1
|
Sun M, Song R, Fang Y, Xu J, Yang Z, Zhang H. DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications. ACS APPLIED MATERIALS & INTERFACES 2024; 16:51899-51915. [PMID: 39314016 DOI: 10.1021/acsami.4c13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.
Collapse
Affiliation(s)
- Mengqiu Sun
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Song
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
| | - Yangwu Fang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
| | - Jiuzhou Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhaoqi Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
| |
Collapse
|
2
|
Tong X, Moradipour M, Novak B, Kamali P, Asare SO, Knutson BL, Rankin SE, Lynn BC, Moldovan D. Experimental and Molecular Dynamics Simulation Study of the Effects of Lignin Dimers on the Gel-to-Fluid Phase Transition in DPPC Bilayers. J Phys Chem B 2019; 123:8247-8260. [DOI: 10.1021/acs.jpcb.9b05525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xinjie Tong
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Mahsa Moradipour
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Brian Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Poorya Kamali
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Shardrack O. Asare
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Barbara L. Knutson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Stephen E. Rankin
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Bert C. Lynn
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Dorel Moldovan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
3
|
Clark KD, Zhu C, Anderson JL. Maximizing Ion-Tagged Oligonucleotide Loading on Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Nucleic Acids. Anal Chem 2019; 91:5945-5952. [PMID: 30995833 DOI: 10.1021/acs.analchem.9b00350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Targeted nucleic acid analysis requires the highly selective extraction of desired DNA fragments in order to minimize interferences from samples with abundant heterogeneous sequences. We previously reported a method based on functionalized oligonucleotide probes known as ion-tagged oligonucleotides (ITOs) that hybridize with complementary DNA targets for subsequent capture using a hydrophobic magnetic ionic liquid (MIL) support. Although the ITO-MIL approach enriched specific DNA sequences in quantities comparable to a commercial magnetic bead-based method, the modest affinity of the ITO for the hydrophobic MIL limited the yield of DNA targets, particularly when stringent wash conditions were applied to remove untargeted DNA. Here, we report the synthesis and characterization of a series of ITOs in which functional groups were installed within the cation and anion components of the tag moiety in order to facilitate loading of the ITO to the MIL support phase. In addition to hydrophobic interactions, we demonstrate that π-π stacking and fluorophilic interactions can be exploited for loading oligonucleotide probes onto MILs. Using a disubstituted ion-tagged oligonucleotide (DTO) possessing two linear C8 groups, nearly quantitative loading of the probe onto the MIL support was achieved. The enhanced stability of the DTO within the MIL solvent permitted successive wash steps without the loss of the DNA target compared to a monosubstituted ITO with a single C8 group that was susceptible to increased loss of analyte. Furthermore, the successful capture of a 120 bp KRAS fragment from human plasma samples followed by real-time quantitative polymerase chain reaction (qPCR) amplification is demonstrated.
Collapse
Affiliation(s)
- Kevin D Clark
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
| | - Chenghui Zhu
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
| | - Jared L Anderson
- Department of Chemistry , Iowa State University , 1605 Gilman Hall , Ames , Iowa 50011 , United States
| |
Collapse
|
4
|
Liu S, Liang A, Wu K, Zeng W, Luo Q, Wang F. Binding of Organometallic Ruthenium Anticancer Complexes to DNA: Thermodynamic Base and Sequence Selectivity. Int J Mol Sci 2018; 19:ijms19072137. [PMID: 30041439 PMCID: PMC6073332 DOI: 10.3390/ijms19072137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/16/2022] Open
Abstract
Organometallic ruthenium(II) complexes [(η⁶-arene)Ru(en)Cl][PF₆] (arene = benzene (1), p-cymene (2), indane (3), and biphenyl (4); en = ethylenediamine) are promising anticancer drug candidates both in vitro and in vivo. In this paper, the interactions between ruthenium(II) complexes and 15-mer single- and double-stranded oligodeoxynucleotides (ODNs) were thermodynamically investigated using high performance liquid chromatography (HPLC) and electrospray ionization mass spectroscopy (ESI-MS). All of the complexes bind preferentially to G₈ on the single strand 5'-CTCTCTT₇G₈T₉CTTCTC-3' (I), with complex 4 containing the most hydrophobic ligand as the most reactive one. To the analogs of I (changing T₇ and/or T₉ to A and/or C), complex 4 shows a decreasing affinity to the G₈ site in the following order: -AG₈T- (K: 5.74 × 10⁴ M-1) > -CG₈C- > -TG₈A- > -AG₈A- > -AG₈C- > -TG₈T- (I) ≈ -CG₈A- (K: 2.81 × 10⁴ M-1). In the complementary strand of I, the G bases in the middle region are favored for ruthenation over guanine (G) bases in the end of oligodeoxynucleotides (ODNs). These results indicate that both the flanking bases (or base sequences) and the arene ligands play important roles in determining the binding preference, and the base- and sequence-selectivity, of ruthenium complex in binding to the ODNs.
