1
|
Alasbahy WM, Shamsi M. In vitro DNA binding, pBR322 cleavage and molecular docking studies of 1,2-diaminobenzene, dichloro glycyl glycinate tin(IV) and zirconium(IV) complexes. J Biomol Struct Dyn 2022; 40:11484-11494. [PMID: 34351843 DOI: 10.1080/07391102.2021.1959402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo design and synthesis of complexes 1,2-diaminobenzene, dichloro glycyl glycinate tin(IV) and zirconium(IV), 1 and 2 as molecular drug entities were carried out. The structure elucidation of 1 and 2 was done by analytical techniques and spectroscopic methods viz. IR, UV-vis, 1H, 13C, 119Sn NMR, ESI-Mass and XRD techniques. In vitro DNA binding studies of 1 and 2 by various biophysical techniques viz electronic absorption, emission spectroscopy and circular dichroism measurements were carried out to evaluate their potential to act as chemotherapeutic candidates; furthermore, cleavage studies with pBR322plasmid DNA and computer-aided molecular docking studies were also done to study the mechanistic pathway and mode of binding at the molecular level. The observed results revealed that complex 1 exhibited greater DNA binding propensity in contrast to complex 2 primarily via electrostatic binding mode. The pBR322 DNA cleavage studies of both the complexes revealed the hydrolytic cleavage mechanism and DNA minor groove binding, which was ascertained by molecular docking studies of the drug candidate. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Manal Shamsi
- Department of Pharmacy, Taiz University, Taiz, Yemen
| |
Collapse
|
2
|
Barma A, Ghosh D, Karmakar P, Roy P. Synthesis and characterization of a mononuclear nickel(II) complex with N,O-donor ligand: Its DNA/HSA protein binding properties and tumor suppressive function. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
3
|
Cao S, Cheng R, Wang D, Zhao Y, Tang R, Yang X, Chen J. Dinuclear copper(II) complexes of “end-off” bicompartmental ligands: Alteration of the chelating arms on ligands to regulate the reactivity of the complexes towards DNA. J Inorg Biochem 2019; 192:126-139. [DOI: 10.1016/j.jinorgbio.2018.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/23/2018] [Accepted: 12/24/2018] [Indexed: 01/08/2023]
|
4
|
Dar AM, Nabi R, Mir S, Gatoo MA, Lone SH. Synthesis of steroidal imidazolidinthiones as potential apoptotic agents: Investigation by theoretical and experimental studies. Bioorg Chem 2018; 79:190-200. [PMID: 29772469 DOI: 10.1016/j.bioorg.2018.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 11/15/2022]
Abstract
New steroidal imidazolidinthione derivatives (4-6) were synthesized from steroidal thiosemicarbazones and dichloroethane. The synthesized compounds were characterized using spectral data analysis. Theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed to gain insights into the molecular structure of the target compounds. MEPS and FMO analysis were carried out. HOMO-LUMO energy gap was determined which helped to evaluate various global descriptors like hardness, chemical potential, electronegativity, nucleophilicity and electrophilicity index, etc. The calculated properties established that the synthesized products are more or less similar in their reactivity behaviour. To explore their biological potential, interaction studies of compounds (4-6) with DNA were carried out using various biophysical techniques. The compounds bind DNA preferentially through electrostatic and hydrophobic interactions with Kb of 3.21 × 103 M-1, 2.79 × 103 M-1 and 2.26 × 103 M-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis of compound 4 demonstrated strong interaction during the concentration dependent cleavage activity with pBR322 DNA. It was observed that these steroidal imidazolidinthiones are minor groove binders of DNA which was validated using molecular docking studies. An in vitro cytotoxicity screening using MTT assay revealed that the compounds (4-6) exhibit potential toxicity against different human cancer cells. Highest antiproliferative effect was observed on HeLa cells by compound 4. The results suggested that compounds 4-6 cause apoptotic cell death by cleaving apoptotic protein caspase-3 and suppress anti-apoptotic protein Bcl-2 in HeLa cancer cells.
Collapse
Affiliation(s)
- Ayaz Mahmood Dar
- Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Department of Chemistry, Govt Degree College Kulgam, Kashmir 192231, India.
| | - Rizwan Nabi
- Department of Chemistry, Indian Institute of Technology Powai, Mumbai 400076, India
| | - Shafia Mir
- Department of Chemistry, OPJS University, Churu 331001, Rajasthan, India
| | - Manzoor Ahmad Gatoo
- Department of Biochemistry JNMC, Aligarh Muslim University, Aligarh 202 002, India
| | - Shabir H Lone
- Department of Chemistry, Govt Degree College Anantnag, Kashmir 192101, India.
| |
Collapse
|
5
|
DNA binding, artificial nuclease activity and cytotoxic studies of newly synthesized steroidal pyrimidines. Int J Biol Macromol 2017; 111:52-61. [PMID: 29292141 DOI: 10.1016/j.ijbiomac.2017.12.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/09/2017] [Accepted: 12/25/2017] [Indexed: 01/07/2023]
Abstract
The new steroidal pyrimidine derivatives (4-6) were synthesized by the reaction of steroidal thiosemicarbazones with (2-methyl) diethyl malonate in absolute ethanol. After characterization by spectral and analytical data, the DNA interaction studies of compounds (4-6) were carried out by UV-vis, fluorescence spectroscopy, hydrodynamic measurements, molecular docking and gel electrophoresis. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.31×103M-1, 1.93×103M-1 and 2.05×103M-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis demonstrated that compound 4 showed a strong interaction during the concentration dependent cleavage activity with pBR322 DNA. The molecular docking study suggested the intercalation of steroidal pyrimidine moiety in the minor groove of DNA. During in vitro cytotoxicity, compounds (4-6) revealed potential toxicity against the different human cancer cells (MTT assay). During DAPI staining, the nuclear fragmentations on cells occurred after treatment with compounds 4 and 5. Western blotting analysis clearly indicates that compound 4 causes apoptosis in MCF-7 cancer cells. The results revealed that compound 4 has better prospectus to act as a cancer chemotherapeutic candidate, which warrants further in vivo anticancer investigations.
