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El-Yazbi AF, Loppnow GR. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids. Anal Chim Acta 2013; 786:116-23. [PMID: 23790300 DOI: 10.1016/j.aca.2013.04.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.
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Affiliation(s)
- Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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2
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El-Yazbi AF, Loppnow GR. A selective, inexpensive probe for UV-induced damage in nucleic acids. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Absorption of UV light by nucleic acids can result in the formation of molecular lesions in DNA and RNA, leading to mutagenesis, carcinogenesis, and cell death. In this work, hairpin oligonucleotide probes, which have previously been shown to be selective for DNA damage, are used. The hypochromic effect, which arises from the formation of the target–hairpin hybrid when there is no damage, is used to measure the amount of UV damage by measuring the amount of single-stranded DNA oligonucleotides. With accumulated UV exposure, the target–hairpin hybrid concentration decreases and the absorbance increases, enabling detection of UV-induced DNA damage. Our results show that the selectivity for DNA damage of the hypochromism probe is comparable with the molecular beacon probes, detecting between one and three lesions in an oligonucleotide. In addition, this probe is more than 10 times cheaper than molecular beacon probes. However, it shows lower sensitivity to DNA damage. This makes its use recommended for high-throughput, qualitative analysis of DNA damage. This introduces a simple, fast, mix-and-read assay for the detection of DNA damage.
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Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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El-Yazbi AF, Loppnow GR. Chimeric RNA–DNA Molecular Beacons for Quantification of Nucleic Acids, Single Nucleotide Polymophisms, and Nucleic Acid Damage. Anal Chem 2013; 85:4321-7. [DOI: 10.1021/ac301669y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
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4
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El-Yazbi AF, Loppnow GR. 2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage. Anal Chim Acta 2012; 726:44-9. [DOI: 10.1016/j.aca.2012.03.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 11/25/2022]
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Murray V, Nguyen TV, Chen JK. The use of automated sequencing techniques to investigate the sequence selectivity of DNA-damaging agents. Chem Biol Drug Des 2012; 80:1-8. [PMID: 22416919 DOI: 10.1111/j.1747-0285.2012.01379.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this review, the use of automated DNA sequencing techniques to determine the sequence specificity of compounds that interact with DNA is discussed. The sequence specificity of a DNA-damaging agent is an essential element in determining the cellular mechanism of action of a drug. A number of DNA-damaging compounds are mutagenic, carcinogenic, as well as being widely used as cancer chemotherapeutic agents. The distribution of lesions in a sequence of DNA can give vital clues in the determination of the precise mechanism of interaction of the agent with DNA. The DNA sequence specificity of a number of DNA-damaging agents has been delineated using automated DNA sequencing technology, and these studies are discussed in this review. The current state-of-the-art methodology involves capillary electrophoresis with laser-induced fluorescence detection usually on an Applied Biosystems ABI 3730 capillary sequencer. This current technique has higher resolution, greater sensitivity, higher precision, more rapid separation times, is safer and easier to perform than previous methods. The two main methods to determine the DNA sequence selectivity of compounds that interact with DNA are described: end labelling and the polymerase stop assay. The interaction of the antitumour drug, bleomycin, with DNA is utilized to illustrate the recent technological advances.
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Affiliation(s)
- Vincent Murray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Abstract
The exposure of DNA to radiation and chemical insults leads to damage and disease. Thus, detection and understanding of DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we examine the sensitivity of different locked nucleic acid (LNA) hairpin probes for detecting UV-induced oligonucleotide damage to LNA composition, target concentration, and ionic strength. We also compare the selectivity of the LNA hairpin probe with a DNA molecular beacon (MB) hairpin probe for detecting DNA damage. Our results show that the selectivity of the LNA hairpin probe to UV-induced nucleic acid damage increases with increasing ionic strength of the buffer and decreases with increasing target concentration and with increasing LNA ratio.
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Affiliation(s)
- Amira El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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Deng B, Wang Y, Zhu P, Xu X, Ning X. Study of the binding equilibrium between Zn(II) and HSA by capillary electrophoresis–inductively coupled plasma optical emission spectrometry. Anal Chim Acta 2010; 683:58-62. [DOI: 10.1016/j.aca.2010.10.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 10/06/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
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Schettino G, Al Rashid ST, Prise KM. Radiation microbeams as spatial and temporal probes of subcellular and tissue response. Mutat Res 2010; 704:68-77. [PMID: 20079877 DOI: 10.1016/j.mrrev.2010.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/22/2009] [Accepted: 01/06/2010] [Indexed: 11/29/2022]
Abstract
Understanding the effects of ionizing radiations are key to determining their optimal use in therapy and assessing risks from exposure. The development of microbeams where radiations can be delivered in a highly temporal and spatially constrained manner has been a major advance. Several different types of radiation microbeams have been developed using X-rays, charged particles and electrons. For charged particles, beams can be targeted with sub-micron accuracy into biological samples and the lowest possible dose of a single particle track can be delivered with high reproducibility. Microbeams have provided powerful tools for understanding the kinetics of DNA damage and formation under conditions of physiological relevance and have significant advantages over other approaches for producing localized DNA damage, such as variable wavelength laser beam approaches. Recent studies have extended their use to probing for radiosensitive sites outside the cell nucleus, and testing for mechanisms underpinning bystander responses where irradiated and non-irradiated cells communicate with each other. Ongoing developments include the ability to locally target regions of 3D tissue models and ultimately to target localized regions in vivo. With future advances in radiation delivery and imaging microbeams will continue to be applied in a range of biological studies.