Collapse
Affiliation(s)
- Suyan Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Aihua Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
5
|
Mansouri-Torshizi H, Zareian-Jahromi S, Ghahghaei A, Shahraki S, Khosravi F, Heidari Majd M. Palladium(II) complexes of biorelevant ligands. Synthesis, structures, cytotoxicity and rich DNA/HSA interaction studies. J Biomol Struct Dyn 2017; 36:2787-2806. [PMID: 28849726 DOI: 10.1080/07391102.2017.1372309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, a pair of new palladium(II) complexes, [Pd(Gly)(Phe)] and [Pd(Gly)(Tyr)], (where Gly is glycine, Phe is phenylalanine, and Tyr is tyrosine) were synthesized and characterized by UV-Vis, FT-IR, elemental analysis, 1H-NMR, and conductivity measurements. The detailed 1H NMR and infrared spectral studies of these Pd(II) complexes ascertain the mode of binding of amino acids to palladium through nitrogen of -NH2 and oxygen of -COO- groups as bidentate chelates. The Pd(II) complexes have been tested for in vitro cytotoxicity activities against cancer cell line of K562. Interactions of these Pd(II) complexes with CT-DNA and human serum albumin were identified through absorption/emission titrations and gel electrophoresis which indicated significant binding proficiency. The binding distance (r) between these synthesized complexes and HSA based on Forster's theory of non-radiation energy transfer were calculated. Alterations of HSA secondary structure induced by complexes were confirmed by FT-IR measurements. The results of emission quenching at three temperatures have revealed that the quenching mechanism of these Pd(II) complexes with CT-DNA and HSA were the static and dynamic quenching mechanism, respectively. Binding constants (Kb), binding site number (n), and the corresponding thermodynamic parameters were calculated and revealed that the hydrogen binding and hydrophobic forces played a major role when Pd(II) complexes interacted with DNA and HSA, respectively. We bid that [Pd(Gly)(Phe)] and [Pd(Gly)(Tyr)] complexes exhibit the groove binding with CT-DNA and interact with the main binding pocket of HSA. The complexes follow the binding affinity order of [Pd(Gly)(Tyr)] > [Pd(Gly)(Phe)] with CT-DNA- and HSA-binding.
Collapse
Affiliation(s)
- Hassan Mansouri-Torshizi
- a Faculty of Science, Department of Chemistry , University of Sistan and Baluchestan , Zahedan , Iran
| | - Sareh Zareian-Jahromi
- a Faculty of Science, Department of Chemistry , University of Sistan and Baluchestan , Zahedan , Iran
| | - Arezou Ghahghaei
- b Faculty of Science, Department of Biology , University of Sistan and Baluchestan , Zahedan , Iran
| | - Somaye Shahraki
- c Department of Chemistry , University of Zabol , Zabol , Iran
| | - Fatemeh Khosravi
- a Faculty of Science, Department of Chemistry , University of Sistan and Baluchestan , Zahedan , Iran
| | | |
Collapse
|
6
|
Chiu MH, Prenner EJ. Differential scanning calorimetry: An invaluable tool for a detailed thermodynamic characterization of macromolecules and their interactions. J Pharm Bioallied Sci 2011; 3:39-59. [PMID: 21430954 PMCID: PMC3053520 DOI: 10.4103/0975-7406.76463] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/05/2010] [Accepted: 10/19/2010] [Indexed: 11/04/2022] Open
Abstract
Differential Scanning Calorimetry (DSC) is a highly sensitive technique to study the thermotropic properties of many different biological macromolecules and extracts. Since its early development, DSC has been applied to the pharmaceutical field with excipient studies and DNA drugs. In recent times, more attention has been applied to lipid-based drug delivery systems and drug interactions with biomimetic membranes. Highly reproducible phase transitions have been used to determine values, such as, the type of binding interaction, purity, stability, and release from a drug delivery mechanism. This review focuses on the use of DSC for biochemical and pharmaceutical applications.
Collapse
Affiliation(s)
- Michael H Chiu
- Department of Biological Sciences, University of Calgary, T2N 1N4 Calgary, AB, Canada
| | | |
Collapse
|
7
|
Abstract
Differential methods of scanning micro-calorimetry and UV spectrophotometry were used for understanding the interaction of natural anti-tumour antibiotic actinomycin D with cluster sites of native and fragmented DNA during thermal melting. At low (micro-molar) concentrations, the actinomycin molecules penetrate into unwound regions of DNA, but not into the double helix. Moreover, they stabilize the fragmented DNA and increase a total melting point. Actinomycin D interacts with fractions of native DNA even at very low concentrations (at the antibiotic/nucleotide ratio of 1:868) and stabilizes the most loose clusters. At high concentrations, it destabilizes the double helix.
