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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. MICROMACHINES 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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2
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Beh RC, Pitsillou E, Liang JJ, Hung A, Karagiannis TC. In silico investigation of DNA minor groove binding bibenzimidazoles in the context of UV A phototherapy. Phys Chem Chem Phys 2021; 24:112-121. [PMID: 34889929 DOI: 10.1039/d1cp04841d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The versatility of DNA minor groove binding bibenzimidazoles extends to applications in cancer therapy, beyond their typical use as DNA stains. In the context of UVA phototherapy, a series of halogenated analogues designated ortho-, meta-, and para-iodoHoechst have been investigated. Phototoxicity involves dehalogenation of the ligands following exposure to UVA light, resulting in the formation of a carbon-centred radical. While the cytotoxic mechanisms have been well established, the nature and severity of DNA damage induced by the ortho-, meta-, and para-iodoHoechst isomers requires clarification. Our aims were to measure and compare the binding constants of iodoHoechst analogues, and to determine the proximity of the carbon-centred radicals formed following photodehalogenation to the C1', C4', and C5' DNA carbons. We performed molecular docking studies, as well as classical molecular dynamics simulations to investigate the interactions of Hoechst ligands with DNA including a well-defined B-DNA dodecamer containing the high affinity AATT minor groove binding site. Docking highlighted the binding of Hoechst analogues to AATT regions in oligonucleotides, nucleosomes, and origami DNA helical bundles. Further, MD simulations demonstrated the stability of Hoechst ligands in the AATT-containing minor groove over microsecond trajectories. Our findings reiterate that the efficiency of dehalogenation per se, rather than the proximity of the carbon-centred radicals to the DNA backbone, is responsible for the extreme phototoxicity of the ortho- isomer compared to the meta- and para-iodoHoechst isomers. More generally, our analyses are in line with the potential utility of ortho-iodoHoechst in DNA-targeted phototherapy, particularly if combined with a cell-specific delivery system.
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Affiliation(s)
- Raymond C Beh
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia. .,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia. .,School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia. .,School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Andrew Hung
- School of Science, College of Science, Engineering & Health, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia. .,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia
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3
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Graphene-based electrochemical genosensor incorporated loop-mediated isothermal amplification for rapid on-site detection of Mycobacterium tuberculosis. J Pharm Biomed Anal 2020; 186:113333. [DOI: 10.1016/j.jpba.2020.113333] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022]
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4
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Rodríguez-Corrales JÁ, Wang J, Winkel BSJ, Brewer KJ. Mechanistic Investigation into DNA Modification by a Ru II ,Rh III Bimetallic Complex. Chembiochem 2018; 19:2216-2224. [PMID: 30088850 DOI: 10.1002/cbic.201800369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Indexed: 11/09/2022]
Abstract
Despite significant progress in the treatment of cancer, there remains an urgent need for more effective therapies that also have less impact on patient wellbeing. Photodynamic therapy employs targeted light activation of a photosensitizer in selected tissues, thereby reducing off-target toxicity. Our group previously reported a RuII ,RhIII bimetallic architecture that displays multifunctional covalent photomodification of DNA in the therapeutic window in an oxygen-independent manner, features that are essential for treating deep and hypoxic tumors. Herein, we explore the mechanism by which a new analogue, [(phen)2 Ru(dpp)Rh(phen)Cl2 ]3+ , or RuII -RhIII , interacts with DNA. We established that RuII -RhIII exhibits "light switch" behavior in the presence of DNA, undergoing strong electrostatic interactions that might involve groove binding. Furthermore, these noncovalent interactions play a major role in the covalent photobinding and photocleavage of DNA, which occur according to an oxygen-independent mechanism. Polymerase chain reaction (PCR) revealed that covalent modification of DNA by RuII -RhIII , especially photobinding, is critical to inhibiting amplification, thus suggesting that the complex could exert its toxic activity by interfering with DNA replication in cells. This new structural motif, with phenanthroline at all three terminal ligand positions, has a number of properties that are promising for the continued refinement of photodynamic-therapy strategies.
