1
|
El-Wakil MH, El-Dershaby HA, Ghazallah RA, El-Yazbi AF, Abd El-Razik HA, Soliman FSG. Identification of new 5-(2,6-dichlorophenyl)-3-oxo-2,3-dihydro-5H-thiazolo[3,2-a]pyrimidine-7-carboxylic acids as p38α MAPK inhibitors: Design, synthesis, antitumor evaluation, molecular docking and in silico studies. Bioorg Chem 2024; 145:107226. [PMID: 38377818 DOI: 10.1016/j.bioorg.2024.107226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
In pursuit of discovering novel scaffolds that demonstrate potential inhibitory activity against p38α MAPK and possess strong antitumor effects, we herein report the design and synthesis of new series of 17 final target 5-(2,6-dichlorophenyl)-3-oxo-2,3-dihydro-5H-thiazolo[3,2-a]pyrimidine-7-carboxylic acids (4-20). Chemical characterization of the compounds was performed using FT-IR, NMR, elemental analyses and mass spectra of some representative examples. With many compounds showing potential inhibitory activity against p38α MAPK, two derivatives, 8 and 9, demonstrated the highest activity (>70 % inhibition) among the series. Derivative 9 displayed IC50 value nearly 2.5 folds more potent than 8. As anticipated, they both showed explicit interactions inside the kinase active site with the key binding amino acid residues. Screening both compounds for cytotoxic effects, they exhibited strong antitumor activities against lung (A549), breast (MCF-7 and MDA MB-231), colon (HCT-116) and liver (Hep-G2) cancers more potent than reference 5-FU. Their noticeable strong antitumor activity pointed out to the possibility of an augmented DNA binding mechanism of antitumor action besides their kinase inhibition. Both 8 and 9 exhibited strong ctDNA damaging effects in nanomolar range. Further mechanistic antitumor studies revealed ability of compounds 8 and 9 to arrest cell cycle in MCF-7 cells at S phase, while in HCT-116 treated cells at G0-G1 and G2/M phases. They also displayed apoptotic induction effects in both MCF-7 and HCT-116 with total cell deaths more than control untreated cells in reference to 5-FU. Finally, the compounds were tested for their anti-migratory potential utilizing wound healing assay. They induced a significant decrease in wound closure percentage after 24 h treatment in the examined cancer cells when compared to untreated control MCF-7 and HCT-116 cells better than 5-FU. In silico computation of physicochemical parameters revealed the drug-like properties of 8 and 9 with no violation to Lipinski's rule of five as well as their tolerable ADMET parameters, thus suggesting their utilization as potential future drug leads amenable for further optimization and development.
Collapse
Affiliation(s)
- Marwa H El-Wakil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt.
| | - Hadeel A El-Dershaby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Rasha A Ghazallah
- Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Alexandria 21521, Egypt
| | - Amira F El-Yazbi
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Heba A Abd El-Razik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Farid S G Soliman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| |
Collapse
|
2
|
El-Yazbi AF, Elgammal FAH, Moneeb MS, Sabry SM. Sensitive MALDI-TOF MS and 'turn-on' fluorescent genosensor for the determination of DNA damage induced by CNS acting drugs. Int J Biol Macromol 2023; 241:124547. [PMID: 37094646 DOI: 10.1016/j.ijbiomac.2023.124547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/26/2023]
Abstract
The genotoxic and carcinogenic adverse effects of various drugs should be considered for assessing drug benefit/risk ratio. On that account, the scope of this study is to examine the kinetics of DNA damage triggered by three CNS acting drugs; carbamazepine, quetiapine and desvenlafaxine. Two precise, simple and green approaches were proposed for probing drug induced DNA impairment; MALDI-TOF MS and terbium (Tb3+) fluorescent genosensor. The results revealed that all the studied drugs induced DNA damage manifested by the MALDI-TOF MS analysis as a significant disappearance of the DNA molecular ion peak with the appearance of other peaks at smaller m/z indicating the formation of DNA strand breaks. Moreover, significant enhancement of Tb3+ fluorescence occurred, proportional to the amount of DNA damage, upon incubation of each drug with dsDNA. Furthermore, the DNA damage mechanism is examined. The proposed Tb3+ fluorescent genosensor showed superior selectivity and sensitivity and is significantly simpler and less expensive than other methods reported for the detection of DNA damage. Moreover, the DNA damaging potency of these drugs was studied using calf thymus DNA in order to clarify the potential safety hazards associated with the studied drugs on natural DNA.
