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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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2
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Danilevich VN, Kozlov SA, Shevchuk TV, Oleinikov VA, Sizova SV, Khodarovich YM, Mulyukin AL. Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection. J Biomol Struct Dyn 2019; 38:3959-3971. [PMID: 31543001 DOI: 10.1080/07391102.2019.1671228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10-50 nm) suitable for transfection was achieved using cations Ni2+, Co2+ or Cu2+ alone or in combination with Ca2+ at the specially selected concentrations (2.0 mM-3.5 mM), low ionic strength, and narrow pH range (8.0-8.5). Other ions - Mn2+, Zn2+, Tb3+, or Gd3+ - caused RNA-cleaving effect that was abolished in the presence of Ni2+, Co2+, Zn2+, or Cu2+. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasily N Danilevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey A Kozlov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Taras V Shevchuk
- Branch of the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Russia
| | - Vladimir A Oleinikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Svetlana V Sizova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Yuriy M Khodarovich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Andrey L Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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3
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He Y, Lopez A, Zhang Z, Chen D, Yang R, Liu J. Nucleotide and DNA coordinated lanthanides: From fundamentals to applications. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.02.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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4
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Andrushchenko V. Eu 3+ as a luminescence probe in DNA studies: Structural and conformational implications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:456-462. [PMID: 30738352 DOI: 10.1016/j.saa.2019.01.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/03/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu3+ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu3+ effect on DNA structure and conformational transitions. It was shown that Eu3+ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ-type form took place. Eu3+ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu3+ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu3+ ions as probes.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám, 2, 16610 Prague, Czech Republic.
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5
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Wu T, Bouř P, Andrushchenko V. Europium (III) as a Circularly Polarized Luminescence Probe of DNA Structure. Sci Rep 2019; 9:1068. [PMID: 30705327 PMCID: PMC6355874 DOI: 10.1038/s41598-018-37680-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
We report as a proof-of-concept the first application of circularly polarized luminescence (CPL) measured with a Raman optical activity (ROA) spectrometer to differentiate several DNA structures without need of sensitizing complexes. The ROA/CPL approach provides sufficiently high CPL intensity to use hydrated Eu3+ ions, thus avoiding DNA structural changes associated with binding of sensitizers and overcoming the sensitizer quenching issue. We showed that deoxyguanosine monophosphate (dGMP), single- and double-stranded DNA provide different CPL spectra, which could be used for their discrimination. Our results demonstrate that ROA/CPL method is a promising approach to measure CPL spectra of complex biomolecules when the use of sensitizers is not possible. The method can be extended to other biomolecules, such as proteins, lipids, sugars, etc.
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Affiliation(s)
- Tao Wu
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
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6
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El-Yazbi AF, Wong A, Loppnow GR. A luminescent probe of mismatched DNA hybridization: Location and number of mismatches. Anal Chim Acta 2017; 994:92-99. [DOI: 10.1016/j.aca.2017.09.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/22/2023]
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7
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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8
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Xu L, Zhou L, Chen X, Shen X, Wang J, Zhang J, Pei R. Luminescence sensitization of Tb 3+-DNA complexes by Ag . SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 180:85-90. [PMID: 28279827 DOI: 10.1016/j.saa.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Terbium ions (Tb3+) with unique photophysical properties have been utilized to develop biosensors with low background and high sensitivity. In this study, the Ag+-sensitized luminescence of Tb3+-DNA complexes was uncovered. The luminescence of Tb3+-DNA complexes could be enhanced by more than 30 times in the presence of Ag+, when Tb3+ was bound with poly(G) and poly(T) whereas not with other homopolymers. This research confirmed that the sensitization resulted from the interaction of Ag+ with certain bases involved in DNA, not just with the reported certain G-quadruplex sequence. The coordination of Ag+ to guanine and thymine bases was expected to increase their rigidities, form Tb3+-DNA-Ag+ ternary structures, and thus enhance energy transfer from guanine and thymine to Tb3+. These findings benefit the development of sensitive luminescence probes for various nucleic acids-related targets.
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Affiliation(s)
- Lijun Xu
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Xing Chen
- Public Health of Guangxi Medical University, Nanning 530021, China
| | - Xiaoqiang Shen
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China; School of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
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Lari M, Biver T, Busto N, Lozano HJ, Leal JM, Secco F, García B. Binding of Al(iii) to synthetic RNA and metal-mediated strand aggregation. Dalton Trans 2017; 46:16671-16681. [DOI: 10.1039/c7dt02830j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic curve of the binding of aluminum to RNA and metal-induced strand aggregation.