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Affiliation(s)
| | - Jing Wang
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061-0212, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061-0212, USA
| | - Karen J Brewer
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061-0212, USA
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5
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Amirbekyan K, Duchemin N, Benedetti E, Joseph R, Colon A, Markarian SA, Bethge L, Vonhoff S, Klussmann S, Cossy J, Vasseur JJ, Arseniyadis S, Smietana M. Design, Synthesis, and Binding Affinity Evaluation of Hoechst 33258 Derivatives for the Development of Sequence-Specific DNA-Based Asymmetric Catalysts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00495] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen Amirbekyan
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Nicolas Duchemin
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Erica Benedetti
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Rinah Joseph
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Aude Colon
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Shiraz A. Markarian
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Stephan Vonhoff
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Janine Cossy
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Jean-Jacques Vasseur
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| | - Stellios Arseniyadis
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
- School
of Biological and Chemical Sciences, Queen Mary University of London, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
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6
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Lobachevsky P, Clark GR, Pytel PD, Leung B, Skene C, Andrau L, White JM, Karagiannis T, Cullinane C, Lee BQ, Stuchbery A, Kibedi T, Hicks RJ, Martin RF. Strand breakage by decay of DNA-bound 124I provides a basis for combined PET imaging and Auger endoradiotherapy. Int J Radiat Biol 2016; 92:686-697. [PMID: 26902391 DOI: 10.3109/09553002.2015.1136852] [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] [Indexed: 01/09/2023]
Abstract
Purpose DNA ligands labelled with 125I induce cytotoxic DNA double-strand breaks (DSB), suggesting a potential for Auger endoradiotherapy. Since the 60-day half-life of 125I is suboptimal for therapy, we have investigated another Auger-emitter 124I, with shorter half-life (4.18 days), and the additional feature of positron-emission, enabling positron emission tomography (PET) imaging. The purpose of this study was to compare the two radionuclides on the basis of DNA DSB per decay. Materials and methods Using a 124I- (or 125I)-labelled minor groove binding DNA ligand, we investigated DNA breakage using the plasmid DNA assay. Biodistribution of the conjugate of the labelled ligand with transferrin was investigated in nude mice bearing a K562 human lymphoma xenograft. Results The probability of DSB per decay was 0.58 and 0.85 for 124I and 125I, respectively, confirming the therapeutic potential of the former. The crystal structure of the ligand DNA complex shows the iodine atom deep within the minor groove, consistent with the high efficiency of induced damage. Biodistribution studies, including PET imaging, showed distinctive results for the conjugate, compared to the free ligand and transferrin, consistent with receptor-mediated delivery of the ligand. Conclusions Conjugation of 124I-labelled DNA ligands to tumor targeting peptides provides a feasible strategy for Auger endoradiotherapy, with the advantage of monitoring tumor targeting by PET imaging.
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Affiliation(s)
- Pavel Lobachevsky
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia
| | - George R Clark
- c School of Chemical Sciences , The University of Auckland , New Zealand
| | - Patrycja D Pytel
- c School of Chemical Sciences , The University of Auckland , New Zealand
| | - Brenda Leung
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Colin Skene
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Laura Andrau
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Jonathan M White
- d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
| | - Tom Karagiannis
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne
| | - Carleen Cullinane
- b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,e Cancer Research Division , Peter MacCallum Cancer Centre , Melbourne
| | - Boon Q Lee
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Andrew Stuchbery
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Tibor Kibedi
- f Department of Nuclear Physics, Research School of Physics and Engineering , Australian National University , Canberra
| | - Rodney J Hicks
- b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,g Centre for Molecular Imaging, Peter MacCallum Cancer Centre , Melbourne , VIC , Australia
| | - Roger F Martin
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre , Melbourne.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne , Melbourne , Australia.,d School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Australia
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7
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K. V. D, V. V, C. R. Rational design and interaction studies of combilexins towards duplex DNA. MOLECULAR BIOSYSTEMS 2016; 12:860-7. [DOI: 10.1039/c5mb00808e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Combilexins interact more strongly with DNA than any other class of DNA binders.