Collapse
Affiliation(s)
- Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt.
| | - Feda A H Elgammal
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
| | - Marwa S Moneeb
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
| | - Suzy M Sabry
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, University of Alexandria, El-Messalah, Alexandria 21521, Egypt
| |
Collapse
|
3
|
Nair S, El-Yazbi AF. Novel genosensor for probing DNA mismatches and UV-induced DNA damage: Sequence-specific recognition. Int J Biol Macromol 2023; 233:123510. [PMID: 36739048 DOI: 10.1016/j.ijbiomac.2023.123510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Human genome is continuously susceptible to changes that may lead to undesirable mutations causing various diseases and cancer. Vast majority of techniques has investigated the discrimination between base-pair mismatched nucleic acid, but many of these techniques are time-consuming, complex, expensive, and limited to the detection of specific type of dsDNA mismatches. In this study, we introduce a simple mix-and-read assay for the sensitive and cost-effective analysis of DNA base mismatches and UV-induced DNA damage using Hoechst genosensor dye (H258). This dye is a minor groove binder that undergoes a drastic conformational change upon binding with mismatch DNA. The difference in binding affinity between perfectly matched and mismatched DNA was studied for sequences at different base mismatch locations and finally, extended for the detection of dsDNA damage by UVC radiation in calf thymus DNA. In addition, a comparative DNA damage kinetic study was performed using H258 (minor groove binder) and EvaGreen (intercalating) dye to get insight on assay selectivity and sensitivity with dye binding mechanism. The result shows good reproducibility making H258 genosensor a cheaper alternative for DNA mismatch and damage studies with possibility of extension for in-vitro detection of hot spots of DNA mutations.
Collapse
Affiliation(s)
- Sindhu Nair
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21526, Egypt.
| |
Collapse
|
4
|
Elzahhar PA, Nematalla HA, Al-Koussa H, Abrahamian C, El-Yazbi AF, Bodgi L, Bou-Gharios J, Azzi J, Al Choboq J, Labib HF, Kheir WA, Abu-Serie MM, Elrewiny MA, El-Yazbi AF, Belal ASF. Inclusion of Nitrofurantoin into the Realm of Cancer Chemotherapy via Biology-Oriented Synthesis and Drug Repurposing. J Med Chem 2023; 66:4565-4587. [PMID: 36921275 DOI: 10.1021/acs.jmedchem.2c01408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Structural modifications of the antibacterial drug nitrofurantoin were envisioned, employing drug repurposing and biology-oriented drug synthesis, to serve as possible anticancer agents. Eleven compounds showed superior safety in non-cancerous human cells. Their antitumor efficacy was assessed on colorectal, breast, cervical, and liver cancer cells. Three compounds induced oxidative DNA damage in cancer cells with subsequent cellular apoptosis. They also upregulated the expression of Bax while downregulated that of Bcl-2 along with activating caspase 3/7. The DNA damage induced by these compounds, demonstrated by pATM nuclear shuttling, was comparable in both MCF7 and MDA-MB-231 (p53 mutant) cell lines. Mechanistic studies confirmed the dependence of these compounds on p53-mediated pathways as they suppressed the p53-MDM2 interaction. Indeed, exposure of radiosensitive prostatic cancer cells to low non-cytotoxic concentrations of compound 1 enhanced the cytotoxic response to radiation indicating a possible synergistic effect. In vivo antitumor activity was verified in an MCF7-xenograft animal model.