Collapse
Affiliation(s)
- Nikolai Vekshin
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| |
Collapse
|
8
|
Vekshin NL. Cluster melting of DNA-actinomycin complexes. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911010234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
9
|
Novakova O, Malina J, Suchankova T, Kasparkova J, Bugarcic T, Sadler PJ, Brabec V. Energetics, conformation, and recognition of DNA duplexes modified by monodentate Ru(II) complexes containing terphenyl arenes. Chemistry 2010; 16:5744-54. [PMID: 20376825 DOI: 10.1002/chem.200903078] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We studied the thermodynamic properties, conformation, and recognition of DNA duplexes site-specifically modified by monofunctional adducts of Ru(II) complexes of the type [Ru(II)(eta(6)-arene)(Cl)(en)](+), in which arene=para-, meta-, or ortho-terphenyl (complexes 1, 2, and 3, respectively) and en=1,2-diaminoethane. It has been shown (J. Med. Chem. 2008, 51, 5310) that 1 exhibits promising cytotoxic effects in human tumor cells, whereas 2 and 3 are much less cytotoxic; concomitantly with the high cytotoxicity of 1, its DNA binding mode involves combined intercalative and monofunctional (coordination) binding modes, whereas less cytotoxic compounds 2 and 3 bind to DNA only through a monofunctional coordination to DNA bases. An analysis of conformational distortions induced in DNA by adducts of 1 and 2 revealed more extensive and stronger distortion and concomitantly greater thermodynamic destabilization of DNA by the adducts of nonintercalating 2. Moreover, affinity of replication protein A to the DNA duplex containing adduct of 1 was pronouncedly lower than to the adduct of 2. On the other hand, another damaged-DNA-binding protein, xeroderma pigmentosum protein A, did not recognize the DNA adduct of 1 or 2. Importantly, the adducts of 1 induced a considerably lower level of repair synthesis than the adducts of 2, which suggests enhanced persistence of the adducts of the more potent and intercalating 1 in comparison with the adducts of the less potent and nonintercalating 2. Also interestingly, the adducts of 1 inhibited DNA polymerization more efficiently than the adducts of 2, and they could also be bypassed by DNA polymerases with greater difficulty. Results of the present work along with those previously published support the view that monodentate Ru(II) arene complexes belong to a class of anticancer agents for which structure-pharmacological relationships might be correlated with their DNA-binding modes.
Collapse
Affiliation(s)
- Olga Novakova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 61265 Brno, Czech Republic
| | | | | | | | | | | | | |
Collapse
|
10
|
Krause-Heuer AM, Grünert R, Kühne S, Buczkowska M, Wheate NJ, Le Pevelen DD, Boag LR, Fisher DM, Kasparkova J, Malina J, Bednarski PJ, Brabec V, Aldrich-Wright JR. Studies of the Mechanism of Action of Platinum(II) Complexes with Potent Cytotoxicity in Human Cancer Cells. J Med Chem 2009; 52:5474-84. [DOI: 10.1021/jm9007104] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anwen M. Krause-Heuer
- Nanoscale Organisation and Dynamics Group, School of Biomedical and Health Sciences, University of Western Sydney, Locked Bag 1797, Penrith South DC, 1797, NSW, Australia
| | - Renate Grünert
- Institute of Pharmacy, University of Greifswald, 17487 Greifswald, Germany
| | - Sybill Kühne
- Institute of Pharmacy, University of Greifswald, 17487 Greifswald, Germany
| | | | - Nial J. Wheate
- Nanoscale Organisation and Dynamics Group, School of Biomedical and Health Sciences, University of Western Sydney, Locked Bag 1797, Penrith South DC, 1797, NSW, Australia
| | | | - Leanne R. Boag
- Nanoscale Organisation and Dynamics Group, School of Biomedical and Health Sciences, University of Western Sydney, Locked Bag 1797, Penrith South DC, 1797, NSW, Australia
| | | | - Jana Kasparkova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | | | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
- Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, CZ-77146 Olomouc, Czech Republic
| | - Janice R. Aldrich-Wright
- Nanoscale Organisation and Dynamics Group, School of Biomedical and Health Sciences, University of Western Sydney, Locked Bag 1797, Penrith South DC, 1797, NSW, Australia
| |
Collapse
|
11
|
Riahi S, Ganjali MR, Bagheri M. Theoretical investigation of interaction between Gatifloxacin and DNA: Implications for anticancer drug design. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2009. [DOI: 10.1016/j.msec.2009.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Kostrhunova H, Florian J, Novakova O, Peacock AFA, Sadler PJ, Brabec V. DNA interactions of monofunctional organometallic osmium(II) antitumor complexes in cell-free media. J Med Chem 2008; 51:3635-43. [PMID: 18494458 DOI: 10.1021/jm701538w] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work is the first in-depth study of osmium binding to DNA and confirms the pharmacological activity of a new class of anticancer metallodrugs. We investigated the interactions between the potential biological target DNA and four osmium(II) arene complexes, of the type [(eta 6-arene)Os(LL)Cl]n+, where arene = biphenyl or p-cymene and LL = ethylenediamine, picolinate, or oxinate in an effort to understand their mechanism of action. Most notably we show that these complexes bind to DNA. DNA adducts of the OsII complexes that exhibit promising cytotoxic effects in ovarian tumor cell lines largely distort its conformation. The data are consistent with DNA binding of the complexes containing biphenyl as the arene ligand that involves combined coordination to guanine residues and noncovalent interactions between the arene ligand and DNA. The results also indicate both a mechanism of action and a detoxification mechanism for OsII arene compounds different from those of cisplatin.
