these simultaneously. Here, we have used a laser tweezers method to investigate such interactions. With a force jump approach, we observe that pyridostatin promotes the folding of telomeric G-quadruplexes. The increased mechanical stability of pyridostatin-bound G-quadruplex permits the determination of a dissociation constant K(d) of 490 ± 80 nM. The free-energy change of binding obtained from a Hess-like process provides an identical K(d) for pyridostatin and a K(d) of 42 ± 3 µM for a weaker ligand RR110. We anticipate that this single-molecule platform can provide detailed insights into the mechanical, kinetic and thermodynamic properties of liganded bio-macromolecules, which have biological relevance.
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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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Tsai YL, Wang ZF, Chen WW, Chang TC. Emulsified BMVC derivative induced filtration for G-quadruplex DNA structural separation. Nucleic Acids Res 2011; 39:e114. [PMID: 21715373 PMCID: PMC3177220 DOI: 10.1093/nar/gkr499] [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: 12/28/2022] Open
Abstract
A novel method based on emulsion/filtration is introduced for G-quadruplex DNA structural separation. We first synthesized a lipophilic analogue of BMVC, 3,6-Bis(1-methyl-4-vinylpyridinium)-9-(12′-bromododecyl) carbazole diiodide (BMVC-12C-Br), which can form an oil-in-water (o/w) phase emulsion. Due to the binding preferences of BMVC-12C-Br emulsion to some specific DNA structures, the large emulsion (∼2 µm) bound DNA was separated from the small free DNA in the filtrate by a 0.22 µm pore size MCE membrane. This method is able to isolate the non-parallel G-quadruplexes from the parallel G-quadruplexes and the linear duplexes from both G-quadruplexes. In addition, this method allows us not only to determine the absence of the parallel G-quadruplexes of d(T2AG3)4 and the presence of the parallel G-quadruplexes of d(T2AG3)2 in K+ solution, but also to verify structural conversion from antiparallel to parallel G-quadruplexes of d[AG3(T2AG3)3] in K+ solution under molecular PEG condition. Moreover, this emulsion can separate the non-parallel G-quadruplexes of d(G3CGCG3AGGAAG5CG3) monomer from the parallel G-quadruplexes of its dimer in K+ solution. Together with NMR spectra, one can simplify the spectra for both the free DNA and the bound DNA to establish a spectrum-structure correlation for further structural analysis.
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Affiliation(s)
- Yu-Lin Tsai
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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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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Xu Y, Suzuki Y, Lönnberg T, Komiyama M. Human telomeric DNA sequence-specific cleaving by G-quadruplex formation. J Am Chem Soc 2010; 131:2871-4. [PMID: 19209856 DOI: 10.1021/ja807313x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Telomere is an emerging target for the treatment of human cancers. Here, we report a structure-based approach to sequence-specific cleaving of human telomeric DNA by G-quadruplex formation. Oligonucleotide with multiphosphonate [DNA-EDTP.Ce(IV)] at the 5' end binds to human telomere DNA by G-quadruplex formation and causes a sequence-specific strand break. These results provide the first proof of concept for targeting the human telomere DNA based on G-quadruplex formation, and this may serve as a starting point for the design of more efficient telomere sequence-specific cleaving reagents by G-quadruplex formation.
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Affiliation(s)
- Yan Xu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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Rosu F, Gabelica V, Smargiasso N, Mazzucchelli G, Shin-Ya K, De Pauw E. Cation involvement in telomestatin binding to g-quadruplex DNA. J Nucleic Acids 2010; 2010. [PMID: 20700418 PMCID: PMC2911584 DOI: 10.4061/2010/121259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 04/13/2010] [Indexed: 11/20/2022] Open
Abstract
The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show the incorporation of one extra ammonium ion in the telomestatin complexes. Experiments on telomestatin alone also show that the telomestatin alone is able to coordinate cations in a similar way as a crown ether. Finally, density functional theory calculations suggest that in the G-quadruplex-telomestatin complex, potassium or ammonium cations are located between the telomestatin and a G-quartet. This study underlines that monovalent cation coordination capabilities should be integrated in the rational design of G-quadruplex binding ligands.