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Affiliation(s)
- Matteo Lari
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | - Tarita Biver
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Natalia Busto
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | | | - José M. Leal
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
| | - Fernando Secco
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56124 Pisa
- Italy
| | - Begoña García
- Departamento de Química
- Universidad de Burgos
- 09001 Burgos
- Spain
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10
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Yang W, Ruan Y, Wu W, Chen P, Xu L, Fu F. A "turn-on" and label-free fluorescent assay for the rapid detection of exonuclease III activity based on Tb(3+)-induced G-quadruplex conjugates. Anal Bioanal Chem 2014; 406:4535-40. [PMID: 24770805 DOI: 10.1007/s00216-014-7830-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/23/2014] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
Abstract
A "turn-on" and label-free fluorescent assay for the specific, rapid, and sensitive detection of 3' → 5' exonuclease III activity is reported in this study. The assay is based on the Tb(3+)-promoted G-quadruplex, which lead to the enhancement of Tb(3+) fluorescence due to the energy transfer from guanines. The proposed assay is highly simple, rapid, and cost-effective, and does not require sophisticated experimental techniques such as gel-based equipment or radioactive labels. It can be used for the rapid detection of exonuclease III activity with a detection limit of 0.8 U and a RSD (n = 6) <5 %. Notably, no dye was covalently conjugated to the DNA strands, which offers the advantages of low-cost and being interference-free.
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Affiliation(s)
- WeiJuan Yang
- Key Lab of Analysis and Detection for Food Safety of Ministry of Education, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
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11
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Wei Y, Liu R, Wang Y, Zhao Y, Cai Z, Gao X. Hairpin oligonucleotides anchored terbium ion: a fluorescent probe to specifically detect lead(II) at sub-nM levels. Analyst 2014; 138:2302-7. [PMID: 23446487 DOI: 10.1039/c3an36795a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A terbium based fluorescent probe was synthesized by coordinating terbium ions with a designed oligonucleotides (5'-ATATGGGGGATAT-3', termed GH5). GH5 improved the fluorescence of terbium ions by four orders of magnitude. The fluorescence enhancement of terbium ions by different oligonucleotides sequences indicated that the polyguanine loop of the hairpin GH5 is key to enhance terbium ion emission. The quantum yield of Tb-GH5 probe was 10.5% and the probe was photo-stable. The result of conductivity titration indicated that the stoichiometry of the probe is 3.5 Tb: 1 GH5, which is confirmed by fluorescence titration. This probe had high sensitivity and specificity for the detection of lead ions. The fluorescence intensity of this probe was linear with respect to lead concentration over a range 0.3-2.1 nM (R(2) = 0.99). The limit of detection for lead ions was 0.1 nM at a signal-to-noise ratio of 3.
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Affiliation(s)
- Yueteng Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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12
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On the use of X-ray absorption spectroscopy to elucidate the structure of lutetium adenosine mono- and triphosphate complexes. Anal Bioanal Chem 2013; 406:1049-61. [PMID: 23727732 DOI: 10.1007/s00216-013-7053-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/07/2013] [Indexed: 10/26/2022]
Abstract
Although the physiological impact of the actinide elements as nuclear toxicants has been widely investigated for half a century, a description of their interactions with biological molecules remains limited. It is however of primary importance to better assess the determinants of actinide speciation in cells and more generally in living organisms to unravel the molecular processes underlying actinide transport and deposition in tissues. The biological pathways of this family of elements in case of accidental contamination or chronic natural exposure (in the case of uranium rich soils for instance) are therefore a crucial issue of public health and of societal impact. Because of the high chemical affinity of those actinide elements for phosphate groups and the ubiquity of such chemical functions in biochemistry, phosphate derivatives are considered as probable targets of these cations. Among them, nucleotides and in particular adenosine mono- (AMP) and triphosphate (ATP) nucleotides occur in more chemical reactions than any other compounds on the earth's surface, except water, and are therefore critical target molecules. In the present study, we are interested in trans-plutonium actinide elements, in particular americium and curium that are more rarely considered in environmental and bioaccumulation studies than early actinides like uranium, neptunium and plutonium. A first step in this strategy is to work with chemical analogues like lanthanides that are not radioactive and therefore allow extended physical chemical characterization to be conducted that are difficult to perform with radioactive materials. We describe herein the interaction of lutetium(III) with adenosine AMP and ATP. With AMP and ATP, insoluble amorphous compounds have been obtained with molar ratios of 1:2 and 1:1, respectively. With an excess of ATP, with 1:2 molar ratio, a soluble complex has been obtained. A combination of spectroscopic techniques (IR, NMR, ESI-MS, EXAFS) together with quantum chemical calculations has been implemented in order to assess the lutetium coordination arrangement for the two nucleotides. In all the complexes described in the article, the lutetium cation is coordinated by the phosphate groups of the nucleotide plus additional putative water molecules with various tridimensional arrangements. With AMP 1:2 and ATP 1:1 solid-state compounds, polynuclear complexes are assumed to be obtained. In contrast, with ATP 1:2 soluble compound, the Lu coordination sphere is saturated by two ATP ligands, and this favors the formation of a mononuclear complex. In order to further interpret the EXAFS data obtained at the Lu LIII edge, model structures have been calculated for the 1:1 and 1:2 ATP complexes. They are discussed and compared to the EXAFS best fit metrical parameters.