Collapse
Affiliation(s)
- Hana Kostrhunova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, Královopolská 135, CZ-61265 Brno, Czech Republic
| | | | | | | | | | | |
Collapse
|
13
|
Bugarcic T, Nováková O, Zerzánková L, Vrána O, Kašpárková J, Habtemariam A, Parsons S, Sadler PJ, Brabec V. Cytotoxicity, Cellular Uptake, and DNA Interactions of New Monodentate Ruthenium(II) Complexes Containing Terphenyl Arenes. J Med Chem 2008; 51:5310-9. [DOI: 10.1021/jm8003043] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tijana Bugarcic
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Olga Nováková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Lenka Zerzánková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Oldřich Vrána
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Jana Kašpárková
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Abraha Habtemariam
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Simon Parsons
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Peter J. Sadler
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| | - Viktor Brabec
- School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, United Kingdom, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic, Laboratory of Biophysics, Department of Experimental Physics, Faculty of Sciences, Palacky University, tr. Svobody 26, CZ-771 46 Olomouc, Czech Republic
| |
Collapse
|
14
|
Guralchuk GY, Sorokin AV, Katrunov IK, Yefimova SL, Lebedenko AN, Malyukin YV, Yarmoluk SM. Specificity of Cyanine Dye L-21 Aggregation in Solutions with Nucleic Acids. J Fluoresc 2007; 17:370-6. [PMID: 17564820 DOI: 10.1007/s10895-007-0201-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
Optical spectroscopy experiments were used to study the features of cyanine dye 3,3'-dimethyl-9-(2-thienyl)-thiacarbocyanine iodide (L-21) aggregation in binary solutions DMF:Tris-HCl buffer (pH = 8) containing nucleic acids (DNA or RNA). The appearance of absorption and luminescence bands associated with J-aggregates and dimers that are formed within the minor groove of DNA has been observed. The model of L-21 J-aggregate structure is proposed. It has been found that dimers are the building blocks of L-21 J-aggregates. Disorientation in dimers caused by the minor groove curvature is reason of observation of Davydov splitting in absorption spectrum of L-21 J-aggregates. In the solution containing DNA the absorption and luminescence bands of L-21 J-aggregates exhibit the specific properties that allows the dye L-21 to be used as a fluorescent probe for DNA detection.
Collapse
Affiliation(s)
- G Ya Guralchuk
- Institute for Scintillation Materials, STC Institute for Single Crystals, NAS of Ukraine, 60 Lenin Ave., 61001 Kharkov, Ukraine
| | | | | | | | | | | | | |
Collapse
|
15
|
Guo L, Qiu B, Chen G. Synthesis and investigation on the interaction with calf thymus deoxyribonucleic acid of a novel fluorescent probe 7-oxobenzo[b][1,10]phenanthroline-12(7H)-sulfonic acid. Anal Chim Acta 2007; 588:123-30. [PMID: 17386801 DOI: 10.1016/j.aca.2007.01.083] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Revised: 01/24/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
Abstract
In this paper, the synthetic route of a potential antitumor reagent, benzo[b][1,10] phenanthrolin-7(12H)-one (BPO), was improved. A sulfonic group was introduced to BPO to form a new compound, 7-oxobenzo[b][1,10]phenan-throline-12(7H)-sulfonic acid (OPSA), in order to enhance its water-solubility. The molecular structure of OPSA has been confirmed by IR, UV, MS, (1)H NMR and elements analysis. It was proved in our experiments that DNA could quench the fluorescence of OPSA and the maximum quenched intensity appeared at 408 nm (lambda(ex)=284 nm). The quenched fluorescence intensity was proportional to the concentration of DNA. Based on this phenomenon, OPSA had been used as the fluorescent probe for detection of calf thymus DNA (ct-DNA) and the corresponding linear response range was from 1.0 to 150.0 microg mL(-1) and the limit of detection (LOD) was 3.8 ng mL(-1). Its interaction with ct-DNA was investigated by fluorescence, absorption and viscosity measurements. When binding to ct-DNA, OPSA showed obvious fluorescence quenching and the quenched intensity was stable with the presence and absence of NaCl. The absorption spectra of OPSA had no evidence of increasing or decreasing when ct-DNA was added. The viscosity of OPSA and ct-DNA mixture showed no obvious change comparing with the viscosity of ct-DNA along. The results suggested that the interaction between OPSA and ct-DNA was groove binding in nature. Scatchard plots constructed from fluorescence titration data gave a binding constant of 8.9 x 10(5) L mol(-1) and a binding site size of 0.35 base pairs per bound drug molecule.
Collapse
Affiliation(s)
- Longhua Guo
- Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou 350002, China
| | | | | |
Collapse
|
16
|
Castelló A, Alvarez E, Carrasco L. Differential cleavage of eIF4GI and eIF4GII in mammalian cells. Effects on translation. J Biol Chem 2006; 281:33206-16. [PMID: 16959778 DOI: 10.1074/jbc.m604340200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two isoforms of the translation initiation factor eIF4G, eIF4GI and eIF4GII, have been described in eukaryotic cells. The exact function of each isoform during the initiation of protein synthesis is still under investigation. We have developed an efficient and reliable method of expressing poliovirus 2Apro, which differentially proteolyzes eIF4GI and eIF4GII in a time- and dose-dependent manner. This system is based on the electroporation of an in vitro transcribed mRNA that contains the encephalomyocarditis virus internal ribosome entry site followed by the sequence of poliovirus 2Apro. In contrast to HeLa cells, expression of this protease in BHK-21 cells induces delayed hydrolysis kinetics of eIF4GI with respect to eIF4GII. Moreover, under these conditions the polyadenylate binding protein is not cleaved. Interestingly, translation of de novo synthesized luciferase mRNA is highly dependent on eIF4GI integrity, whereas ongoing translation is inhibited at the same time as eIF4GII cleavage. Moreover, reinitiation of a preexisting mRNA translation after polysome run-off is dependent on the integrity of eIF4GII. Notably, de novo translation of heat shock protein 70 mRNA depends little on eIF4GI integrity but is more susceptible to eIF4GII hydrolysis. Finally, translation of an mRNA containing encephalomyocarditis virus internal ribosome entry site when the two isoforms of eIF4G are differentially hydrolyzed has been examined.