Collapse
|
6
|
Dar AM, Uzzaman S, Ahmad MS, Khan Y. Steroidal imidazoles: Synthesis, characterization, molecular docking studies with DNA and in vitro cytotoxicity. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
7
|
Kotera N, Granzhan A, Teulade-Fichou MP. Comparative study of affinity and selectivity of ligands targeting abasic and mismatch sites in DNA using a fluorescence-melting assay. Biochimie 2016; 128-129:133-7. [PMID: 27523781 DOI: 10.1016/j.biochi.2016.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/08/2016] [Indexed: 11/29/2022]
Abstract
Recently, several families of small-molecule ligands have been developed to selectively target DNA pairing defects, such as abasic sites and mismatched base pairs, with the aim to interfere with the DNA repair and the template function of the DNA. However, the affinity and selectivity (with respect to well-matched DNA) of these ligands has barely been evaluated in a systematic way. Herein, we report a comparative study of binding affinity and selectivity of a representative panel of 16 ligands targeting abasic sites and a T-T mismatch in DNA, using a fluorescence-monitored melting assay. We demonstrate that bisintercalator-type macrocyclic ligands are characterized by moderate affinity but exceptionally high selectivity with respect to well-matched DNA, whereas other reported ligands show either modest selectivity or rather low affinity in identical conditions.
Collapse
Affiliation(s)
- Naoko Kotera
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR9187, INSERM U1196, F-91405, Orsay, France
| |
Collapse
|
8
|
Spectroscopic, Viscositic, DNA Binding and Cytotoxic Studies of Newly Synthesized Steroidal Imidazolidines. J Fluoresc 2015; 26:639-49. [DOI: 10.1007/s10895-015-1750-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
|
9
|
In vitro cytotoxcity and interaction of new steroidal oxadiazinanones with calf thymus DNA using molecular docking, gel electrophoresis and spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 148:340-350. [DOI: 10.1016/j.jphotobiol.2015.04.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/23/2022]
|
10
|
Gup R, Gökçe C, Dilek N. Seven-coordinated cobalt(II) complexes with 2,6-diacetylpyridine bis(4-hydroxybenzoylhydrazone): synthesis, characterisation, DNA binding and cleavage properties. Supramol Chem 2015. [DOI: 10.1080/10610278.2015.1051978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ramazan Gup
- Department of Chemistry, Faculty of Science, Mugla Sιtkι Koçman University, 48100 Mugla, Turkey
| | - Cansu Gökçe
- Department of Chemistry, Faculty of Science, Mugla Sιtkι Koçman University, 48100 Mugla, Turkey
| | - Nefise Dilek
- Department of Physics, Faculty of Arts and Sciences, Aksaray University, 68100 Aksaray, Turkey
| |
Collapse
|
11
|
Seven coordinated cobalt(II) complexes with 2,6-diacetylpyridine bis(4-acylhydrazone) ligands: Synthesis, characterization, DNA-binding and nuclease activity. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.03.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Gup R, Gökçe C, Dilek N. Synthesis, structural characterization and DNA interaction of zinc complex from 2,6-diacetylpyridine dihydrazone and {4-[(2E)-2-(hydroxyimino)acetyl]phenoxy} acetic acid. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 144:42-50. [DOI: 10.1016/j.jphotobiol.2015.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 11/16/2022]
|
13
|
Sureshbabu P, Tjakraatmadja AAJS, Hanmandlu C, Elavarasan K, Kulak N, Sabiah S. Mononuclear Cu(ii) and Zn(ii) complexes with a simple diamine ligand: synthesis, structure, phosphodiester binding and DNA cleavage studies. RSC Adv 2015. [DOI: 10.1039/c4ra15717f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mononuclear Cu(ii) and Zn(ii) complexes with simple 1,2-diaminocylohexane were synthesized. They interact with phosphodiesters and CT-DNA. Cu(ii) complex with ascorbate efficiently cleaves supercoiled DNA up to Form III at 25 µM under oxidative pathway.