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Lan T, Lu Y. Metal Ion-Dependent DNAzymes and Their Applications as Biosensors. Met Ions Life Sci 2012; 10:217-48. [DOI: 10.1007/978-94-007-2172-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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14
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Tan H, Chen Y. Ag(+)-enhanced fluorescence of lanthanide/nucleotide coordination polymers and Ag(+) sensing. Chem Commun (Camb) 2011; 47:12373-5. [PMID: 22012124 DOI: 10.1039/c1cc16003f] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The weak fluorescence of lanthanide/nucleotide coordination polymers was greatly enhanced by Ag(+) in aqueous solution, which has been used for highly sensitive sensing of Ag(+).
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Affiliation(s)
- Hongliang Tan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P R China
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15
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Huang P, Mao J, Yang L, Yu P, Mao L. Bioelectrochemically Active Infinite Coordination Polymer Nanoparticles: One-Pot Synthesis and Biosensing Property. Chemistry 2011; 17:11390-3. [DOI: 10.1002/chem.201101634] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/29/2011] [Indexed: 02/01/2023]
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16
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Li YZ, Chang WB, Ci YX. Structure effect of nucleotides in terbium(III)-nucleotide fluorescent reaction New evidence for the binding sites of terbium(III) on nucleotides. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.19930110606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Tong C, Xiang G, Bai Y. Interaction of paraquat with calf thymus DNA: a terbium(III) luminescent probe and multispectral study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:5257-5262. [PMID: 20402507 DOI: 10.1021/jf1000748] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Terbium(III), as a good luminescent probe, was developed for the study of the interaction between paraquat and calf thymus DNA (ctDNA) when the binding mode of small molecules to DNA was electrostatic binding. This interaction was further investigated using an ethidium bromide (EB) probe, UV absorption spectra, and circular dichroism spectra. On the basis of Scatchard plots constructed from fluorescence titration data of the ctDNA-Tb(3+) system in the presence of paraquat, the binding constants between paraquat and ctDNA were obtained. The results showed that the electrostatic attraction between positively charged sodium ion and negatively charged phosphate groups could inhibit the binding of paraquat to ctDNA, and competitive inhibition between Tb(3+) and paraquat also existed when they were bound to ctDNA. The effects of paraquat on the fluorescence intensity of the EB-ctDNA system indicated that the intercalation binding of paraquat to ctDNA could be excluded. This conclusion could be further supported by both the absorption spectra of paraquat in the presence of ctDNA and the CD spectra of the paraquat-ctDNA system.
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Affiliation(s)
- Changlun Tong
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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Worlinsky JL, Basu S. Detection of Quadruplex DNA by Luminescence Enhancement of Lanthanide Ions and Energy Transfer from Lanthanide Chelates. J Phys Chem B 2009; 113:865-8. [DOI: 10.1021/jp8100464] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jill L. Worlinsky
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, Pennsylvania 17870
| | - Swarna Basu
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, Pennsylvania 17870
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Kim HK, Li J, Nagraj N, Lu Y. Probing metal binding in the 8-17 DNAzyme by TbIII luminescence spectroscopy. Chemistry 2008; 14:8696-703. [PMID: 18688837 DOI: 10.1002/chem.200701789] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Metal-dependent cleavage activities of the 8-17 DNAzyme were found to be inhibited by Tb(III) ions, and the apparent inhibition constant in the presence of 100 microM of Zn(II) was measured to be 3.3+/-0.3 microM. The apparent inhibition constants increased linearly with increasing Zn(II) concentration, and the inhibition effect could be fully rescued with addition of active metal ions, indicating that Tb(III) is a competitive inhibitor and that the effect is completely reversible. The sensitized Tb(III) luminescence at 543 nm was dramatically enhanced when Tb(III) was added to the DNAzyme-substrate complex. With an inactive DNAzyme in which the GT wobble pair was replaced with a GC Watson-Crick base pair, the luminescence enhancement was slightly decreased. In addition, when the DNAzyme strand was replaced with a complete complementary strand to the substrate, no significant luminescence enhancement was observed. These observations suggest that Tb(III) may bind to an unpaired region of the DNAzyme, with the GT wobble pair playing a role. Luminescence lifetime measurements in D(2)O and H(2)O suggested that Tb(III) bound to DNAzyme is coordinated by 6.7+/-0.2 water molecules and two or three functional groups from the DNAzyme. Divalent metal ions competed for the Tb(III) binding site(s) in the order Co(II)>Zn(II)>Mn(II)>Pb(II)>Ca(II) approximately Mg(II). This order closely follows the order of DNAzyme activity, with the exception of Pb(II). These results indicate that Pb(II), the most active metal ion, competes for Tb(III) binding differently from other metal ions such as Zn(II), suggesting that Pb(II) may bind to a different site from that for the other metal ions including Zn(II) and Tb(III).