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Affiliation(s)
- Dileep K. V.
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram
- Trivandrum-695016
- India
| | - Vijeesh V.
- Department of Biotechnology and Microbiology and Inter-University Centre for Bioscience
- Kannur University
- Palayad P O
- India
| | - Remya C.
- Department of Biotechnology and Microbiology and Inter-University Centre for Bioscience
- Kannur University
- Palayad P O
- India
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8
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Zhang F, Tsunoda M, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Takénaka A. O6-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine. ACTA ACUST UNITED AC 2014; 70:1669-79. [DOI: 10.1107/s1399004714006178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/19/2014] [Indexed: 11/10/2022]
Abstract
N-Nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation ofO6-carboxymethylguanine (O6-CMG) in DNA.O6-CMG has been identified in DNA derived from human colon tissue and its occurrence has been linked to diets high in red and processed meats, implying an association with the induction of colorectal cancer. By analogy toO6-methylguanine,O6-CMG is expected to be mutagenic, inducing G-to-A mutations that may be the molecular basis of increased cancer risk. Previously, the crystal structure of the DNA dodecamer d(CGCG[O6-CMG]ATTCGCG) has been reported, in whichO6-CMG forms a Watson–Crick-type pair with thymine similar to the canonical A:T pair. In order to further investigate the versatility ofO6-CMG in base-pair formation, the structure of the DNA dodecamer d(CGC[O6-CMG]AATTTGCG) containingO6-CMG at a different position has been determined by X-ray crystallography using four crystal forms obtained under conditions containing different solvent ions (Sr2+, Ba2+, Mg2+, K+or Na+) with and without Hoechst 33258. The most striking finding is that the pairing modes ofO6-CMG with T are quite different from those previously reported. In the present dodecamer, the T bases are displaced (wobbled) into the major groove to form a hydrogen bond between the thymine N3N—H and the carboxyl group ofO6-CMG. In addition, a water molecule is bridged through two hydrogen bonds between the thymine O2atom and the 2-amino group ofO6-CMG to stabilize the pairing. These interaction modes commonly occur in the four crystal forms, regardless of the differences in crystallization conditions. The previous and the present results show thatO6-CMG can form a base pair with T in two alternative modes: the Watson–Crick type and a high-wobble type, the nature of which may depend on the DNA-sequence context.
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9
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Fornander LH, Wu L, Billeter M, Lincoln P, Nordén B. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule? J Phys Chem B 2013; 117:5820-30. [DOI: 10.1021/jp400418w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Louise H. Fornander
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Lisha Wu
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Martin Billeter
- Department of Chemistry and
Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Bengt Nordén
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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10
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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Balagurumoorthy P, Xu X, Wang K, Adelstein SJ, Kassis AI. Effect of distance between decaying (125)I and DNA on Auger-electron induced double-strand break yield. Int J Radiat Biol 2012; 88:998-1008. [PMID: 22732063 DOI: 10.3109/09553002.2012.706360] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To determine the possible effects of (125)I-to-DNA distance on the magnitude and mechanism of Auger-electron induced-double-strand break (DSB) production. MATERIALS AND METHODS We have synthesized a series of (125)I-labeled Hoechst (H) derivatives ((125)IE-H, (125)IB-H, (125)I-C(8)-H and (125)I-C(12)-H). While all four molecules share a common DNA minor groove binding bis-benzimidazole motif, they are designed to position (125)I at varying distances from the DNA helix. Each Hoechst derivative was incubated at 4°C in phosphate buffered saline (PBS) together with supercoiled (SC) (3)H-pUC19 plasmid DNA (ratio 3:1) ± the •OH scavenger dimethyl sulfoxide (DMSO) (0.2 M). Aliquots were analyzed on agarose gels over time and DSB yields per decay of (125)I atom were determined. Docking of the iodinated compounds on a DNA molecule was carried out to determine the distance between the iodine atom and the central axis