Collapse
Affiliation(s)
- Popuri Sureshbabu
- Department of Chemistry
- Pondicherry University
- Pondicherry-605 014
- India
| | | | | | - K. Elavarasan
- Department of Chemistry
- Pondicherry University
- Pondicherry-605 014
- India
| | - Nora Kulak
- Institute of Chemistry and Biochemistry
- Freie Universtität Berlin
- Germany
| | | |
Collapse
|
14
|
Khan RA, Arjmand F, Tabassum S, Monari M, Marchetti F, Pettinari C. Organometallic ruthenium(II) scorpionate as topo IIα inhibitor; in vitro binding studies with DNA, HPLC analysis and its anticancer activity. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.05.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
15
|
Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
16
|
Tabassum S, Asim A, Khan RA, Hussain Z, Srivastav S, Srikrishna S, Arjmand F. Chiral heterobimetallic complexes targeting human DNA-topoisomerase Iα. Dalton Trans 2013; 42:16749-16761. [PMID: 24077532 DOI: 10.1039/c3dt51209f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The chiral monometallic Cu(II) (1) and Zn(II) (2) and heterobimetallic Cu(II)-Sn(IV) and Zn(II)-Sn(IV) complexes with tridentate chiral Schiff base -ONO-ligand in the presence of nitrogen donor heterocyclic ligand imidazole; were prepared and characterized by various physico-chemical and spectroscopic methods. Preliminary complex-DNA interaction studies employing optical methods revealed that 3 displayed a higher propensity towards the drug target DNA double helix and recommended predominantly an electrostatic mode of interaction as well as a groove binding affinity of the complex with CT-DNA. This was quantified by Kb and KSV values of complexes 1-4, which demonstrated a multifold increase in complex 3 binding to CT DNA and clearly demonstrates its potency to act as a chemotherapeutic agent. Furthermore, the gel electrophoretic patterns of supercoiled pBR322 DNA with varying concentrations of complex 3 exhibits the ability to cleave DNA and follow a freely diffusible radical mechanism. The antiproliferative effects of complex 3 on human hepatoma cancer cells (Huh7) was investigated. Human Topo I inhibition assay by complex 3 was performed and results confirmed significantly good activity at lower concentrations than some of the classical Topo I inhibitors. Additionally, complex 3 was investigated for the expression of MMP-2 and TGF-β by real time PCR. The cellular uptake of complex 3 by HeLa cells was studied by confocal microscopy.
Collapse
Affiliation(s)
- Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | | | | | | | | | | | | |
Collapse
|
17
|
Khan RA, Yadav S, Hussain Z, Arjmand F, Tabassum S. Carbohydrate linked organotin(IV) complexes as human topoisomerase Iα inhibitor and their antiproliferative effects against the human carcinoma cell line. Dalton Trans 2013; 43:2534-48. [PMID: 24310209 DOI: 10.1039/c3dt51973b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dimethyltin(IV) complexes with ethanolamine (1) and biologically significant N-glycosides (2 and 3) were designed and synthesized. The structural elucidation of complexes 1-3 was done using elemental and spectroscopic methods; in addition, complex 1 was studied by single crystal X-ray diffraction studies. The in vitro DNA binding profile of complexes 2 and 3 was carried out by employing different biophysical methods to ascertain the feasibility of glycosylated complexes. Further, the cleaving ability of 2 and 3 was investigated by the agarose gel electrophoretic mobility assay with supercoiled pBR322 DNA, and demonstrated significantly good nuclease activity. Furthermore, both the complexes exhibited significant inhibitory effects on the catalytic activity of human Topo I at lower concentration than standard drugs. Computer-aided molecular docking techniques were used to ascertain the mode and mechanism of action towards the molecular target DNA and Topo I. The cytotoxicity of 2 and 3 against human hepatoma cancer cells (Huh7) was evaluated, which revealed significant regression in cancerous cells as compared with the standard drug. The antiproliferative activities of 2 and 3 were tested against human hepatoma cancer cells (Huh7), and results showed significantly good activity. Additionally, to validate the remarkable antiproliferative activity of complexes 2 and 3, specific regulatory gene expression (MMP-2 and TGF-β) was obtained by real time PCR.
Collapse
Affiliation(s)
- Rais Ahmad Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh - 202002, India.
| | | | | | | | | |
Collapse
|
18
|
Tabassum S, Amir S, Arjmand F, Pettinari C, Marchetti F, Masciocchi N, Lupidi G, Pettinari R. Mixed-ligand Cu(II)–vanillin Schiff base complexes; effect of coligands on their DNA binding, DNA cleavage, SOD mimetic and anticancer activity. Eur J Med Chem 2013; 60:216-32. [PMID: 23291123 DOI: 10.1016/j.ejmech.2012.08.019] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 07/26/2012] [Accepted: 08/13/2012] [Indexed: 10/28/2022]
|
19
|
Sarkar A, Paital AR, Khan RA, Arjmand F, Bertolasi V, Mathonière C, Clérac R, Ray D. Ligand dependent self-assembly of hydroxido-bridged dicopper units templated by sodium ion. Dalton Trans 2013; 42:12495-506. [DOI: 10.1039/c3dt51095f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Suntharalingam K, Hunt DJ, Duarte AA, White AJP, Mann DJ, Vilar R. A tri-copper(II) complex displaying DNA-cleaving properties and antiproliferative activity against cancer cells. Chemistry 2012; 18:15133-41. [PMID: 23059789 DOI: 10.1002/chem.201202482] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Indexed: 11/07/2022]
Abstract
A new disubstituted terpyridine ligand and the corresponding tri-copper(II) complex have been prepared and characterised. The binding affinity and binding mode of this tri-copper complex (as well as the previously reported mono- and di-copper analogues) towards duplex DNA were determined by using UV/Vis spectroscopic titrations and fluorescent indicator displacement (FID) assays. These studies showed the three complexes to bind moderately (in the order of 10(4) M(-1)) to duplex DNA (ct-DNA and a 26-mer sequence). Furthermore, the number of copper centres and the nature of the substituents were found to play a significant role in defining the binding mode (intercalative or groove binding). The nuclease potential of the three complexes was investigated by using circular plasmid DNA as a substrate and analysing the products by agarose-gel electrophoresis. The cleaving activity was found to be dependent on the number of copper centres present (cleaving potency was in the order: tri-copper>di-copper>mono-copper). Interestingly, the tri-copper complex was able to cleave DNA without the need of external co-reductants. As this complex displayed the most promising nuclease properties, cell-based studies were carried out to establish if there was a direct link between DNA cleavage and cellular toxicity. The tri-copper complex displayed high cytotoxicity against four cancer cell lines. Of particular interest was that it displayed high cytotoxicity against the cisplatin-resistant MOLT-4 leukaemia cell line. Cellular uptake studies showed that the tri-copper complex was able to enter the cell and more importantly localise in the nucleus. Immunoblotting analysis (used to monitor changes in protein levels related to the DNA damage response pathway) and DNA-flow cytometric studies suggested that this tri-copper(II) complex is able to induce cellular DNA damage.