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Affiliation(s)
- Hee-Kyung Kim
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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Costa D, Luísa Ramos M, Burrows HD, José Tapia M, da Graça Miguel M. Using lanthanides as probes for polyelectrolyte–metal ion interactions. Hydration changes on binding of trivalent cations to nucleotides and nucleic acids. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Horrocks WD, Albin M. Lanthanide Ion Luminescence in Coordination Chemistry and Biochemistry. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9780470166321.ch1] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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22
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Galezowska E, Gluszynska A, Juskowiak B. Luminescence study of G-quadruplex formation in the presence of Tb3+ ion. J Inorg Biochem 2007; 101:678-85. [PMID: 17289149 DOI: 10.1016/j.jinorgbio.2006.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 12/13/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
The interactions of Tb3+ with the quadruplex-forming oligonucleotide bearing human telomeric repeat sequence d(G(3)T(2)AG(3)T(2)AG(3)T(2)AG(3)), (htel21), have been studied using luminescence spectroscopy and circular dichroism (CD). Enhanced luminescence of Tb3+, resulting from energy transfer from guanines, indicated encapsulation of Tb3+ ion in the central cavity of quadruplex core. The ability of lanthanide ions (Eu3+ and Tb3+) to mediate formation of quadruplex structure has been further evidenced by the fluorescence energy transfer measurements with the use of oligonucleotide probe labeled with fluorescein and rhodamine FRET partners, FAM-htel21-TAMRA. The CD spectra revealed that Tb3+/htel21 quadruplex possesses antiparallel strand orientation, similarly as sodium quadruplex. Tb3+ binding equilibria have been investigated in the absence and the presence of competing metal cations. At low Tb3+ concentration (8 microM) Tb3+/htel21 quadruplex stability is very high (5 x 10(6) M(-1)) and stoichiometry of 5-7 Tb3+ ions per one quadruplex molecule is observed. Luminescence and CD titration experiments suggested that the cavity of quadruplex accommodates two Tb3+ ions and the remaining Tb3+ ions bind probably to TTA loops of quadruplex. Higher concentration of Tb3+ (above 10 microM) results in the excessive binding of Tb3+ ions that finally destabilizes quadruplex, which undergoes transformation into differently organized assemblies. Such assemblies (probably possessing multiple positive charge) exhibit kinetic stability, which is manifested by a very slow kinetics of displacement of Tb3+ ion by competing cations (Li+, Na+, K+).
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Affiliation(s)
- Elzbieta Galezowska
- Department of Analytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland
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Yi L, Zhao H, Sun C, Chen S, Jin L. Flow-injection chemiluminescence study of Ce(IV)-Na2SO3-Tb(III)-fluoquinolone antibiotic system with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:2541-2546. [PMID: 12963449 DOI: 10.1016/s1386-1425(02)00439-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A novel flow injection chemiluminescence (CL) system is developed to determine DNA. According to the fact that DNA linearly quenches the CL intensity of Ce(IV)-Na(2)SO(3)-Tb(III)-fluoquinolone antibiotic (FLUQ) system, DNA concentration is determined. The calibration graphs are linear in the range of 0.04-10 microg/ml (for both natural and denatured DNA), and the 3sigma limits of detection are 7.8 ng/ml (natural DNA) and 9.5 ng/ml (denatured DNA). According to fluorescence spectrum and CL spectrum, and through studying the reaction of Ce(IV)-Na(2)SO(3)-Tb(III)-FLUQ with nucleotides and bases, we conclude that DNA counteracts the energy transfer from FLUQ to Tb(III), and this function is related to both bases and phosphate groups in DNA.