Collapse
Affiliation(s)
- Alfredo Castelló
- Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias and Centro Nacional de Biotecnología Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | | | | |
Collapse
|
17
|
Novakova O, Kasparkova J, Bursova V, Hofr C, Vojtiskova M, Chen H, Sadler PJ, Brabec V. Conformation of DNA Modified by Monofunctional Ru(II) Arene Complexes: Recognition by DNA Binding Proteins and Repair. Relationship to Cytotoxicity. ACTA ACUST UNITED AC 2005; 12:121-9. [PMID: 15664521 DOI: 10.1016/j.chembiol.2004.11.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 11/03/2004] [Accepted: 11/05/2004] [Indexed: 11/17/2022]
Abstract
We analyzed DNA duplexes modified at central guanine residues by monofunctional Ru(II) arene complexes [(eta(6)-arene)Ru(II)(en)(Cl)](+) (arene = tetrahydroanthracene or p-cymene, Ru-THA or Ru-CYM, respectively). These two complexes were chosen as representatives of two different classes of Ru(II) arene compounds for which initial studies revealed different binding modes: one that may involve DNA intercalation (tricyclic-ring Ru-THA) and the other (mono-ring Ru-CYM) that may not. Ru-THA is approximately 20 times more toxic to cancer cells than Ru-CYM. The adducts of Ru-THA and Ru-CYM have contrasting effects on the conformation, thermodynamic stability, and polymerization of DNA in vitro. In addition, the adducts of Ru-CYM are removed from DNA more efficiently than those of Ru-THA. Interestingly, the mammalian nucleotide excision repair system has low efficiency for excision of ruthenium adducts compared to cisplatin intrastrand crosslinks.
Collapse
Affiliation(s)
- Olga Novakova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Novakova O, Chen H, Vrana O, Rodger A, Sadler PJ, Brabec V. DNA interactions of monofunctional organometallic ruthenium(II) antitumor complexes in cell-free media. Biochemistry 2003; 42:11544-54. [PMID: 14516206 DOI: 10.1021/bi034933u] [Citation(s) in RCA: 278] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modifications of natural DNA in a cell-free medium by antitumor monodentate Ru(II) arene compounds of the general formula [(eta(6)-arene)Ru(en)Cl](+) (arene = biphenyl, dihydroanthracene, tetrahydroanthracene, p-cymene, or benzene; en = ethylenediamine) were studied by atomic absorption, melting behavior, transcription mapping, circular and linear dichroism, plasmid unwinding, competitive ethidium displacement, and differential pulse polarography. The results indicate that these complexes bind preferentially to guanine residues in double-helical DNA. The data are consistent with DNA binding of the complexes containing biphenyl, dihydroanthracene, or tetrahydroanthracene ligands that involves combined coordination to G N7 and noncovalent, hydrophobic interactions between the arene ligand and DNA, which may include arene intercalation and minor groove binding. In contrast, the single hydrocarbon rings in the p-cymene and benzene ruthenium complexes cannot interact with double-helical DNA by intercalation. Interestingly, the adducts of the complex containing p-cymene ligand, which has methyl and isopropyl substituents, distort the conformation and thermally destabilize double-helical DNA distinctly more than the adducts of the three multiring ruthenium arene compounds. It has been suggested that the different character of conformational alterations induced in DNA, and the resulting thermal destabilization, may affect differently further "downstream" effects of damaged DNA and consequently may result in different biological effects of this new class of metal-based antitumor compounds. The results point to a unique profile of DNA binding for Ru(II) arene compounds, suggesting that a search for new anticancer compounds based on this class of complexes may also lead to an altered profile of biological activity in comparison with that of metal-based antitumor drugs already used in the clinic or currently on clinical trials.
Collapse
Affiliation(s)
- Olga Novakova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | | | | | | | | | | |
Collapse
|
19
|
Zhong W, Yu JS, Liang Y. Chlorobenzylidine-herring sperm DNA interaction: binding mode and thermodynamic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:1281-1288. [PMID: 12659897 DOI: 10.1016/s1386-1425(02)00301-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The interaction of chlorobenzylidine with herring sperm DNA has been investigated by fluorescence, absorption, DNA melting experiment and differential scanning calorimetry (DSC). When bound to DNA, chlorobenzylidine shows hypochromism and red shift in absorption spectra, fluorescence quenching and polarization increasing in fluorescence spectra and increasing in DNA melting temperature. These spectral characteristics strongly support intercalation of chlorobenzylidine into herring sperm DNA. Scatchard plots constructed from fluorescence titration data give a binding constant of 3.2 x 10(4) M(-1) and a binding site size of six base pairs per bound drug molecule. The intercalative interaction is exothermic with a van't Hoff enthalpy of -30.6 kJ mol(-1). This result is obtained from DSC experiment. In addition, DeltaG degrees =-28.5 kJ mol(-1), and DeltaS degrees =-7.1 J mol(-1) K(-1). These results show that the binding of chlorobenzylidine to herring sperm DNA is exothermic.