Collapse
|
21
|
Lujan SA, Williams JS, Pursell ZF, Abdulovic-Cui AA, Clark AB, Nick McElhinny SA, Kunkel TA. Mismatch repair balances leading and lagging strand DNA replication fidelity. PLoS Genet 2012; 8:e1003016. [PMID: 23071460 PMCID: PMC3469411 DOI: 10.1371/journal.pgen.1003016] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/22/2012] [Indexed: 11/24/2022] Open
Abstract
The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases, α, δ, and ε. Current evidence suggests that DNA polymerase ε (Pol ε) is the primary leading strand replicase, whereas Pols α and δ primarily perform lagging strand replication. The fact that these polymerases differ in fidelity and error specificity is interesting in light of the fact that the stability of the nuclear genome depends in part on the ability of mismatch repair (MMR) to correct different mismatches generated in different contexts during replication. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first use the strand-biased ribonucleotide incorporation propensity of a Pol ε mutator variant to confirm that Pol ε is the primary leading strand replicase in Saccharomyces cerevisiae. We then use polymerase-specific error signatures to show that MMR efficiency in vivo strongly depends on the polymerase, the mismatch composition, and the location of the mismatch. An extreme case of variation by location is a T-T mismatch that is refractory to MMR. This mismatch is flanked by an AT-rich triplet repeat sequence that, when interrupted, restores MMR to >95% efficiency. Thus this natural DNA sequence suppresses MMR, placing a nearby base pair at high risk of mutation due to leading strand replication infidelity. We find that, overall, MMR most efficiently corrects the most potentially deleterious errors (indels) and then the most common substitution mismatches. In combination with earlier studies, the results suggest that significant differences exist in the generation and repair of Pol α, δ, and ε replication errors, but in a generally complementary manner that results in high-fidelity replication of both DNA strands of the yeast nuclear genome. The stability of complex and highly organized nuclear genomes partly depends on the ability of mismatch repair (MMR) to correct a variety of different mismatches generated as the leading and lagging strand templates are copied by three polymerases, each with different fidelity. Here we provide the first comparison, to our knowledge, of the efficiency of MMR of leading and lagging strand replication errors. We first confirm that Pol ε is the primary leading strand replicase, complementing earlier assignment of Pols α and δ as the primary lagging strand replicases. We then show that MMR efficiency in vivo strongly depends on the polymerase that generates the mismatch and on the composition and location of mismatches. In one extreme case, a flanking triplet repeat sequence eliminates MMR altogether. Overall, MMR is most efficient for mismatches generated at the highest rates and having the most deleterious potential, thereby ultimately achieving high-fidelity replication of both DNA strands.
Collapse
Affiliation(s)
- Scott A. Lujan
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Jessica S. Williams
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Zachary F. Pursell
- Department of Biochemistry, Tulane University, New Orleans, Louisiana, United States of America
| | - Amy A. Abdulovic-Cui
- Department of Biology, Augusta State University, Augusta, Georgia, United States of America
| | - Alan B. Clark
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | | | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
22
|
Chiral nano heterobimetallic DNA receptors: In vitro binding studies, cleavage activity and DNA condensation studies (TEM and AFM imaging). J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
23
|
Synthesis of Aryl-1,2,4,5-tetrazinane-3-thiones, in vitro DNA binding studies, nuclease activity and its antimicrobial activity. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
24
|
Tabassum S, Sharma GC, Arjmand F. New modulated design and synthesis of chiral CuII/SnIV bimetallic potential anticancer drug entity: in vitro DNA binding and pBR322 DNA cleavage activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 90:208-217. [PMID: 22343081 DOI: 10.1016/j.saa.2012.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 12/23/2011] [Accepted: 01/16/2012] [Indexed: 05/31/2023]
Abstract
A new chiral ligand scaffold L derived from (R)-2-amino-2-phenyl ethanol and diethyl oxalate was isolated and thoroughly characterized by various spectroscopic methods. The ligand L was allowed to react with CuCl(2)·2H(2)O and NiCl(2)·6H(2)O to achieve monometallic complexes 1 and 2, respectively. Subsequently modulation of 1 and 2 was carried out in the presence of SnCl(4)·5H(2)O to obtain heterobimetallic potential drug candidates 3 and 4 possessing (Cu(II)/Sn(IV) and Ni(II)/Sn(IV)) metallic cores, respectively and characterized by elemental analysis and spectroscopic data including (1)H, (13)C and (119)Sn NMR in case of 3 and 4. In vitro DNA binding studies revealed that complex 3 avidly binds to DNA as quantified by K(b) and K(sv) values. Complex 3 exhibits a remarkable DNA cleavage activity (concentration dependent) with pBR322 DNA and the cleavage activity of 3 was significantly enhanced in the presence of activators and follows the order H(2)O(2)>Asc>MPA>GSH. Complex 3 cleave pBR322 DNA via hydrolytic pathway and accessible to major groove of DNA.