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Affiliation(s)
- Lin Yi
- Department of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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24
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25
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Walter NG, Yang N, Burke JM. Probing non-selective cation binding in the hairpin ribozyme with Tb(III). J Mol Biol 2000; 298:539-55. [PMID: 10772868 DOI: 10.1006/jmbi.2000.3691] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Catalysis by the hairpin ribozyme is stimulated by a wide range of both simple and complex metallic and organic cations. This independence from divalent metal ion binding unequivocally excludes inner-sphere coordination to RNA as an obligatory role for metal ions in catalysis. Hence, the hairpin ribozyme is a unique model to study the role of outer-sphere coordinated cations in folding of a catalytically functional RNA structure. Here, we demonstrate that micromolar concentrations of a deprotonated aqueous complex of the lanthanide metal ion terbium(III), Tb(OH)(aq)(2+), reversibly inhibit the ribozyme by competing for a crucial, yet non-selective cation binding site. Tb(OH)(aq)(2+) also reports a likely location of this binding site through backbone hydrolysis, and permits the analysis of metal binding through sensitized luminescence. We propose that the critical cation-binding site is located at a position within the catalytic core that displays an appropriately-sized pocket and a high negative charge density. We show that cationic occupancy of this site is required for tertiary folding and catalysis, yet the site can be productively occupied by a wide variety of cations. It is striking that micromolar Tb(OH)(aq)(2+) concentrations are compatible with tertiary folding, yet interfere with catalysis. The motif implicated here in cation-binding has also been found to organize the structure of multi-helix loops in evolutionary ancient ribosomal RNAs. Our findings, therefore, illuminate general principles of non-selective outer-sphere cation binding in RNA structure and function that may have prevailed in primitive ribozymes of an early "RNA world".
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Affiliation(s)
- N G Walter
- Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, The University of Vermont, 306 Stafford Hall, Burlington, VT, 05405, USA.
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26
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Lin C, Yang J, Wu X, Zhang G, Liu R, Cao X, Han R. Enhanced fluorescence of the terbium–gadolinium–nucleic acids system and the determination of nucleic acids. Anal Chim Acta 2000. [DOI: 10.1016/s0003-2670(99)00653-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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28
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Chatterji D, Gopal V. Fluorescence spectroscopy analysis of active and regulatory sites of RNA polymerase. Methods Enzymol 1996; 274:456-78. [PMID: 8902825 DOI: 10.1016/s0076-6879(96)74037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D Chatterji
- Center for Cellular and Molecular Biology, Hyderabad, India
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29
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Jolles B, Laigle A, Liquier J, Chinsky L. Evaluation of the structural modifications induced by mitomycin C on nucleic acids. Biophys Chem 1993; 46:179-85. [PMID: 8513119 DOI: 10.1016/0301-4622(93)85025-d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The interaction of poly(dG-dC).poly(dG-dC) with mitomycin C, an antitumor antibiotic, has been studied by various spectroscopic methods: circular dichroism, Fourier transform infrared resonance Raman scattering and using fluorescence emission of terbium bound to unpaired guanines as local conformation probe. The results allowed us to confirm the lack of long range modification of the DNA secondary structure upon binding. They also brought first information concerning the modification of the local structure of the nucleic acid at the level of mono- or bifunctional adducts.
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Affiliation(s)
- B Jolles
- Laboratoire de Physique et Chimie Biomoléculaires (C.N.R.S. URA 198), Université Pierre et Marie Curie, Paris, France
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30
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Blagoy Y, Levitsky I, Rubin Y. Spectra-kinetic investigation POLY(G) and DNA with luminescence probes: energy migration and changes of structure at low temperatures. J Mol Struct 1993. [DOI: 10.1016/0022-2860(93)80330-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Blagoy Y, Levitsky I, Rubin Y, Slavin V. One-dimensional migration of triplet excitations in polymers at low temperatures: polyquanylic acid—lTb3+ complex. Chem Phys Lett 1993. [DOI: 10.1016/0009-2614(93)85399-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Nagesh N, Bhargava P, Chatterji D. Terbium(III)-induced fluorescence of four-stranded G4-DNA. Biopolymers 1992; 32:1421-4. [PMID: 1420968 DOI: 10.1002/bip.360321015] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- N Nagesh
- Centre for Cellular and Molecular Biology, Hyderabad, India
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33
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Klakamp SL, Horrocks WD. Lanthanide ion luminescence as a probe of DNA structure. 2. Non- guanine-containing oligomers and nucleotides. J Inorg Biochem 1992; 46:193-205. [PMID: 1517731 DOI: 10.1016/0162-0134(92)80029-u] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oligo(dC)8, oligo(dA)8, and oligo(dT)8 as well as d-CMP, d-AMP, and d-TMP, when complexed to Eu(3+), possess two classes of Eu(3+) binding environment. The binding environments consist of two classes, tight sites which coordinate two H2O molecules, and weaker sites which coordinate six or seven, analogous to the previously studied guanine-containing molecules. It is inferred that the tight class of Eu(3+) ion site observed with these oligomers and nucleotides corresponds to dimeric or polymeric structures. Comparison of the results for the guanine and non-guanine containing oligomers suggests that Eu(3+) possibly coordinates base nitrogen atoms in the former and in an outer sphere mode (hydrogen bonding via the H2O molecules coordinated to Eu(3+)) in the species examined here.
