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Huang C, Ma Z, Lin J, Gong X, Zhang F, Wu X, Wang F, Zheng W, Zhao Y, Wu K. Tandem Mass Spectrometry Reveals Preferential Ruthenation of Thymines in Human Telomeric G-Quadruplex DNA by an Organometallic Ruthenium Anticancer Complex. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chao Huang
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Ziqi Ma
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Jiafan Lin
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Xianxian Gong
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Fengfeng Zhang
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Xiaoqin Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Wei Zheng
- Peking University Health Science Center, Beijing 100191, People’s Republic of China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing; CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Kui Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, People’s Republic of China
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Nozeret K, Loll F, Escudé C, Boutorine AS. Polyamide fluorescent probes for visualization of repeated DNA sequences in living cells. Chembiochem 2015; 16:549-54. [PMID: 25639955 DOI: 10.1002/cbic.201402676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/07/2022]
Abstract
DNA imaging in living cells usually requires transgenic approaches that modify the genome. Synthetic pyrrole-imidazole polyamides that bind specifically to the minor groove of double-stranded DNA (dsDNA) represent an attractive approach for in-cell imaging that does not necessitate changes to the genome. Nine hairpin polyamides that target mouse major satellite DNA were synthesized. Their interactions with synthetic target dsDNA fragments were studied by thermal denaturation, gel-shift electrophoresis, circular dichroism, and fluorescence spectroscopy. The polyamides had different affinities for the target DNA, and fluorescent labeling of the polyamides affected their affinity for their targets. We validated the specificity of the probes in fixed cells and provide evidence that two of the probes detect target sequences in mouse living cell lines. This study demonstrates for the first time that synthetic compounds can be used for the visualization of the nuclear substructures formed by repeated DNA sequences in living cells.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum national d'Histoire naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris Cedex 05 (France)
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Kar RK, Suryadevara P, Jana J, Bhunia A, Chatterjee S. Novel G-quadruplex stabilizing agents: in-silico approach and dynamics. J Biomol Struct Dyn 2013; 31:1497-518. [DOI: 10.1080/07391102.2012.742246] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. J Comput Aided Mol Des 2012; 26:289-99. [PMID: 22456858 DOI: 10.1007/s10822-012-9548-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)₄. Here we report the relative stabilities of these structures under K⁺ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.
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Bazzicalupi C, Chioccioli M, Sissi C, Porcù E, Bonaccini C, Pivetta C, Bencini A, Giorgi C, Valtancoli B, Melani F, Gratteri P. Modeling and Biological Investigations of an Unusual Behavior of Novel Synthesized Acridine-Based Polyamine Ligands in the Binding of Double Helix and G-Quadruplex DNA. ChemMedChem 2010; 5:1995-2005. [DOI: 10.1002/cmdc.201000332] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhang Z, Dai J, Veliath E, Jones RA, Yang D. Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures. Nucleic Acids Res 2010; 38:1009-21. [PMID: 19946019 PMCID: PMC2817458 DOI: 10.1093/nar/gkp1029] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/19/2009] [Accepted: 10/20/2009] [Indexed: 12/21/2022] Open
Abstract
Human telomeric DNA G-quadruplex has been considered as an attractive target for cancer therapeutic intervention. The telomeric sequence shows intrinsic structure polymorphism. Here we report a novel intramolecular G-quadruplex structure formed by a variant human telomeric sequence in K(+) solution. This sequence forms a basket-type intramolecular G-quadruplex with only two G-tetrads but multiple-layer capping structures formed by loop residues. While it is shown that this structure can only be detected in the specifically truncated telomeric sequences without any 5'-flanking residues, our results suggest that this two-G-tetrad conformation is likely to be an intermediate form of the interconversion of different telomeric G-quadruplex conformations.
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Affiliation(s)
- Zhenjiang Zhang
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721 and Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Jixun Dai
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721 and Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Elizabeth Veliath
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721 and Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Roger A. Jones
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721 and Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA
| | - Danzhou Yang
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721 and Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA
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Dai J, Punchihewa C, Ambrus A, Chen D, Jones RA, Yang D. Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Nucleic Acids Res 2007; 35:2440-50. [PMID: 17395643 PMCID: PMC1874667 DOI: 10.1093/nar/gkm009] [Citation(s) in RCA: 299] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We report the NMR solution structure of the intramolecular G-quadruplex formed in human telomeric DNA in K+. The hybrid-type telomeric G-quadruplex consists of three G-tetrads linked with mixed parallel–antiparallel G-strands, with the bottom two G-tetrads having the same G-arrangement (anti:anti:syn:anti) and the top G-tetrad having the reversed G-arrangement (syn:syn:anti:syn). The three TTA loop segments adopt different conformations, with the first TTA assuming a double-chain-reversal loop conformation, and the second and third TTA assuming lateral loop conformations. The NMR structure is very well defined, including the three TTA loops and the two flanking sequences at 5′- and 3′-ends. Our study indicates that the three loop regions interact with the core G-tetrads in a specific way that defines and stabilizes the unique human telomeric G-quadruplex structure in K+. Significantly, a novel adenine triple platform is formed with three naturally occurring adenine residues, A21, A3 and A9, capping the top tetrad of the hybrid-type telomeric G-quadruplex. This adenine triple is likely to play an important role in the formation of a stable human telomeric G-quadruplex structure in K+. The unique human telomeric G-quadruplex structure formed in K+ suggests that it can be specifically targeted for anticancer drug design.