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Affiliation(s)
- Giuseppe Schettino
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast BT97BL, UK
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Fundador E, Rusling J. Detection of labeled abasic sites in damaged DNA by capillary electrophoresis with laser-induced fluorescence. Anal Bioanal Chem 2007; 387:1883-90. [PMID: 17206410 DOI: 10.1007/s00216-006-1041-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/19/2006] [Accepted: 11/22/2006] [Indexed: 11/29/2022]
Abstract
Removal of nucleobases from the DNA backbone leads to the formation of abasic sites. The rate of abasic site formation is significantly increased for chemically damaged nucleobases. Thus, abasic sites serve as general biomarkers for the quantification of DNA damage. Herein, we show that capillary electrophoresis with laser-induced fluorescence (CE-LIF) can be used to detect the amount of abasic sites with very high sensitivity. For proof of concept, DNA was incubated with methylmethane sulfonate (MMS) and the damaged bases were removed by incubation at 80 degrees C. The resulting abasic sites were then tagged with a fluorescent aldehyde-reactive probe (FARP). The DNA was precipitated with ethanol, and then analyzed by CE-LIF. CE-LIF and HPLC analysis shows that the fluorescently tagged DNA (DNA-FARP) had a peak area directly proportional to the amount of N-7 methyl guanines. The CE-LIF method had a detection limit of 1.2 abasic sites per 1,000,000 bases or ca. 20 attomoles of abasic sites. This provides a general method for detecting DNA damage that is not only faster but also has comparable or better sensitivity than the alternative ELISA-like method.
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Affiliation(s)
- Erwin Fundador
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA
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Abstract
Many protein-protein interactions involved in signal transduction occur through the interaction of modular protein domains in one molecule with short linear sequences of amino acids ("motifs") in another. Although protein domains are recognized by a variety of computational tools, bioinformatic approaches alone have not been successful in identifying the short sequence motifs to which domains bind. A new approach, applying motif-determining algorithms to smaller subproteomic collections of proteins that are already known to associate with each other in high-throughput protein-protein interaction screens, now appears to be capable of capturing a reasonably large number of low-affinity core motif sequences. Application of this approach to the genomes of yeast, fruit flies, nematodes, and humans has doubled the number of known or suspected protein-protein interaction motifs.
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Affiliation(s)
- Michael B Yaffe
- Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, E18-580, Cambridge, MA 02138, USA.
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Pan W, Liu Y, Huang Y, Yao S. Determination of difenidol hydrochloride by capillary electrophoresis with electrochemiluminescence detection. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 831:17-23. [PMID: 16364700 DOI: 10.1016/j.jchromb.2005.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 11/05/2005] [Accepted: 11/11/2005] [Indexed: 11/24/2022]
Abstract
A novel and sensitive method for the determination of difenidol hydrochloride has been established using capillary electrophoresis coupled with end-column electrogenerated chemiluminescence (ECL) detection, based on the ECL reaction of tris(2,2'-bypyridine)ruthenium(II) (Ru(bpy)(3)(2+)) with the tertiary amino groups of the difenidol analyte. Parameters that affect separation and detection were optimized. Calibration curve was linear over the range from 1 x 10(-6)M to 6 x 10(-5)M with a detection limit of 1 x 10(-7)M (S/N=3). Separation of difenidol hydrochloride from clomifene citrate and lidocaine was achieved using the proposed method. This method was successfully utilized to the assay of the active ingredients of the "difenidol hydrochloride" tablets and to the investigation on the interaction of difenidol hydrochloride with hemoglobin. The number of binding sites and the binding constant were estimated as (11.2 and 2.5) x 10(3)M(-1), respectively.
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Affiliation(s)
- Wen Pan
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, Hunan Province, China
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Babu C V S, Song EJ, Babar SME, Wi MH, Yoo YS. Capillary electrophoresis at the omics level: Towards systems biology. Electrophoresis 2006; 27:97-110. [PMID: 16421959 DOI: 10.1002/elps.200500511] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Emerging systems biology aims at integrating the enormous amount of existing omics data in order to better understand their functional relationships at a whole systems level. These huge datasets can be obtained through advances in high-throughput, sensitive, precise, and accurate analytical instrumentation and technological innovation. Separation sciences play an important role in revealing biological processes at various omic levels. From the perspective of systems biology, CE is a strong candidate for high-throughput, sensitive data generation which is capable of tackling the challenges in acquiring qualitative and quantitative knowledge through a system-level study. This review focuses on the applicability of CE to systems-based analytical data at the genomic, transcriptomic, proteomic, and metabolomic levels.