of DNA. RESULTS In the absence of DMSO, the results show that the DSB yields decrease monotonically as the (125)I atom is distanced - by 10.5 Å to 13.9 Å - from the DNA helix ((125)IEH: 0.52 ± 0.01; (125)IB-H: 0.24 ± 0.03; (125)I-C(8)-H: 0.18 ± 0.02; (125)I-C(12)-H: 0.10 ± 0.00). In the presence of DMSO, DSB yields for (125)IEH (0.49 ± 0.02) and (125)IB-H (0.26 ± 0.04) remain largely unchanged indicating that DSB are entirely produced by direct effects. Strikingly, (125)I-C(8)-H or (125)I-C(12)-H, did not produce detectable DSB in the presence of DMSO under similar conditions suggesting when (125)I atom is positioned > 12 Å from the DNA, DSB are entirely produced by indirect effects. CONCLUSION These results suggest that at a critical distance between the (125)I atom and the DNA helix, DSB production switches from an 'all' direct to an 'all' indirect mechanism, the latter situation being comparable to the decay of (125)I free in solution. These experimental findings were correlated with theoretical expectations based on microdosimetry.
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12
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Modelling topoisomerase I inhibition by minor groove binders. Bioorg Med Chem 2011; 19:1450-7. [PMID: 21273082 DOI: 10.1016/j.bmc.2011.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 01/03/2011] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
Abstract
Topoisomerase inhibition is an extremely useful target for anticancer and antimicrobial drugs, and an undesirable side effect of some drugs targeting other proteins. Published modelling studies are sparse, and have used small data sets with relatively low molecular diversity. Given the important role of minor groove binding in the mechanism of topoisomerase I inhibition, we have conducted the first 3D QSAR study of topoisomerase I inhibition of a large, diverse set of minor groove binders using the minor groove binding conformation as the alignment template. The highly significant QSAR models resulting from this alignment identify the roles played by molecular features, most importantly the hydrogen bond donor properties.
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13
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Nagatani N, Yamanaka K, Saito M, Koketsu R, Sasaki T, Ikuta K, Miyahara T, Tamiya E. Semi-real time electrochemical monitoring for influenza virus RNA by reverse transcription loop-mediated isothermal amplification using a USB powered portable potentiostat. Analyst 2011; 136:5143-50. [DOI: 10.1039/c1an15638a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Bazhulina NP, Nikitin AM, Rodin SA, Surovaya AN, Kravatsky YV, Pismensky VF, Archipova VS, Martin R, Gursky GV. Binding of Hoechst 33258 and its derivatives to DNA. J Biomol Struct Dyn 2009; 26:701-18. [PMID: 19385699 DOI: 10.1080/07391102.2009.10507283] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present work, we employed UV-VIS spectroscopy, fluorescence methods, and circular dichroism spectroscopy (CD) to study the interaction of dye Hoechst 33258, Hoechst 33342, and their derivatives to poly[d(AT)].poly[d(AT)], poly(dA).poly(dT), and DNA dodecamer with the sequence 5'-CGTATATATACG-3'. We identified three types of complexes formed by Hoechst 33258, Hoechst 33342, and methylproamine with DNA, corresponding to the binding of each drug in monomer, dimer, and tetramer forms. In a dimer complex, two dye molecules are sandwiched in the same place of the minor DNA groove. Our data show that Hoechst 33258, Hoechst 33342, and methylproamine also form complexes of the third type that reflects binding of dye associates (probably tetramers) to DNA. Substitution of a hydrogen atom in the ortho position of the phenyl ring by a methyl group has a little effect on binding of monomers to DNA. However it reduces strength of binding of tetramers to DNA. In contrast, a Hoechst derivative containing the ortho-isopropyl group in the phenyl ring exhibits a low affinity to poly(dA).poly(dT) and poly[d(AT)].poly[d(AT)] and binds to DNA only in the monomer form. This can be attributed to a sterical hindrance caused by the ortho-isopropyl group for side-by-side accommodation of two dye molecules in the minor groove. Our experiments show that mode of binding of Hoechst 33258 derivatives and their affinity for DNA depend on substituents in the ortho position of the phenyl ring of the dye molecule. A statistical mechanical treatment of binding of Hoechst 33258 and its derivatives to a polynucleotide lattice is described and used for determination of binding parameters of Hoechst 33258 and its derivatives to poly[d(AT)].poly[d(AT)] and poly(dA).poly(dT).