Collapse
Affiliation(s)
- Wenying Zhong
- State Key Laboratory of Coordination Chemistry, Laboratory of Mesoscopic Materials Science, Nanjing University, 210093, Nanjing, People's Republic of China
| | | | | |
Collapse
|
20
|
Bjorndal MT, Fygenson DK. DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel-based assay. Biopolymers 2002; 65:40-4. [PMID: 12209471 DOI: 10.1002/bip.10220] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We measured the effect of the intercalating oxazole yellow DNA dye quinolinium,4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]-1-[3-(trimethylammonio)propyl]-,diiodide (YO-PRO) and its homodimer (YOYO) on the melting of self-complementary DNA duplexes using a gel-based assay. The assay, which requires a self-complementary DNA sequence, is independent of the optical properties of the molecules in solution. The melting temperature of the DNA is observed to increase in direct proportion to the number of occupied intercalation sites on the DNA, irrespective of whether the dye molecules are in monomer or dimer form. The increase is approximately 2.5 degrees C for each intercalation site occupied in the presence of 38 mM [Na(+)], for dye/duplex ratios in which less than 1/5 of the available intercalation sites are occupied.
Collapse
Affiliation(s)
- Michael T Bjorndal
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
21
|
Berge T, Jenkins NS, Hopkirk RB, Waring MJ, Edwardson JM, Henderson RM. Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy. Nucleic Acids Res 2002; 30:2980-6. [PMID: 12087184 PMCID: PMC117064 DOI: 10.1093/nar/gkf409] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Atomic force microscopy (AFM) has been used to examine perturbations in the tertiary structure of DNA induced by the binding of ditercalinium, a DNA bis-intercalator with strong anti-tumour properties. We report AFM images of plasmid DNA of both circular and linearised forms showing a difference in the formation of supercoils and plectonemic coils caused at least in part by alterations in the superhelical stress upon bis-intercalation. A further investigation of the effects of drug binding performed with 292 bp mixed-sequence DNA fragments, and using increment in contour length as a reliable measure of intercalation, revealed saturation occurring at a point where sufficient drug was present to interact with every other available binding site. Moment analysis based on the distribution of angles between segments along single DNA molecules showed that at this level of bis-intercalation, the apparent persistence length of the molecules was 91.7 +/- 5.7 nm, approximately twice as long as that of naked DNA. We conclude that images of single molecules generated using AFM provide a valuable supplement to solution-based techniques for evaluation of physical properties of biological macromolecules.
Collapse
Affiliation(s)
- Torunn Berge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
| | | | | | | | | | | |
Collapse
|
22
|
|
23
|
Lobo BA, Rogers SA, Choosakoonkriang S, Smith JG, Koe G, Middaugh CR. Differential scanning calorimetric studies of the thermal stability of plasmid DNA complexed with cationic lipids and polymers. J Pharm Sci 2002; 91:454-66. [PMID: 11835205 DOI: 10.1002/jps.10025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The thermal stabilities of supercoiled (SC) and linear/open circular (LIN/OC) forms of plasmid DNA when complexed with cationic lipids or cationic polymers used for cellular transfection were assessed using differential scanning calorimetry. Differences in the stability of SC DNA produced by the cationic lipids DOTAP (1,2-dioleoyltrimethyl ammoniumpropane chloride), DSTAP (1,2-distearyltrimethyl ammoniumpropane chloride), and DDAB (dimethyldioctadecylammonium bromide) upon complexation suggest possible effects of headgroup structure on the stability of SC DNA and minimal effects of lipid acyl chain saturation/unsaturation. Complexation of DNA with the cationic polymers polyethylenimine (PEI) or poly-L-lysine (PLL) (but not poly-L-arginine) resulted in a decreased stability of SC DNA when the DNA was in charge excess, although all polymers stabilized SC DNA when the polymer was in charge excess. The effects of these cationic polymers on the stability of SC DNA can be explained by changes produced in the tertiary structure of SC DNA upon binding and may reflect the importance of the topological constraint of supercoiling upon the stability of the resulting complexes.
Collapse
Affiliation(s)
- Brian A Lobo
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
| | | | | | | | | | | |
Collapse
|
24
|
Krautbauer R, Pope LH, Schrader TE, Allen S, Gaub HE. Discriminating small molecule DNA binding modes by single molecule force spectroscopy. FEBS Lett 2002; 510:154-8. [PMID: 11801245 DOI: 10.1016/s0014-5793(01)03257-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Drugs may interact with double stranded DNA via a variety of binding modes, each mode giving rise to a specific pharmacological function. Here we demonstrate the ability of single molecule force spectroscopy to discriminate between different interaction modes by measuring the mechanical properties of DNA and their modulation upon the binding of small molecules. Due to the unique topology of double stranded DNA and due to its base pair stacking pattern, DNA undergoes several well-characterised structural transitions upon stretching. We show that small molecule binding markedly affects these transitions in ways characteristic to the binding mode and that these effects can be detected at the level of an individual molecule. The minor groove binder berenil, the crosslinker cisplatin and the intercalator ethidium bromide are compared.
Collapse
Affiliation(s)
- Rupert Krautbauer
- Lehrstuhl für Angewandte Physik and CeNS, Luwig-Maximilians Universität, Munich, Germany
| | | | | | | | | |
Collapse
|
25
|
Ueta H, Maeda Y, Kawai Y. Features of distamycin preferential binding sites on natural DNA predicted using differential scanning calorimetry. Biosci Biotechnol Biochem 2001; 65:1261-4. [PMID: 11440155 DOI: 10.1271/bbb.65.1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interaction of distamycin with ColE1 DNA was examined by using differential scanning calorimetry (DSC) taking the helix-coil transition theory of DNA into consideration. Our results here strongly indicate that the affinity of distamycin to DNA, at a low distamycin concentration, depends highly on the DNA sequence, and preferential binding occurs to the sites of four to six successive A-T pairs having two or more successive G-C pairs on both their ends.