Collapse
Affiliation(s)
- Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University (AMU), Aligarh, Uttar Pradesh, India.
| | | | | |
Collapse
|
25
|
Parveen S, Arjmand F. De novo design, synthesis and spectroscopic characterization of chiral benzimidazole-derived amino acid Zn(II) complexes: Development of tryptophan-derived specific hydrolytic DNA artificial nuclease agent. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 85:53-60. [PMID: 22000640 DOI: 10.1016/j.saa.2011.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/18/2011] [Accepted: 09/04/2011] [Indexed: 05/31/2023]
Abstract
Novel ternary dizinc(II) complexes 1-3, derived from 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol and l-form of amino acids (viz., tryptophan, leucine and valine) were synthesized and characterized by spectroscopic (IR, (1)H NMR, UV-vis, ESI-MS) and other analytical methods. To evaluate the biological preference of chiral drugs for inherently chiral target DNA, interaction of 1-3 with calf thymus DNA in Tris-HCl buffer was studied by various biophysical techniques which reveal that all these complexes bind to CT DNA non-covalently via electrostatic interaction. The higher K(b) value of L-tryptophan complex 1 suggested greater DNA binding propensity. Further, to evaluate the mode of action at the molecular level, interaction studies of complexes 1 and 2 with nucleotides (5'-GMP and 5'-TMP) were carried out by UV-vis titrations, (1)H and (31)P NMR which implicates the preferential selectivity of these complexes to N3 of thymine rather than N7 of guanine. Furthermore, complex 1 exhibits efficient DNA cleavage with supercoiled pBR322. The complex 1 cleaves DNA efficiently involving hydrolytic cleavage pathway. Such chiral synthetic hydrolytic nucleases with asymmetric centers are gaining considerable attention owing to their importance in biotechnology and drug design, in particular to cleave DNA with sequence selectivity different from that of the natural enzymes.
Collapse
Affiliation(s)
- Shazia Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | | |
Collapse
|
26
|
Arjmand F, A. J. Synthesis, characterization and in vitro DNA binding studies of tin(IV) complexes of tert-butyl 1-(2-hydroxy-1-phenylethylamino)-3-methyl-1-oxobutan-2-yl carbamate. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
Panja A, Matsuo T, Nagao S, Hirota S. DNA Cleavage by the Photocontrolled Cooperation of ZnII Centers in an Azobenzene-Linked Dizinc Complex. Inorg Chem 2011; 50:11437-45. [DOI: 10.1021/ic201244y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anangamohan Panja
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| |
Collapse
|
28
|
Arjmand F, Sharma GC, Muddassir M, Tabassum S. Synthesis and enantiopreferential DNA-binding profile of late 3d transition metal R- and S-enantiomeric complexes derived from N,N-bis-(1-benzyl-2-ethoxyethane): Validation of R-enantiomer of copper(II) complex as a human topoisomerase II inhibitor. Chirality 2011; 23:557-567. [PMID: 21695735 DOI: 10.1002/chir.20970] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 04/12/2011] [Indexed: 09/12/2023]
Abstract
To evaluate the biological preference of chiral drug candidates for molecular target DNA, new potential metal-based chemotherapeutic agents 1-3 (a and b) of late 3d transition metals Ni(II), Cu(II), and Zn(II), respectively, derived from (R)- and (S)-2-amino-2-phenylethanol with CH(2) CH(2) linker were synthesized and thoroughly characterized. Interaction studies of 1-3 (a and b) with calf thymus DNA in Tris buffer were studied by electronic absorption titrations, luminescence titrations, cyclic voltammetry, and circular dichroism. The results reveal that the extent of DNA binding of R-enantiomer of copper 1a was highest in comparison to rest of the complexes via electrostatic interaction mode. The nuclease activity of 1(a and b) with supercoiled pBR322 DNA was further examined by gel electrophoresis, which reveals that complex 1a exhibits a remarkable DNA cleavage activity (concentration dependent) with pBR322DNA, and the cleavage activity of both enantiomers of complex 1 was significantly enhanced in the presence of activators. The activating efficiency follows the order Asc > H(2) O(2) > MPA for 1a, and reverse order was observed for 1b, because of the differences in enantioselectivity and conformation. Further, it was observed that cleavage reaction involves singlet oxygen species and superoxide radicals via oxidative cleavage mechanism. In addition, complex 1a exhibits significant inhibitory effects on the topoisomerase II (topo II) activity at a very low concentration ∼24 μM, which suggest that complex 1a is indeed catalytic inhibitor or (poison) of human topo II.