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Affiliation(s)
- N P Bazhulina
- V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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15
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Lobachevsky PN, White J, Leung M, Skene C, White J, Martin RF. Plasmid breakage by (125)I-labelled DNA ligands: effect of DNA-iodine atom distance on breakage efficiency. Int J Radiat Biol 2009; 84:991-1000. [PMID: 19061123 DOI: 10.1080/09553000802478091] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE The aim of the study is to establish the relationship between the efficiency of DNA double-stranded breakage by (125)I-labelled DNA ligands and the distance from the decaying atom to the helical axis. MATERIALS AND METHODS Two new iodinated minor groove binding ligands were synthesized which, on the basis of molecular modelling studies, place the iodine atom at different distances from the DNA helical axis (namely 7.4 and 11.2 A degrees ). Plasmid DNA breakage experiments, in both buffer-only and buffer + 2M dimethylsulfoxide (DMSO), were used to determine the efficiency of induction of internal double-stranded breaks (DSB) of the two new ligands, as well as that for (125)I-Hoechst 33258, which is characterized by a helical axis-iodine atom distance of 9.1 A degrees . RESULTS The results showed a progressive decrease in the efficiency of DNA DSB induction with the axis-iodine atom distance, for both incubation conditions. The distance-damage relationship was somewhat steeper than previously predicted from the theoretical studies by Humm and Charlton, based on radical-mediated damage. Another distinctive trend was revealed by comparison of breakage efficiency with and without DMSO. The extent of DMSO protection increased significantly with DNA-iodine distance. CONCLUSIONS The steeper than predicted decrease in DSB induction with DNA-iodine distance is consistent with a substantial contribution to DNA breakage of the charge neutralization effect (arising from the transient positive charge left on the daughter Te atom), and the expectation that this contribution would be very dependent on the distance of the site of hole injection from the base-pair pi-stack. An important caveat to the results and conclusions is the need to confirm the estimated helical axis-iodine distances with X-ray crystallography studies, and for further exemplification with a more extensive collection of DNA ligands.
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Affiliation(s)
- Pavel N Lobachevsky
- Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, Melbourne, Australia
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Ahmed MU, Saito M, Hossain MM, Rao SR, Furui S, Hino A, Takamura Y, Takagi M, Tamiya E. Electrochemical genosensor for the rapid detection of GMO using loop-mediated isothermal amplification. Analyst 2009; 134:966-72. [DOI: 10.1039/b812569d] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Araúzo-Bravo MJ, Sarai A. Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Nucleic Acids Res 2008; 36:376-86. [PMID: 18039704 PMCID: PMC2241865 DOI: 10.1093/nar/gkm892] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 09/22/2007] [Accepted: 10/03/2007] [Indexed: 11/13/2022] Open
Abstract
DNA-binding drugs have numerous applications in the engineered gene regulation. However, the drug-DNA recognition mechanism is poorly understood. Drugs can recognize specific DNA sequences not only through direct contacts but also indirectly through sequence-dependent conformation, in a similar manner to the indirect readout mechanism in protein-DNA recognition. We used a knowledge-based technique that takes advantage of known DNA structures to evaluate the conformational energies. We built a dataset of non-redundant free B-DNA crystal structures to calculate the distributions of adjacent base-step and base-pair conformations, and estimated the effective harmonic potentials of mean force (PMF). These PMFs were used to calculate the conformational energy of drug-DNA complexes, and the Z-score as a measure of the binding specificity. Comparing the Z-scores for drug-DNA complexes with those for free DNA structures with the same sequence, we observed that in several cases the Z-scores became more negative upon drug binding. Furthermore, the specificity is position-dependent within the drug-bound region of DNA. These results suggest that DNA conformation plays an important role in the drug-DNA recognition. The presented method provides a tool for the analysis of drug-DNA recognition and can facilitate the development of drugs for targeting a specific DNA sequence.