Collapse
Affiliation(s)
- Perihan A Elzahhar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Hisham A Nematalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Damanhour University, Damanhour 22516, Egypt
| | - Houssam Al-Koussa
- Department of Pharmacology and Toxicology, American University of Beirut, Beirut 11072020, Lebanon
| | - Carla Abrahamian
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Amira F El-Yazbi
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Larry Bodgi
- Department of Radiation Oncology, American University of Beirut Medical Center, Beirut 11072020, Lebanon.,Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 11072020, Lebanon
| | - Jolie Bou-Gharios
- Department of Radiation Oncology, American University of Beirut Medical Center, Beirut 11072020, Lebanon.,Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 11072020, Lebanon
| | - Joyce Azzi
- Department of Radiation Oncology, American University of Beirut Medical Center, Beirut 11072020, Lebanon.,Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 11072020, Lebanon
| | - Joelle Al Choboq
- Department of Radiation Oncology, American University of Beirut Medical Center, Beirut 11072020, Lebanon.,Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 11072020, Lebanon
| | - Hala F Labib
- Department of Pharmaceutical Chemistry, College of Pharmacy, Arab Academy of Science Technology and Maritime Transport, Alexandria 21913, Egypt
| | - Wassim Abou Kheir
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 11072020, Lebanon
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
| | - Mohamed A Elrewiny
- Faculty of Pharmacy and the Research and Innovation Hub, Alamein International University, Alamein 5060335, Egypt
| | - Ahmed F El-Yazbi
- Department of Pharmacology and Toxicology, American University of Beirut, Beirut 11072020, Lebanon.,Faculty of Pharmacy and the Research and Innovation Hub, Alamein International University, Alamein 5060335, Egypt.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Ahmed S F Belal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| |
Collapse
|
5
|
Two novel "release-on-demand" fluorescent biosensors for probing UV-induced DNA damage induced in single stranded and double stranded DNA: Comparative study. Int J Biol Macromol 2022; 215:657-664. [PMID: 35777509 DOI: 10.1016/j.ijbiomac.2022.06.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/25/2022] [Indexed: 11/22/2022]
Abstract
Light in the UVC spectral region damages both single-strand (ssDNA) and double-strand DNA (dsDNA), and contributes to the formation of mutagenic photoproducts. In-vivo studies show greater damage for ssDNA compared to dsDNA. However, excited-state spectroscopy shows that dsDNA has longer excited-state lifetime than ssDNA, which increases the probability of damage for dsDNA. However, lack of a direct comparison of in-vitro ssDNA and dsDNA damage rates precludes the development of a model that elucidates the molecular factors responsible for damage. In this work, two novel sensitive "release-on-demand" biosensors are developed for the selective probing of DNA-damage and comparing the rate of DNA damage in ssDNA and dsDNA. The two biosensors involve the use of EvaGreen and Hoechst dyes for the sensitive probing of DNA-damage. The results show that ssDNA is damaged at a faster rate than dsDNA in the presence of UVC light (200-295 nm). Furthermore, we examined the effect of G/C composition on the damage rate for mostly A/T ssDNA and dsDNA oligonucleotides. Our results show that DNA damage rates are highly dependent on the fraction of guanines in the sequence, but that in-vitro dsDNA always exhibits an overall slower rate of damage compared to ssDNA, essentially independent of sequence.