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Affiliation(s)
- Frédéric Rosu
- Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, 4000 Liège, Belgium
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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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Shinohara KI, Sannohe Y, Kaieda S, Tanaka KI, Osuga H, Tahara H, Xu Y, Kawase T, Bando T, Sugiyama H. A Chiral Wedge Molecule Inhibits Telomerase Activity. J Am Chem Soc 2010; 132:3778-82. [DOI: 10.1021/ja908897j] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ken-ichi Shinohara
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Yuta Sannohe
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Shuji Kaieda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Ken-ichi Tanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hideji Osuga
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hidetoshi Tahara
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Takashi Kawase
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku Kyoto 606-8502, Japan, Department of Materials Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani Wakayama 640-8510, Japan, Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8553, Japan, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba Meguro-ku Tokyo 153-8904, Japan, and Institute for Integrated Cell-Material
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Pierce SE, Wang J, Jayawickramarajah J, Hamilton AD, Brodbelt JS. Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats. Chemistry 2010; 15:11244-55. [PMID: 19746468 DOI: 10.1002/chem.200901047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.
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Affiliation(s)
- Sarah E Pierce
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
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Shahabuddin MS, Nambiar M, Moorthy BT, Naik PL, Choudhary B, Advirao GM, Raghavan SC. A novel structural derivative of natural alkaloid ellipticine, MDPSQ, induces necrosis in leukemic cells. Invest New Drugs 2010; 29:523-33. [DOI: 10.1007/s10637-009-9379-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/17/2009] [Indexed: 11/24/2022]
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46
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Liu Y, Wilson WD. Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection. Methods Mol Biol 2010; 613:1-23. [PMID: 19997874 DOI: 10.1007/978-1-60327-418-0_1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
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47
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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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48
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Maiti M, Kumar GS. Polymorphic nucleic Acid binding of bioactive isoquinoline alkaloids and their role in cancer. J Nucleic Acids 2009; 2010. [PMID: 20814427 PMCID: PMC2915887 DOI: 10.4061/2010/593408] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 12/20/2022] Open
Abstract
Bioactive alkaloids occupy an important position in applied chemistry and play an indispensable role in medicinal chemistry. Amongst them, isoquinoline alkaloids like berberine, palmatine and coralyne of protoberberine group, sanguinarine of the benzophenanthridine group, and their derivatives represent an important class of molecules for their broad range of clinical and pharmacological utility. In view of their extensive occurrence in various plant species and significantly low toxicities, prospective development and use of these alkaloids as effective anticancer agents are matters of great current interest. This review has focused on the interaction of these alkaloids with polymorphic nucleic acid structures (B-form, A-form, Z-form, HL-form, triple helical form, quadruplex form) and their topoisomerase inhibitory activity reported by several research groups using various biophysical techniques like spectrophotometry, spectrofluorimetry, thermal melting, circular dichroism, NMR spectroscopy, electrospray ionization mass spectroscopy, viscosity, isothermal titration calorimetry, differential scanning calorimetry, molecular modeling studies, and so forth, to elucidate their mode and mechanism of action for structure-activity relationships. The DNA binding of the planar sanguinarine and coralyne are found to be stronger and thermodynamically more favoured compared to the buckled structure of berberine and palmatine and correlate well with the intercalative mechanism of sanguinarine and coralyne and the partial intercalation by berberine and palmatine. Nucleic acid binding properties are also interpreted in relation to their anticancer activity.
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Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), Kolkata 700032, India
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Deiters A. Small molecule modifiers of the microRNA and RNA interference pathway. AAPS JOURNAL 2009; 12:51-60. [PMID: 19937410 DOI: 10.1208/s12248-009-9159-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 10/30/2009] [Indexed: 12/14/2022]
Abstract
Recently, the RNA interference (RNAi) pathway has become the target of small molecule inhibitors and activators. RNAi has been well established as a research tool in the sequence-specific silencing of genes in eukaryotic cells and organisms by using exogenous, small, double-stranded RNA molecules of approximately 20 nucleotides. Moreover, a recently discovered post-transcriptional gene regulatory mechanism employs microRNAs (miRNAs), a class of endogenously expressed small RNA molecules, which are processed via the RNAi pathway. The chemical modulation of RNAi has important therapeutic relevance, because a wide range of miRNAs has been linked to a variety of human diseases, especially cancer. Thus, the activation of tumor-suppressive miRNAs and the inhibition of oncogenic miRNAs by small molecules have the potential to provide a fundamentally new approach for the development of cancer therapeutics.
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Affiliation(s)
- Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA.
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Dohno C, Yamamoto T, Nakatani K. Photoswitchable Unsymmetrical Ligand for DNA Hetero-Mismatches. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900323] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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