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Affiliation(s)
- Suresh Babu C V
- Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, Cheongryang, Seoul, Korea
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Purschke M, Kasten-Pisula U, Brammer I, Dikomey E. Human and rodent cell lines showing no differences in the induction but differing in the repair kinetics of radiation-induced DNA base damage. Int J Radiat Biol 2004; 80:29-38. [PMID: 14761848 DOI: 10.1080/09553000310001642885] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PURPOSE To compare the induction and repair of radiation-induced base damage in human and rodent cell lines. MATERIAL AND METHODS Experiments were performed with two human (normal fibroblasts HSF1 and tumour HeLa cells) and two rodent (mouse L929 and hamster CHO-K1) cell lines. Base damage was determined with the alkaline comet assay combined with the repair enzyme formamidopyrimidine-glycosylase (Fpg). Proteins were detected by Western blot. RESULTS The induction of Fpg-sensitive sites was measured in human and rodent cell lines for doses up to 8 or 5 Gy, respectively. Comets were analysed in terms of tail moments, which were transformed into Gy-equivalents. The amount of Fpg-sensitive sites increased linearly with doses up to 4 Gy, whereby the ratio of single-strand breaks (ssb) to Fpg-sensitive sites was nearly identical for human and rodent cells with ssb:Fpg-sensitive sites=1:0.41+/-0.07 and 1:0.45+/-0.05, respectively. For doses exceeding 4 Gy, the amount of Fpg-sensitive sites did not increase further, indicating a dose limit up to which the comet assay can be used to detect Fpg-sensitive sites. Repair of Fpg-sensitive sites was studied for an X-ray dose of 4 Gy. For all four cell lines, the repair was measured to be completed 24 h after irradiation, but with pronounced differences in the kinetics. In both rodent cell lines, 50% of Fpg-sensitive sites were removed after t((1/2))=25+/-10 min in contrast to t((1/2))=80+/-20 min in the two human cell lines. The two species also differed in the level of polymerase ss with, on average, a three- to fivefold higher level in rodent cells compared with human cells. CONCLUSIONS Repair of radiation-induced Fpg-sensitive sites was much faster in rodent than in human cells, which might result from the higher level of polymerase ss found in rodent cells.
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Affiliation(s)
- M Purschke
- Institute of Biophysics and Radiobiology, University-Hospital Hamburg-Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
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Lin YW, Chiu TC, Chang HT. Laser-induced fluorescence technique for DNA and proteins separated by capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 793:37-48. [PMID: 12880853 DOI: 10.1016/s1570-0232(03)00363-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent developments in capillary electrophoresis (CE) in conjunction with laser-induced fluorescence (LIF) using long-wavelength (maximum excitation wavelength>500 nm) dyes are reviewed. These dyes are particularly of interest when conducting the analyses of biopolymers by CE-LIF using He-Ne lasers. These systems are benefited from low background, low costs, easy maintenance, and compactness. Derivatizations of DNA and proteins with fluorescent or nonfluorescent chemicals can be carried out prior to, during, or after separations. With the advantages of sensitivity, rapidity, and high efficiency, the applications of CE-LIF to the analysis of polymerase chain reaction products, DNA sequencing, trace analysis of proteins, and single cell analysis have been presented.
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Affiliation(s)
- Yang-Wei Lin
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, Taiwan
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Weinfeld M, Xing JZ, Lee J, Leadon SA, Cooper PK, Le XC. Factors influencing the removal of thymine glycol from DNA in gamma-irradiated human cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2002; 68:139-49. [PMID: 11554293 DOI: 10.1016/s0079-6603(01)68096-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The toxic and mutagenic effects of ionizing radiation are believed to be caused by damage to cellular DNA. We have made use of a novel immunoassay for thymine glycol to examine the removal of this lesion from the DNA of irradiated human cells. Because of the sensitivity of the assay, we have been able to keep the radiation doses at or below the standard clinical dose of 2 Gy. Our initial observations indicated that although removal of thymine glycol is > 80% complete by 4 h post-irradiation with 2 Gy, there is a lag of 30-60 min before repair commences. However, if cells are irradiated with 0.25 Gy 4 h prior to the 2-Gy dose, removal of the thymine glycols commences immediately after the second irradiation, suggesting that repair of thymine glycol is inducible. Our current studies are directed at two aspects of the repair process, (1) factors involved in the repair process leading up to and including glycosylase-mediated removal of thymine glycol and (2) the control of the inducible response. We have observed that mutation of the XPG gene drastically reduced the level and rate of global removal of thymine glycol (induced by 2-Gy irradiation), and there was no evidence for an inducible response. Similar results were seen with a Cockayne syndrome B (CSB) cell line. We have also examined repair in quiescent and phytohemagglutinin-stimulated human lymphocytes. Both show similar kinetics for the rate of removal of thymine glycol under induced and noninduced conditions.
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Affiliation(s)
- M Weinfeld
- Experimental Oncology Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
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