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Affiliation(s)
| | - Akinori Sarai
- Department of Biosciences and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
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Singh A, Chen K, Adelstein SJ, Kassis AI. Synthesis of Coumarin–Polyamine-Based Molecular Probe for the Detection of Hydroxyl Radicals Generated by Gamma Radiation. Radiat Res 2007; 168:233-42. [PMID: 17638412 DOI: 10.1667/rr0948.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 03/15/2007] [Indexed: 11/03/2022]
Abstract
To develop a molecular probe for detection of hydroxyl radicals in the vicinity of DNA, the coumarin-polyamine complexes, N(1),N(12)-bis[2-oxo-2H-chromene-3-carbonyl]-1,12-diamine-4,9-diazadodecane (5) and tris[2-(2-oxo-2H-chromene-3-carboxamido)ethyl]amine (7), and their hydroxylated derivatives, N(1),N(12)-bis[7-hydroxy-2-oxo-2H-chromene-3-carbonyl]-1,12-diamine-4,9-diazadodecane (6) and tris[2-(7-hydroxy-2-oxo-2H-chromene-3-carboxamido)ethyl]amine (8), have been synthesized. Using computer-generated molecular modeling, the derivatives have been docked onto DNA dodecamer d(CGCGAATTCGCG)(2), the ligand-DNA complexes have been minimized, and the free binding energies (DeltaG(binding)) and inhibition constants (K(i)) have been calculated. Compound 7 is not water-soluble at the concentrations required for the project. When aqueous solutions of 5 are irradiated with gamma rays, the relationship between induced fluorescence and dose is linear in the range of 0 to 10 Gy. The fluorescence emission spectrum of irradiated 5 is similar to that of its dihydroxy derivative 6, indicating conversion of 5 to 6, and induction of fluorescence records formation of hydroxyl radicals in aqueous solution. The dicoumarin-polyamine 5, a novel compound for the detection of hydroxyl radicals close to DNA, is a sensitive and quantitative probe with potential for applications in biological systems.
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Affiliation(s)
- Amarjit Singh
- Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
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Yasui LS, Chen K, Wang K, Jones TP, Caldwell J, Guse D, Kassis AI. Using Hoechst 33342 to target radioactivity to the cell nucleus. Radiat Res 2007; 167:167-75. [PMID: 17390724 DOI: 10.1667/rr0584.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have explored the use of Hoechst 33342 (H33342) to carry radioactivity to the cell nucleus. H33342 enters cells and targets DNA at adenine-thymine-rich regions of the minor groove. Considerable membrane blebbing and ruffling occur in CHO cells within minutes after its addition to the culture medium in micromolar quantities. Blue vesicles are apparent in the cell cytoplasm, and by 30 min the nuclei are stained dark blue. Upon its binding to DNA, a visible emission shift of the dye can be observed with fluorescence microscopy. We have radioiodinated (125I) H33342 and specifically irradiated nuclear DNA by incubating CHO cells with 125I-H33342 at 37 degrees C and accumulating 125I decays at -90 degrees C. At various times, the cells are thawed and assayed for survival (clonogenicity) and DSB (gamma-H2AX) formation. 125I-H33342 decay leads to a monoexponential decrease in cell survival with a D0 of 122 125I decays per cell and a linear increase in DNA DSB induction (equivalent to 15 gamma-H2AX foci/cell). Cell death is not modified by the radioprotective effects of H33342 because we use considerably lower concentrations than those that provide a slight protection against gamma radiation. We conclude that cell killing by 125I-H33342 and the induction of gamma-H2AX foci are highly correlated.