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Affiliation(s)
- S L Klakamp
- Department of Chemistry, Pennsylvania State University, University Park
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34
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Klakamp SL, Horrocks WD. Lanthanide ion luminescence as a probe of DNA structure. 1. Guanine-containing oligomers and nucleotides. J Inorg Biochem 1992; 46:175-92. [PMID: 1517730 DOI: 10.1016/0162-0134(92)80028-t] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Laser-induced Eu(3+) luminescence spectroscopy is used to probe the interaction of Eu(3+) ion with guanine-containing nucleotides and single-stranded oligomers. By using time-resolved and non-time-resolved Eu(3+) luminescence techniques, two classes of Eu(3+) binding site are observed in oligo(dG)10, oligo(dG)8, oligo(dG)6, oligo(dG)4, and d-GMP. One class of site binds Eu(3+) ions more strongly than the other. Since the "tight" class of bound Eu(3+) ions have two coordinated water molecules, it is inferred that six or seven atoms from the oligomers are coordinating the Eu(3+). The "weaker" class of Eu(3+) ion sites involve the coordination of six or seven water molecules and therefore, are coordinated by one or two atoms from the oligomer. The tight class of Eu(3+) binding site is attributed to an interstrand association of Eu(3+) with the oligomers forming dimeric or polymeric structures. The dissociation constants (Kd) for the 1:1 complexes Eu(d-GMP)+ and Eu(d-GTP)- have been determined as well as the Kd for the dimerization reaction of Eu(d-GMP)+. The Tb(3+) luminescence enhancement properties of these molecules are also examined in relation to their EU(3+) binding characteristics.
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Affiliation(s)
- S L Klakamp
- Department of Chemistry, Pennsylvania State University, University Park
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35
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Fluorescence enhancement of terbium(III) by nucleotides and polyhomonucleotides in the presence of phenanthroline. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf00321699] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Tajmir-Riahi HA. Interaction of La (III) and Tb (III) ions with purine nucleotides: evidence for metal chelation (N-7-M-PO3) and the effect of macrochelate formation on the nucleotide sugar conformation. Biopolymers 1991; 31:1065-75. [PMID: 1664746 DOI: 10.1002/bip.360310906] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction of the La (III) and Tb (III) ions with adenosine-5'-monophosphate (5'-AMP), guanosine-5'-monophosphate (5'-GMP), and 2'-deoxyguanosine-5'-monophosphate (5'-dGMP) anions with metal/nucleotide ratios of 1 and 2 has been studied in aqueous solution in acidic and neutral pHs. The solid complexes were isolated and characterized by Fourier transform ir and 1H-nmr spectroscopy. The lanthanide (III)-nucleotide complexes are polymeric in nature both in the solid and aqueous solutions. In the metal-nucleotide complexes isolated from acidic solution, the nucleotide binding is via the phosphate group (inner sphere) and an indirect metal-N-7 interaction (outer-sphere) with the adenine N-1 site protonated. In the complexes obtained from neutral solution, metal chelation through the N-7 and the PO3(2-) group is prevailing. In aqueous solution, an equilibrium between the inner and outer sphere metal-nucleotide interaction has been observed. The ribose moiety shows C2'-endo/anti pucker in the free AMP anion and in the lanthanide (III)-AMP complexes, whereas the GMP anion with C2'-endo/anti sugar conformation exhibits a mixture of the C2'-endo/anti and C3'-endo/anti sugar puckers in the lanthanide (III)-GMP salts. The deoxyribose has O4'-endo/anti sugar pucker in the free dGMP anion and a C3'-endo/anti, in the lanthanide (III)-dGMP complexes.
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Affiliation(s)
- H A Tajmir-Riahi
- Centre de recherche en photobiophysique, Université du Québec à Trois-Rivières, Canada
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37
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Ci YX, Li YZ, Chang WB. Fluorescence reaction of terbium(III) with nucleic acids in the presence of phenanthroline. Anal Chim Acta 1991. [DOI: 10.1016/s0003-2670(00)84680-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Ringer DP, Etheredge JL, Dalrymple BL, Niedbalski JS. Fluorescence of phosphotyrosine--terbium(III) complexes. Biochem Biophys Res Commun 1990; 168:267-73. [PMID: 1691639 DOI: 10.1016/0006-291x(90)91703-u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phosphotyrosine, a biologically important protein residue, was investigated for the ability to enhance terbium (Tb3+) fluorescence. Spectroscopic analysis of the Tb3+: phosphotyrosine interaction indicated the development of a new excitation peak at 275 nm and strong Tb+ fluorescence enhancement at 488 and 540 nm that was linear over a range from 0.5 to 100 microM amino acid. Subsequent experiments comparing the ability of phosphotyrosine, phosphothreonine, phosphoserine and 20 other common non-phosphorylated amino acids showed that only phosphotyrosine produced significant Tb3+ fluorescence enhancement. Analysis of various phospho-sugars and nucleotides showed (with the expected exception of GMP) that they produced little or no significant fluorescence enhancement, indicating a further selectiveness for the phosphotyrosine: Tb3+ fluorescence enhancement event. These results establish a basis for the future use of Tb3+ fluorescence enhancement as a unique probe for the investigation of phosphotyrosine residues.