Collapse
Affiliation(s)
- Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | | | | | | |
Collapse
|
29
|
Pan X, Liao Y, Liu Y, Chang P, Liao L, Yang L, Li H. Transcription of AAT•ATT triplet repeats in Escherichia coli is silenced by H-NS and IS1E transposition. PLoS One 2010; 5:e14271. [PMID: 21151567 PMCID: PMC3000339 DOI: 10.1371/journal.pone.0014271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/15/2010] [Indexed: 11/18/2022] Open
Abstract
Background The trinucleotide repeats AAT•ATT are simple DNA sequences that potentially form different types of non-B DNA secondary structures and cause genomic instabilities in vivo. Methodology and Principal Findings The molecular mechanism underlying the maintenance of a 24-triplet AAT•ATT repeat was examined in E.coli by cloning the repeats into the EcoRI site in plasmid pUC18 and into the attB site on the E.coli genome. Either the AAT or the ATT strand acted as lagging strand template in a replication fork. Propagations of the repeats in either orientation on plasmids did not affect colony morphology when triplet repeat transcription using the lacZ promoter was repressed either by supplementing LacIQin trans or by adding glucose into the medium. In contrast, transparent colonies were formed by inducing transcription of the repeats, suggesting that transcription of AAT•ATT repeats was toxic to cell growth. Meanwhile, significant IS1E transposition events were observed both into the triplet repeats region proximal to the promoter side, the promoter region of the lacZ gene, and into the AAT•ATT region itself. Transposition reversed the transparent colony phenotype back into healthy, convex colonies. In contrast, transcription of an 8-triplet AAT•ATT repeat in either orientation on plasmids did not produce significant changes in cell morphology and did not promote IS1E transposition events. We further found that a role of IS1E transposition into plasmids was to inhibit transcription through the repeats, which was influenced by the presence of the H-NS protein, but not of its paralogue StpA. Conclusions and Significance Our findings thus suggest that the longer AAT•ATT triplet repeats in E.coli become vulnerable after transcription. H-NS and its facilitated IS1E transposition can silence long triplet repeats transcription and preserve cell growth and survival.
Collapse
Affiliation(s)
- Xuefeng Pan
- School of Life Science, Beijing Institute of Technology, Beijing, China.
| | | | | | | | | | | | | |
Collapse
|
30
|
Arjmand F, Muddassir M. A mechanistic approach for the DNA binding of chiral enantiomeric L- and D-tryptophan-derived metal complexes of 1,2-DACH: cleavage and antitumor activity. Chirality 2010; 23:250-9. [PMID: 20928895 DOI: 10.1002/chir.20907] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 06/16/2010] [Indexed: 01/23/2023]
Abstract
A new chiral series of potential antitumor metal-based complexes 1-3(a and b) of L- and D-tryptophan have been synthesized and thoroughly characterized. Both enantiomers of 1-3 bind DNA noncovalently via phosphate interaction with slight preference of metal center for covalent coordination to nucleobases. The K(b) values of L-enantiomer, however, possess higher propensity for DNA binding in comparison with the D-enantiomeric analogs. The relative trend in K(b) values is as follows: 2(a) > 2(b) > 3(a) > 1(a) > 3(b) > 1(b). These observations together with the findings of circular dichoric and fluorescence studies reveal maximal potential of L-enantiomeric form of copper complex to bind DNA, thereby exerting its therapeutic effect. The complex 2a exhibits a remarkable DNA cleavage activity with pBR322DNA in the presence of different activators such as H(2) O(2) , ascorbic acid, 3-mercaptopropionic acid, and glutathione, suggesting the involvement of active oxygen species for the DNA scission. In vitro anticancer activity of complexes 1-3(a) were screened against 14 different human carcinoma cell lines of different histological origin, and the results reveal that 2a shows significant antitumor activity in comparison with both 1a and 3a and is particularly selective for MIAPACA2 (pancreatic cancer cell line).
Collapse
Affiliation(s)
- Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | | |
Collapse
|
31
|
Arjmand F, Muddassir M. Design and synthesis of heterobimetallic topoisomerase I and II inhibitor complexes: in vitro DNA binding, interaction with 5'-GMP and 5'-TMP and cleavage studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2010; 101:37-46. [PMID: 20638859 DOI: 10.1016/j.jphotobiol.2010.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 06/11/2010] [Accepted: 06/21/2010] [Indexed: 10/19/2022]
Abstract
New potential cancer chemotherapeutic complexes Cu-Sn(2)/Zn-Sn(2) 3 and 4 were designed and prepared as topoisomerases inhibitors; their in vitro DNA binding studies were carried out which reveal strong electrostatic binding via phosphate backbone of DNA helix, in addition to other binding modes viz. coordinate covalent and partial intercalation. To throw insight to molecular binding event at the target site, UV-vis titrations of 3 and 4 with mononucleotides of interest, viz, 5'-GMP and 5'-TMP were carried out, (in case of 4) by (1)H and (31)P NMR. Cleavage studies employing gel electrophoresis demonstrate both the complexes 3 and 4 are efficient cleavage agents and are specific groove binders (complex 3 binds to both major and minor groove while complex 4 is specifically minor groove binder only). In addition, the complexes show high inhibition activity against topoisomerase I and II. However, complex 4 exhibits significant inhibitory effects on the Topo I activity at a very low concentration approximately 2.5 microM.
Collapse
Affiliation(s)
- Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India.