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Affiliation(s)
- Linda S Yasui
- Northern Illinois University, Department of Biological Sciences, DeKalb, Illinois 60115, USA.
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Ahmed MU, Idegami K, Chikae M, Kerman K, Chaumpluk P, Yamamura S, Tamiya E. Electrochemical DNA biosensor using a disposable electrochemical printed (DEP) chip for the detection of SNPs from unpurified PCR amplicons. Analyst 2007; 132:431-8. [PMID: 17471389 DOI: 10.1039/b615242b] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we are reporting for the first time the elucidation of single nucleotide polymorphisms (SNPs) of clinically important alleles from consenting human subjects using a disposable electrochemical printed (DEP) chip in connection with differential pulse voltammetry (DPV) and a redox active molecule Hoechst 33258 [H33258, 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi(1H-benzimidazole)]. Post-PCR products were analyzed directly without any purification process. The aggregation of the DNA-H33258 complex causes a significant drop in the peak current intensity of H33258 oxidation. The phenomenon of DNA aggregation induced by H33258 in addition to changes in anodic current peak are used to detect SNPs. Since laborious probe immobilization was not required, our biosensor offers several benefits due to its simplicity and rapid response as a promising device for genetic analysis.
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Affiliation(s)
- Minhaz Uddin Ahmed
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa 923-1292, Japan
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Balagurumoorthy P, Chen K, Bash RC, Adelstein SJ, Kassis AI. Mechanisms Underlying Production of Double-Strand Breaks in Plasmid DNA after Decay of125I-Hoechst. Radiat Res 2006; 166:333-44. [PMID: 16881734 DOI: 10.1667/rr3591.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Previously, the kinetics of strand break production by (125)I-labeled m-iodo-p-ethoxyHoechst 33342 ((125)IEH) in supercoiled (SC) plasmid DNA had demonstrated that approximately 1 DSB is produced per (125)I decay both in the presence and absence of the hydroxyl radical scavenger DMSO. In these experiments, an (125)IEH:DNA molar ratio of 42:1 was used. We now hypothesize that this DSB yield (but not the SSB yield) may be an overestimate due to subsequent decays occurring in any of the 41 (125)IEH molecules still bound to nicked (N) DNA. To test our hypothesis, (125)IEH was incubated with SC pUC19 plasmids ((125)IEH:DNA ratio of approximately 3:1) and the SSB and DSB yields were quantified after the decay of (125)I. As predicted, the number of DSBs produced per (125)I decay is one-half that reported previously ( approximately 0.5 compared to approximately 1, +/- DMSO) whereas the number of SSBs ( approximately 3/(125)I decay) is similar to that obtained previously ( approximately 90% are generated by OH radicals). Direct visualization by atomic force microscopy confirms formation of L and N DNA after (125)IEH decays in SC DNA and supports the strand break yields reported. These findings indicate that although SSB production is independent of the number of (125)IEH bound to DNA, the DSB yield can be augmented erroneously by (125)I decays occurring in N DNA. Further analysis indicates that 17% of SSBs and 100% of DSBs take place within the plasmid molecule in which an (125)IEH molecule decays, whereas 83% of SSBs are formed in neighboring plasmid DNA molecules.