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Affiliation(s)
- D P Ringer
- Samuel Roberts Noble Foundation, Inc. Ardmore, Oklahoma 73402
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39
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Abstract
Terbium (Tb3+) fluorescence was used to investigate local non-denaturation perturbations of double-helical DNA structure induced in this nucleic acid by various physical and chemical agents. It has been shown that the interaction of Tb3+ with DNA into which single-strand or double-strand breaks have been introduced by DNase I or by low doses of ionizing radiation does not influence the fluorescence of the lanthanide cation. On the other hand, interaction of terbium with DNA modified by the antitumour drug cis-diamminedichloroplatinum(II) at low levels of binding and by low doses of ultraviolet radiation (wavelength 254 nm) has been shown to result in substantial enhancement of the fluorescence of this cation. It has been proposed that the terbium fluorescent probe can also be exploited successfully for the purpose of analysing the guanine bases present in distorted double-stranded regions of DNA, in which only the vertical stacking of the base-pairs is altered.
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Affiliation(s)
- Z Balcarová
- Institute of Biophysics, Czechoslovak Academy of Sciences, Brno
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40
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EVANS CH, RUSSEL AP, WESTCOTT VC. APPROACHES TO PARAMAGNETIC SEPARATIONS IN BIOLOGY AND MEDICINE. PARTICULATE SCIENCE AND TECHNOLOGY 1989. [DOI: 10.1080/02726358908906527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Simpkins H, Figliomeni M, Rosen M. The interaction of platinum and anthrapyrazole antitumor drugs with mouse thymocytes studied by terbium fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 972:25-32. [PMID: 2846072 DOI: 10.1016/0167-4889(88)90098-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fluorescent lanthanide, terbium has been employed to study the effect of a series of platinum and anthracycline drugs and an anthrapyrazole (oxanthrazole) on terbium binding to mouse thymocytes. It was observed that terbium fluorescence intensity was markedly decreased by two platinum drugs (cis-dichlorodiammine platinum(II) (cis-DDP) and cis-dichloro-trans-dihydroxybis(isopropylammine) platinum(IV) (CHIP)) and an anthrapyrazole (oxanthrazole), but that the lipophylic derivative cis-diammine-1,1-cyclobutanedicarboxylate platinum(II) had a small but significant effect and the anthracyclines (at low concentrations) had no effect. The calcium channel blocker, verapamil also had no effect. The effect of cis-DDP was markedly dependent on ionic strength in contradistinction to CHIP. The decreases in phosphorescence decay produced by cis-DDP also showed a marked dependence on ionic strength. It is proposed that cis-DDP interacts with the membrane primarily by a charge effect, but that CHIP may produce a conformational change in the membrane. These data are interesting, since the lipophylic platinum drugs (CHIP and CBDCA) also increased significantly the amount of bound intracellular calcium, but all the drugs decreased mitogen-stimulated calcium uptake into mouse thymocytes.
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Affiliation(s)
- H Simpkins
- Department of Pathology, State University of New York, NY 11203-2093
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42
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43
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Wenzel TJ, Collette LM. Lanthanide ions as luminescent chromophores for the liquid chromatographic detection of polynucleotides and nucleic acids. J Chromatogr A 1988; 436:299-307. [PMID: 3356764 DOI: 10.1016/s0021-9673(00)94587-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Europium(III) and terbium(III) can be used as luminescent chromophores for the liquid chromatographic detection of certain nucleotides and nucleic acids. The method is dependent upon an energy transfer from the nucleic acid to the lanthanide ion. Of the base moieties, only xanthine, guanine, and thiouridine have appropriate excited state energy levels for efficient energy transfer. The lanthanide ion can be added in a pre- or post-column mode. The applicability of the method was demonstrated for the detection of homologous polynucleotides such as poly X and poly G. The method was also used to detect transfer RNA from Escherichia coli.
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Affiliation(s)
- T J Wenzel
- Department of Chemistry, Bates College, Lewiston, ME 04240
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44
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Al-Hakeem M, Sommer SS. Terbium identifies double-stranded RNA on gels by quenching the fluorescence of intercalated ethidium bromide. Anal Biochem 1987; 163:433-9. [PMID: 3661991 DOI: 10.1016/0003-2697(87)90245-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report that the lanthanide cation terbium quenches the fluorescence of ethidium bromide bound to double-stranded RNA by 40-fold, whereas the quenching of double-stranded and single-stranded DNA is under 2.5-fold and the quenching of single-stranded RNA is under 5-fold. This observation was used to develop a convenient method of detecting dsRNA among other nucleic acids in an agarose or polyacrylamide gel. The sensitivity of the method is approximately 4 ng/mm2.