| | | |
Collapse
|
32
|
Wang JT, Zheng XH, Ji LN, Mao ZW. High nuclease activity of a copper(II)-bipyridyl complex containing cytosine pendants. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.492216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jin-Tao Wang
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, P.R. China
| | - Xiao-Hui Zheng
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, P.R. China
| | - Liang-Nian Ji
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, P.R. China
| | - Zong-Wan Mao
- a MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, P.R. China
| |
Collapse
|
33
|
Arjmand F, Sayeed F. Synthesis, characterization and DNA-binding studies of mono and heterobimetallic complexes CuSn2/ZnSn2 and their DNA cleavage activity. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.11.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
34
|
Wang JT, Xia Q, Zheng XH, Chen HY, Chao H, Mao ZW, Ji LN. An effective approach to artificial nucleases using copper(ii) complexes bearing nucleobases. Dalton Trans 2010; 39:2128-36. [DOI: 10.1039/b915392f] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
35
|
Balu B, Blair PL, Adams JH. Identification of the transcription initiation site reveals a novel transcript structure for Plasmodium falciparum maebl. Exp Parasitol 2008; 121:110-4. [PMID: 18950624 DOI: 10.1016/j.exppara.2008.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 08/12/2008] [Accepted: 10/01/2008] [Indexed: 10/21/2022]
Abstract
Strict regulation of gene expression is critical for the development of the malaria parasite within multiple host cell types. However, much remains unexplored regarding gene regulation in Plasmodium falciparum with only a few components of the gene regulation machinery identified thus far. Better characterization of transcript structures with precise mapping of transcript ends will greatly aid in the search of conserved regulatory sequences in the genome. Transcript analysis of maebl, a member of the ebl gene family, in P. falciparum intra-erythrocytic stages has revealed a unique transcript structure for maebl. The 5'-untranslated region of maebl transcript is exceptionally long (>2 kb) with a small multi-exon open reading frame, annotated as a putative mitochondrial ATP synthase (PF11_0485) in the Plasmodium database. Northern blot hybridizations and RT-PCR analysis confirmed a bicistronic message for maebl along with PF11_0485. We further identified the minimal maebl promoter to be upstream of PF11_0485 by using transient chloramphenicol acetyl transferase (CAT) reporter assays. The occurrence of a bicistronic mRNA in Plasmodium is both novel and unusual for a lower eukaryote and adds on to the complexity of gene regulation in malaria parasites.
Collapse
Affiliation(s)
- Bharath Balu
- Global Health and Infectious Disease Research, Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL 33612, USA
| | | | | |
Collapse
|
36
|
Ouyang D, Yi L, Liu L, Mu HT, Xi Z. In vitro expansion of DNA triplet repeats with bulge binders and different DNA polymerases. FEBS J 2008; 275:4510-21. [DOI: 10.1111/j.1742-4658.2008.06593.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Rahimian M, Miao Y, Wilson WD. Influence of DNA structure on adjacent site cooperative binding. J Phys Chem B 2008; 112:8770-8. [PMID: 18582108 DOI: 10.1021/jp801997v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Previous NMR studies of Hoechst 33258 with the d(CTTTTGCAAAAG)2 sequence have shown very strong (K2 >> K1) cooperativity between two adjacent binding sites (Searle, M. S.; Embrey, K. J. Nucleic Acids Res. 1990, 18 (13), 3753- 3762). In contrast, surface plasmon resonance (SPR) results with the hairpin analog of the same sequence show significantly reduced cooperativity. In an effort to explain the difference, two-dimensional (2-D) NMR experiments were done on both duplex and hairpin. Hoechst 33258 and an amidine analog, DB183, show very strong cooperativity with the duplex DNA but much weaker cooperativity with the hairpin. The significantly lower thermal melting temperature (Tm) of the duplex (34.8 degrees C) in comparison to its hairpin analog (62.3 degrees C) supports the idea of a dynamic difference between the two DNA structures that can influence cooperativity in binding. These results confirm the role of conformational entropy in positive cooperativity in some DNA interactions.
Collapse
Affiliation(s)
- Maryam Rahimian
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30303, USA
| | | | | |
Collapse
|
38
|
Liu L, Yi L, Yang X, Yu Z, Wen X, Xi Z. Synthesis and spectroscopic characterization of binaphthol aminosugars for stimulation of DNA strand slippage synthesis. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
39
|
Chen J, Wang X, Shao Y, Zhu J, Zhu Y, Li Y, Xu Q, Guo Z. A Trinuclear Copper(II) Complex of 2,4,6-Tris(di-2-pyridylamine)-1,3,5-triazine Shows Prominent DNA Cleavage Activity. Inorg Chem 2007; 46:3306-12. [PMID: 17355128 DOI: 10.1021/ic0614162] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly water soluble 3:2 complex of copper(II) and 2,4,6-tris(di-2-pyridylamine)-1,3,5-triazine (TDAT) has been synthesized and structurally characterized. The complex crystallized in a triclinic P1 space group with a molecular formula of [Cu3(TDAT)2Cl3]Cl3.2H2O (1), where each copper ion is coordinated by four pyridine nitrogen atoms and an apical chloride. The trinuclear complex is stable at physiological relevant conditions. It can bind to DNA through electrostatic attraction and cleave efficiently the supercoiled pBR322 DNA into its nicked and linear forms at micromolar concentrations. Active oxygen intermediates such as hydroxyl radicals and singlet oxygen generated in the presence of 1 may act as active species for the DNA scission.
Collapse
Affiliation(s)
- Jingwen Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Mun JH, Kim DJ, Choi HK, Gish J, Debellé F, Mudge J, Denny R, Endré G, Saurat O, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR. Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 2006; 172:2541-55. [PMID: 16489220 PMCID: PMC1456377 DOI: 10.1534/genetics.105.054791] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 02/09/2006] [Indexed: 11/18/2022] Open
Abstract
Microsatellites are tandemly repeated short DNA sequences that are favored as molecular-genetic markers due to their high polymorphism index. Plant genomes characterized to date exhibit taxon-specific differences in frequency, genomic location, and motif structure of microsatellites, indicating that extant microsatellites originated recently and turn over quickly. With the goal of using microsatellite markers to integrate the physical and genetic maps of Medicago truncatula, we surveyed the frequency and distribution of perfect microsatellites in 77 Mbp of gene-rich BAC sequences, 27 Mbp of nonredundant transcript sequences, 20 Mbp of random whole genome shotgun sequences, and 49 Mbp of BAC-end sequences. Microsatellites are predominantly located in gene-rich regions of the genome, with a density of one long (i.e., > or = 20 nt) microsatellite every 12 kbp, while the frequency of individual motifs varied according to the genome fraction under analysis. A total of 1,236 microsatellites were analyzed for polymorphism between parents of our reference intraspecific mapping population, revealing that motifs (AT)n, (AG)n, (AC)n, and (AAT)n exhibit the highest allelic diversity. A total of 378 genetic markers could be integrated with sequenced BAC clones, anchoring 274 physical contigs that represent 174 Mbp of the genome and composing an estimated 70% of the euchromatic gene space.