Collapse
Affiliation(s)
- H Ueta
- College of Science and Engineering, Iwaki Meisei University, Fukushima, Japan
| | | | | |
Collapse
|
26
|
Hodgkinson CP, Wright MC, Paine AJ. Fibronectin-mediated hepatocyte shape change reprograms cytochrome P450 2C11 gene expression via an integrin-signaled induction of ribonuclease activity. Mol Pharmacol 2000; 58:976-81. [PMID: 11040044 DOI: 10.1124/mol.58.5.976] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A major limitation to the use of rat hepatocytes in the study of drug metabolism and toxicity is the rapid loss of CYPs. We demonstrate that the culture of rat hepatocytes results in a rapid loss of liver-specific CYP2C11 mRNA and transcripts encoding the general housekeeping gene copper-zinc superoxide dismutase (CuZnSOD) as well as poly(A(+)) mRNA. These losses are accelerated by fibronectin, which has no effect on the transcription of CYP2C11 and CuZnSOD. However, fibronectin, an extracellular matrix protein involved in cell adhesion and spreading, induces ribonuclease (RNase) activity. Fibronectin also increases hepatocyte diameter and data are presented that cell spreading is involved in the loss of both CYP2C11 and CuZnSOD mRNAs. The use of functional blocking antibodies demonstrates that fibronectin is operating through its alpha(5)beta(1) integrin receptor and genistein, a tyrosine kinase inhibitor, prevents hepatocyte spreading, RNase induction, and CYP2C11 mRNA loss. Collectively, the data indicate that hepatocytes in vitro actively promote the extinction of their phenotype via the autocrine effects of fibronectin rather than the current consensus that they simply lose differentiated function, such as CYP2C11 expression, through the absence of extracellular matrix proteins. The substrate specificity of the ribonuclease induced is also considered.
Collapse
Affiliation(s)
- C P Hodgkinson
- Department of Biochemistry, University of Southampton, Southampton, United Kingdom
| | | | | |
Collapse
|
27
|
Jamieson ER, Lippard SJ. Structure, Recognition, and Processing of Cisplatin-DNA Adducts. Chem Rev 1999; 99:2467-98. [PMID: 11749487 DOI: 10.1021/cr980421n] [Citation(s) in RCA: 2332] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- E R Jamieson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | | |
Collapse
|
28
|
Castelli F, De Guidi G, Giuffrida S, Miano P, Sortino S. Molecular mechanisms of photosensitization XIII: a combined differential scanning calorimetry and DNA photosensitization study in non steroidal antiinflammatory drugs-DNA interaction. Int J Pharm 1999; 184:21-33. [PMID: 10425348 DOI: 10.1016/s0378-5173(99)00094-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A combined differential scanning calorimetry (DSC) and photosensitization study has been carried out on the interaction of several NSAID on DNA, both from calf thymus and pBR 322 plasmid. The investigated compounds were both non-steroidal anti-inflammatory drugs as well as compounds related to NSAIDs for structural similar properties, to find evidence for their ability to interact with DNA as a function of steric hindrance and polarity of the chemical structures. The considered NSAIDs were diflunisal (DFN, a salicylic derivative), naproxen (NAP), ketoprofen (KPF), suprofen (SPF) and tiaprofenic acid (TIA, arylpropionic acids). The structural criterion used was related to three different aromatic groups, biphenyl, naphthalene and benzophenone (BZP). In fact drug-DNA interaction can be revealed by variations of the enthalpies and temperatures of unfolding of DNA obtained by comparison of calorimetric peaks, where a decrease of the enthalpy is associated with the drug-DNA interaction, by engaging electrostatic bonds. Testing their ability in inducing DNA cleavage when UVA irradiated can evidence the photosensitizing properties of the drug. A good correlation was found between calorimetric and photosensitization studies. From the results obtained it can be reasonably supposed that the photocleavage depends only on the drug molecules bound to DNA.
Collapse
Affiliation(s)
- F Castelli
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 8, 95125, Catania, Italy.
| | | | | | | | | |
Collapse
|
29
|
Bischoff G, Bischoff R, Birch-Hirschfeld E, Gromann U, Lindau S, Meister WV, de A Bambirra S, Bohley C, Hoffmann S. DNA-drug interaction measurements using surface plasmon resonance. J Biomol Struct Dyn 1998; 16:187-203. [PMID: 9833660 DOI: 10.1080/07391102.1998.10508239] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (HPD) with synthetic self-complementary DNA (36-b.p.; 5'-biotin-spacer-[d(CGCTATATAGCG)]3-3') were studied by SPR (Surface Plasmon Resonance). Monolayers of biotinylated DNA were immobilized on a streptavidin-dextran-gold triple-layer. Small portions of the drugs (approximately 30 pmol/ml) were injected in continuous flow. The mass corresponded to the amount of the bound molecules. Injections of 50 mM sodium hydroxide pulses separated the DNA double strands, releasing the effector molecules. Subsequent treatments with the effectors gave reproducible results. The maximum interaction between drug and DNA was observed in the case of Tilorone. 41 molecules could bind to the 36-b.p. DNA duplex. To investigate the microscopic behavior in condensed nucleic acid phases, SFM (Scanning Force Microscopy)-imaging and polarizing microscopic observations of DNA-effector complexes were carried out. Supplementary UV-absorption thermal denaturation curves of DNA with the above-mentioned effectors in dilute solutions were measured. As an additional aid to understand the geometries of DNA-drug interactions, computer simulations were performed and compared with the experimental data.