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Affiliation(s)
- M Al-Hakeem
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905
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45
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Burns VW. Energy transfer in polynucleotide homopolymers and copolymers. Biopolymers 1986. [DOI: 10.1002/bip.360251208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Pearlman LF, Simpkins H. The differential effects produced by daunomycin and adriamycin on RNA, polynucleotides, single stranded, supercoiled DNA, and nucleosomes. Biochem Biophys Res Commun 1985; 131:1033-40. [PMID: 2413842 DOI: 10.1016/0006-291x(85)91343-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Terbium, a sensitive probe whose fluorescence is strongly enhanced when bound to unpaired guanine and xanthine bases, has been employed to study the effects of adriamycin and daunomycin on a variety of nucleotide substrates. After treatment with either drug at concentrations of less than or equal to 1:500, the fluorescence of the probe was substantially abrogated. Daunomycin, however, produced a markedly greater effect than adriamycin with rRNA, linear calf thymus DNA, and polyriboguanylic acid. The difference between the drugs was experimentally significant, suggesting that changing the C9 side group from a methyl (daunomycin) to an alcohol (adriamycin) may result in a changed base sequence specificity. The distinction was also evident when changes in electrophoretic mobility of supercoiled and nucleosomal DNA was monitored, but only at much higher (1:25) drug:DNA ratios.
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47
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Stokke T, Steen HB. Neither adriamycin nor actinomycin D displaces Tb3+ from DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 825:416-8. [PMID: 4016123 DOI: 10.1016/0167-4781(85)90070-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The decay of fluorescence of Tb3+ bound to DNA was measured in the absence and presence of adriamycin and actinomycin D. The decay for Tb3+ bound to DNA was mainly exponential (lifetime: tau = 0.96 ms). In the presence of adriamycin or actinomycin D, the Tb3+ fluorescence decayed much faster, indicating that excitation energy was transferred from Tb3+ to the drugs. Extrapolation of the decay curves to zero time showed that the number of strongly emitting, DNA-bound terbium ions was not reduced by the presence of adriamycin or actinomycin D. Hence, these drugs do not seem to displace Tb3+ bound to DNA.
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48
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Burns VW. Heavy-atom effects on energy transfer from polynucleotides to terbium (III). Biopolymers 1985; 24:1293-300. [PMID: 2992622 DOI: 10.1002/bip.360240715] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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49
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Ringer DP, Etheredge JL, Kizer DE. The influence of DNA sequence on terbium (III) fluorescence enhancement by DNA. J Inorg Biochem 1985; 24:137-45. [PMID: 4045443 DOI: 10.1016/0162-0134(85)80005-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The synthetic DNA duplexes, poly(dA-dC):poly(dG-dT), poly(dG):poly(dC), poly(dG-dC):poly(dG-dC), and poly(dG-m5dC):poly(dG-m5dC), were analyzed as double- and single-strand polymers for the ability to enhance terbium fluorescence. Using conditions which limited the enhancement of Tb3+ fluorescence to that from DNA-guanosines, our results showed that (a) guanosines in single-strand DNA enhanced terbium fluorescence equally well irrespective of the primary sequence surrounding them, and (b) guanosines in either left- (Z-form) or right- (B-form) handed double helixes failed to enhance terbium fluorescence.
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50
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Gersanovski D, Colson P, Houssier C, Fredericq E. Terbium(3+) as a probe of nucleic acids structure. Does it alter the DNA conformation in solution? BIOCHIMICA ET BIOPHYSICA ACTA 1985; 824:313-23. [PMID: 3986206 DOI: 10.1016/0167-4781(85)90037-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
At low ionic strength, Tb3+ binding strongly alters the secondary structure of DNA. Circular dichroism and electro-optical techniques are more sensitive than fluorescence to study these alterations in double-stranded DNA, at low Tb3+/DNA phosphate (I/P) ratios. Both techniques yield the following conclusion: as I/P is increased, native and sonicated DNA undergo a transition from the B- to psi-form, the latter being a compact structure characteristic of aggregated DNA. Our study of alkylated DNA establishes that the accessibility of N-7 guanine to Tb3+ is clearly required for structural alterations in an aggregated state to occur. The chelation of the phosphate group and of the N-7 guanine by Tb3+ simultaneously alters the geometry of the sugar-phosphate backbone and the stacking interaction between the bases in double-stranded DNA.
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