Collapse
Affiliation(s)
- Jeong-Hwan Mun
- Department of Plant Pathology, University of California, Davis 95616, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Trotta E, Del Grosso N, Erba M, Melino S, Cicero D, Paci M. Interaction of DAPI with individual strands of trinucleotide repeats. Effects of replication in vitro of the AAT x ATT triplet. ACTA ACUST UNITED AC 2004; 270:4755-61. [PMID: 14622264 DOI: 10.1046/j.1432-1033.2003.03877.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The structural changes produced by the minor-groove binding ligand DAPI (4',6-diamidine-2-phenylindole) on individual strands of trinucleotide repeat sequences were detected by electrophoretic band-shift analysis and related to their effects on DNA replication in vitro. Among the 20 possible single-stranded trinucleotide repeats, only the T-rich strand of the AAT.ATT triplet exhibits an observable fluorescence band and a change in electrophoretic mobility due to the drug binding. This is attributable to the property of DAPI that favours folding of the random coil ATT strand into a fast-migrating hairpin structure by a minor-groove binding mechanism. Electrophoretic characteristics of AAT, ACT, AGT, ATG and ATC are unchanged by DAPI, suggesting the crucial role of T.T with respect to A.A, C.C and G.G mismatch, in favouring the binding properties and the structural features of the ATT-DAPI complexes. Primer extension experiments, using the Klenow fragment of DNA polymerase I, demonstrate that such a selective structural change at ATT targets presents a marked property to stall DNA replication in vitro in comparison with the complementary AAT and a random GC-rich sequence. The results suggest a novel molecular mechanism of action of the DNA minor-groove binding ligand DAPI.
Collapse
Affiliation(s)
- Edoardo Trotta
- Istituto di Neurobiologia e Medicina Molecolare, Consiglio Nazionale delle Ricerche, Roma, Italy.
| | | | | | | | | | | |
Collapse
|
42
|
Kaushik M, Kukreti S. Temperature induced hyperchromism exhibited by Hoechst 33258: evidence of drug aggregation from UV-melting method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:3123-3129. [PMID: 14583287 DOI: 10.1016/s1386-1425(03)00115-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
UV-thermal denaturation is a simple optical method widely employed for determination of DNA stability and interaction with ligands. Thermal denaturation of DNA and DNA-ligand complex is usually monitored at 260 nm. These data are generally presented as a function of the absorption increase of DNA alone with no consideration of the temperature dependent hyperchromism of the free ligand. Since not every ligand has absorption at 260 nm, usually this property of the ligand is ignored. Here, we report the temperature dependent hyperchromicity exhibited by Hoechst 33258 in the presence and absence of DNA. The presence of Hoechst, added to the duplex (monophasic profile, T(m)=75 degrees C) in various ratios generates a new transition at lower temperature displaying biphasic thermal transition profiles. We attributed this new transition (hyperchromic), a mere contribution from Hoechst, which might exist in aggregated forms. The extent of drug aggregation/self-association is concentration dependent. We suggest that prior to UV-melting studies the thermal dependence of the free ligand should be investigated.
Collapse
Affiliation(s)
- Mahima Kaushik
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | | |
Collapse
|
43
|
Spacková N, Cheatham TE, Ryjácek F, Lankas F, Van Meervelt L, Hobza P, Sponer J. Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 2003; 125:1759-69. [PMID: 12580601 DOI: 10.1021/ja025660d] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An extended set of nanosecond-scale molecular dynamics simulations of DNA duplex sequences in explicit solvent interacting with the minor groove binding drug 4',6-diamidino-2-phenylindole (DAPI) are investigated for four different and sequence specific binding modes. Force fields for DAPI have been parametrized to properly reflect its internal nonplanarity. Sequences investigated include the binding modes observed experimentally, that is, AATT in d(CGCGAATTCGCG)(2) and ATTG in d(GGCCAATTGG)(2) and alternative shifted binding modes ATTC and AATT, respectively. In each case, stable MD simulations are obtained, well reproducing specific hydration patterns seen in the experiments. In contrast to the 2.4 A d(CGCGAATTCGCG)(2) crystal structure, the DAPI is nonplanar, consistent with its gas-phase geometry and the higher resolution crystal structure. The simulations also suggest that the DAPI molecule is able to adopt different conformational substates accompanied by specific hydration patterns that include long-residing waters. The MM_PBSA technology for estimating relative free energies was utilized. The most consistent free energy results were obtained with an approach that uses a single trajectory of the DNA-DAPI complex to estimate all free energy terms. It is demonstrated that explicit inclusion of a subset of bound water molecules shifts the calculated relative binding free energies in favor of both crystallographically observed binding modes, underlining the importance of structured hydration.
Collapse
Affiliation(s)
- Nad'a Spacková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, and National Center for Biomolecular Research, Královopolská 135, 612 65 Brno, Czech Republic
| | | | | | | | | | | | | |
Collapse
|