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Affiliation(s)
- Jixun Dai
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Chandanamali Punchihewa
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Attila Ambrus
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Ding Chen
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Roger A. Jones
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Danzhou Yang
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA, Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724, USA and BIO5 Institute, The University of Arizona, 1140 E. South Campus Dr, Tucson, AZ 85721, USA
- *To whom correspondence should be addressed. +1 520 626 5969+1 520 626 6988
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Nelson SM, Ferguson LR, Denny WA. DNA and the chromosome - varied targets for chemotherapy. CELL & CHROMOSOME 2004; 3:2. [PMID: 15157277 PMCID: PMC421739 DOI: 10.1186/1475-9268-3-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 05/24/2004] [Indexed: 12/29/2022]
Abstract
The nucleus of the cell serves to maintain, regulate, and replicate the critical genetic information encoded by the genome. Genomic DNA is highly associated with proteins that enable simple nuclear structures such as nucleosomes to form higher-order organisation such as chromatin fibres. The temporal association of regulatory proteins with DNA creates a dynamic environment capable of quickly responding to cellular requirements and distress. The response is often mediated through alterations in the chromatin structure, resulting in changed accessibility of specific DNA sequences that are then recognized by specific proteins. Anti-cancer drugs that target cellular DNA have been used clinically for over four decades, but it is only recently that nuclease specific drugs have been developed to not only target the DNA but also other components of the nuclear structure and its regulation. In this review, we discuss some of the new drugs aimed at primary DNA sequences, DNA secondary structures, and associated proteins, keeping in mind that these agents are not only important from a clinical perspective but also as tools for understanding the nuclear environment in normal and cancer cells.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - Lynnette R Ferguson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
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Stefl R, Cheatham TE, Spacková N, Fadrná E, Berger I, Koca J, Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys J 2003; 85:1787-804. [PMID: 12944293 PMCID: PMC1303352 DOI: 10.1016/s0006-3495(03)74608-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The formation of a cation-stabilized guanine quadruplex (G-DNA) stem is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. Here, we investigate the formation of a parallel stranded G-DNA stem consisting of four strands of d(GGGG) using molecular dynamics simulations with explicit inclusion of counterions and solvent. Due to the limitations imposed by the nanosecond timescale of the simulations, rather than watching for the spontaneous formation of G-DNA, our approach probes the stability of possible supramolecular intermediates (including two-, three-, and four-stranded assemblies with out-of-register base pairing between guanines) on the formation pathway. The simulations suggest that "cross-like" two-stranded assemblies may serve as nucleation centers in the initial formation of parallel stranded G-DNA quadruplexes, proceeding through a series of rearrangements involving trapping of cations, association of additional strands, and progressive slippage of strands toward the full stem. To supplement the analysis, approximate free energies of the models are obtained with explicit consideration of the integral cations. The approach applied here serves as a prototype for qualitatively investigating other G-DNA molecules using molecular dynamics simulation and free-energy analysis.
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Affiliation(s)
- Richard Stefl
- National Center for Biomolecular Research, Masaryk University, 612 37 Brno, Czech Republic
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Thorpe JH, Teixeira SCM, Gale BC, Cardin CJ. Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution. Nucleic Acids Res 2003; 31:844-9. [PMID: 12560479 PMCID: PMC149190 DOI: 10.1093/nar/gkg168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 11/21/2002] [Accepted: 11/21/2002] [Indexed: 11/13/2022] Open
Abstract
Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.
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Affiliation(s)
- James H Thorpe
- The University of Reading, School of Chemistry, Whiteknights, Reading, Berkshire RG6 6AD, UK
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Lindstrom UM, Chandrasekaran RA, Orbai L, Helquist SA, Miller GP, Oroudjev E, Hansma HG, Kool ET. Artificial human telomeres from DNA nanocircle templates. Proc Natl Acad Sci U S A 2002; 99:15953-8. [PMID: 12444252 PMCID: PMC138546 DOI: 10.1073/pnas.252396199] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human telomerase is a reverse-transcriptase enzyme that synthesizes the multikilobase repeating hexamer telomere sequence (TTAGGG)n at the ends of chromosomes. Here we describe a designed approach to mimicry of telomerase, in which synthetic DNA nanocircles act as essentially infinite catalytic templates for efficient synthesis of long telomeres by DNA polymerase enzymes. Results show that the combination of a nanocircle and a DNA polymerase gives a positive telomere-repeat amplification protocol assay result for telomerase activity, and similar to the natural enzyme, it is inhibited by a known telomerase inhibitor. We show that artificial telomeres can be engineered on human chromosomes by this approach. This strategy allows for the preparation of synthetic telomeres for biological and structural study of telomeres and proteins that interact with them, and it raises the possibility of telomere engineering in cells without expression of telomerase itself. Finally, the results provide direct physical support for a recently proposed rolling-circle mechanism for telomerase-independent telomere elongation.
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Affiliation(s)
- Ulf M Lindstrom
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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