Collapse
Affiliation(s)
- G Bischoff
- Martin Luther University, Halle-Wittenberg, Institute of Biochemistry, Halle (Saale), Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Adam W, Arnold MA, Grimm GN, Saha-Mölter CR, Dall'Acqua F, Miolo G, Vedaldi D. 4-Terf-Butylperoxymethyl-9-Methoxypsoralen as Intercalating Photochemical Alkoxyl-Radical Source for Oxidative DNA Damage. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb02507.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
31
|
Adam W, Grimm GN, Saha-Möller CR, Dall'Acqua F, Miolo G, Vedaldi D. DNA damage by tert-butoxyl radicals generated in the photolysis of a water-soluble, DNA-binding peroxyester acting as a radical source. Chem Res Toxicol 1998; 11:1089-97. [PMID: 9760284 DOI: 10.1021/tx980089a] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photolysis of the water-soluble perester 1 leads to tert-butoxyl radicals as confirmed by EPR studies with the spin trap 5, 5-dimethylpyrroline N-oxide (DMPO). In the presence of DNA, oxidative cleavage of the latter was demonstrated by the formation of strand breaks in supercoiled pBR 322 DNA and by a substantial decrease of the melting temperature of salmon testes DNA. Guanidine, released from, for example, oxazolone and oxoimidazolidine on base treatment, was observed with calf thymus DNA and 2'-deoxyguanosine. These DNA modifications were effectively inhibited by the radical scavenger di-tert-butylcresol or the hydrogen atom donor glutathione. Photosensitization by the arene chromophore was excluded since the corresponding ester 2 caused no DNA damage, nor were the photoproducts of the perester 1 active. The efficacy of the perester 1 in oxidizing DNA derives from the fact that the tert-butoxyl radicals are photolytically generated in the immediate vicinity of the DNA, due to electrostatic binding of the cationic perester to the DNA, as confirmed by fluorescence measurements. These results demonstrate that the photolysis of perester 1 provides a suitable source of tert-butoxyl radicals in aqueous media, a necessary prerequisite for biochemical investigations.
Collapse
Affiliation(s)
- W Adam
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
| | | | | | | | | | | |
Collapse
|
32
|
Shanado Y, Kato J, Ikeda H. Escherichia coli HU protein suppresses DNA-gyrase-mediated illegitimate recombination and SOS induction. Genes Cells 1998; 3:511-20. [PMID: 9797453 DOI: 10.1046/j.1365-2443.1998.00208.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The HU protein is an abundant DNA binding protein of bacteria and is a major constituent of the bacterial nucleoid. HU protein is known to be involved in several fundamental biological functions, including DNA supercoiling, DNA replication, site-specific DNA inversion, and transposition. It is generally thought that a functional relationship exists between HU protein and DNA gyrase. RESULTS We found that an hupA hupB double mutant displays enhanced spontaneous illegitimate recombination during the formation of lambdabio transducing phage in Escherichia coli. Nucleotide sequence analysis of the resulting transducing phages showed that the E. coli bio and lambda recombination sites did not have any homologous sequence. This mutation also enhanced the spontaneous expression of SOS functions. Furthermore, either overproduced GyrA protein or a temperature-sensitive gyrB mutation suppressed the illegitimate recombination enhanced by the defect of HU protein. CONCLUSION These results show that the defect of HU induces illegitimate recombination and SOS response, which are probably mediated by DNA gyrase, implying that HU protein plays roles in suppression of illegitimate recombination and SOS response through interaction with DNA gyrase.
Collapse
Affiliation(s)
- Y Shanado
- Department of Molecular Biology, The Institute of Medical Science, The University of Tokyo, PO Takanawa, Tokyo 108-8639, Japan
| | | | | |
Collapse
|
33
|
Ririe KM, Rasmussen RP, Wittwer CT. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 1997; 245:154-60. [PMID: 9056205 DOI: 10.1006/abio.1996.9916] [Citation(s) in RCA: 1011] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A microvolume fluorometer integrated with a thermal cycler was used to acquire DNA melting curves during polymerase chain reaction by fluorescence monitoring of the double-stranded DNA specific dye SYBR Green I. Plotting fluorescence as a function of temperature as the thermal cycler heats through the dissociation temperature of the product gives a DNA melting curve. The shape and position of this DNA melting curve are functions of the GC/AT ratio, length, and sequence and can be used to differentiate amplification products separated by less than 2 degrees C in melting temperature. Desired products can be distinguished from undesirable products, in many cases eliminating the need for gel electrophoresis. Analysis of melting curves can extend the dynamic range of initial template quantification when amplification is monitored with double-stranded DNA specific dyes. Complete amplification and analysis of products can be performed in less than 15 min.
Collapse
Affiliation(s)
- K M Ririe
- Idaho Technology Inc., Idaho Falls 83402, USA
| | | | | |
Collapse
|