Collapse
|
6
|
El-Yazbi AF, Khalil HA, Belal TS, El-Kimary EI. Inexpensive bioluminescent genosensor for sensitive determination of DNA damage induced by some commonly used sunscreens. Anal Biochem 2022; 651:114700. [DOI: 10.1016/j.ab.2022.114700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/01/2022]
|
7
|
Nair SG, El-Yazbi AF, El-Yazbi AF. Investigation of nucleic acid damage induced by a novel ruthenium anti-cancer drug using multiple analytical techniques: Sequence specificity and damage kinetics. Int J Biol Macromol 2021; 198:68-76. [PMID: 34963625 DOI: 10.1016/j.ijbiomac.2021.12.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/21/2022]
Abstract
Cis-diacetonitrilo-bis(bipyridine) ruthenium(II) chloride is a recently introduced cis-platin analogue that has anti-cancer properties with lower side effects. However, the sequence dependence of its DNA damaging mechanism is unclear. Here, we present a simple, sensitive, multiplexed mix-and-read assay for ascertaining the molecular mechanism of DNA damage induced by the studied ruthenium complex (Ru-complex). The damage kinetics and sequence specificity for the Ru-complex induced DNA damage are examined by studying the induced damage in various oligonucleotide sequences by EvaGreen-DNA intercalator probe. High-through-put measurements were established using a 96-well microplate platform that allows multiple sequences to be measured simultaneously. The results show that the extent of damage increases with an increasing number of guanines, with considerable amount of damage at GA, GT and GC sites, in particular. Furthermore, the interaction of Ru-complex with DNA was confirmed using thermal analysis and MALDI-TOF-MS. Results indicate that the activated Ru-complex preferentially binds via both mono- and di-adduct formation at G and GG sites, respectively. Moreover, the developed method was successfully applied for the determination of the potency of the studied Ru-complex to induce DNA damage in K-Ras and N-Ras family of genes, one of the most common oncogenic events in cancer.
Collapse
Affiliation(s)
- Sindhu G Nair
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Ahmed F El-Yazbi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria 21561, Egypt; Faculty of Pharmacy, Alalamein International University, Alalamein, Egypt
| | - Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21526, Egypt.
| |
Collapse
|
8
|
Novel inexpensive ‘turn-on’ fluorescent biosensor for the sensitive detection of DNA damage induced by epirubicin. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
9
|
El-Wakil MH, El-Yazbi AF, Ashour HM, Khalil MA, Ismail KA, Labouta IM. Discovery of a novel DNA binding agent via design and synthesis of new thiazole hybrids and fused 1,2,4-triazines as potential antitumor agents: Computational, spectrometric and in silico studies. Bioorg Chem 2019; 90:103089. [DOI: 10.1016/j.bioorg.2019.103089] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
|
10
|
|
11
|
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.
Collapse
Affiliation(s)
- Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Nair SG, Loppnow GR. Multiplexed, UVC-induced, sequence-dependent DNA damage detection. Photochem Photobiol 2013; 89:884-90. [PMID: 23441594 DOI: 10.1111/php.12066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/22/2013] [Indexed: 12/12/2022]
Abstract
The exposure of DNA to ultraviolet (UV) radiation causes sequence-dependent damage. Thus, there is a need for an analytical technique that can detect damage in large numbers of DNA sequences simultaneously. In this study, we have designed an assay for UVC-induced DNA damage in multiple oligonucleotides simultaneously by using a 96-well plate and a novel automated sample mover. The UVC-induced DNA damage is measured using smart probes, analogs of molecular beacons in which guanosine nucleotides act as the fluorescence quencher. Our results show that the oligonucleotide damage constants obtained with this method are reproducible and similar to those obtained in cuvettes. The calibration curve for poly-dT shows good linearity (R(2) = 0.96), with limits of detection (LOD) and quantification (LOQ) equal to 55 and 183 nm, respectively. The results show that the damage kinetics upon irradiation is sensitive to the different types of photoproducts formed in the different sequences used; i.e. poly-A oligonucleotides containing guanine are damaged at a faster rate than poly-A oligonucleotides containing either thymine or cytosine. Thus, detecting DNA damage in a 96-well plate and quantifying the damage with smart probes are a simple, fast and inexpensive mix-and-read technique for multiplexed, sequence-specific DNA damage detection.
Collapse
Affiliation(s)
- Sindhu G Nair
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | |
Collapse
|
15
|
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]
|
16
|
Shire ZJ, Loppnow GR. Molecular Beacon Probes of Oligonucleotides Photodamaged by Psoralen. Photochem Photobiol 2012; 88:645-50. [DOI: 10.1111/j.1751-1097.2012.01109.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|