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Lobachevsky PN, Martin RF. DNA Breakage by Decay of Auger Electron Emitters: Experiments with123I-iodoHoechst 33258 and Plasmid DNA. Radiat Res 2005; 164:766-73. [PMID: 16296882 DOI: 10.1667/rr3469.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Auger electron-emitting isotope 123I is of interest in the context of potential exploitation of Auger electron emitters in radioimmunotherapy. The efficiency of induction of cytotoxic lesions by decay of DNA-associated 125I, the prototype Auger electron emitter, is well established, but its long half-life (60 days) is a limitation. However, the advantage of the much shorter half-life of 123I (13.2 h) might be outweighed by its "weaker" Auger electron cascade with an average of 8-11 Auger electrons, compared to about 15-21 electrons for 125I. Accordingly, the efficiency of DNA breakage for DNA-associated 123I was investigated by incubation of 123I-iodoHoechst 33258 with plasmid DNA. The efficiency of double-strand break induction by decay of 123I was 0.62 compared to 0.82 per decay of 125I in the same experimental system. In the presence of dimethylsulfoxide, the values were 0.54 and 0.65 for decay of 123I and 125I, respectively. The results also showed that at a very low ligand/plasmid molar ratio (<1), the majority of cleavage seemed to occur at a particular site on the plasmid molecule, indicating preferential binding of the 123I-ligand to a unique site or a cluster of neighboring sites.
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Affiliation(s)
- Pavel N Lobachevsky
- Trescowthick Research Laboratories, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
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Chen K, Adelstein SJ, Kassis AI. Molecular simulation of ligand-binding with DNA: implications for 125I-labeled pharmaceutical design. Int J Radiat Biol 2005; 80:921-6. [PMID: 15764403 DOI: 10.1080/09553000400017630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE By using computer-assisted molecular modeling software, to assess the effects of structural modification on the interaction of 125I-labeled iodoHoechst ligands and DNA and to design new analogs with specified distances between the Auger-electron-emitting 125I atom and the DNA central axis. MATERIALS AND METHODS The Lamarckian genetic algorithm (AutoDock 3.0) was used to model the interaction between DNA and m-iodo-p-methoxyHoechst (IMH), a ligand whose binding to the minor groove of DNA has been demonstrated (crystal structure) and which is available in the Protein Data Bank. m-Iodo-p-ethoxyHoechst (IEH), a radioligand we had previously synthesized and characterized, was then docked onto DNA, the IEH-DNA complex minimized, and the binding free energy and inhibition constant (Ki) estimated and compared with those for IMH-DNA. Using the protocol, several novel iodoHoechst analogs (IH-A and IH-B) were designed. Finally, Insight II was used to measure the distances between the iodine atom (e.g. 125I) of these Hoechst analogs and of 5-iodo-2'-deoxyuridine (IdUrd) and the central axis of the targeted DNA, and these values were correlated with the expected/measured DSB yield following 125I decay. RESULTS The docking of IMH and DNA leads to a ligand-DNA complex approximately 1 A RMSD (root mean square deviation) from the crystal-structure position, and the IEH-DNA complex also has a small RMSD (1.27 A). The distances between the 125I atom and the DNA central axis are estimated as 8.61 A for IMH, 9.20 A for IEH and 5.7A for IdUrd. For the newly designed analogs, the distances from the 125I atom to the central DNA axis are 10.92 A for IH-A and 16.39 A for IH-B. CONCLUSION These software programs can predict the reactivity of newly designed radiolabelled molecules with their targeted DNA molecules by molecular modeling prior to their chemical synthesis.
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Affiliation(s)
- Kai Chen
- Harvard Medical School, 200 Longwood Avenue, Armenise Building, D2-137, Boston, MA 02115-5729, USA
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Chen K, Adelstein SJ, Kassis AI. Molecular modeling of the interaction of iodinated Hoechst analogs with DNA: implications for new radiopharmaceutical design. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.08.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Adhikary A, Buschmann V, Müller C, Sauer M. Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA. Nucleic Acids Res 2003; 31:2178-86. [PMID: 12682368 PMCID: PMC153736 DOI: 10.1093/nar/gkg308] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ensemble and single-molecule fluorescence measurements of 2'-(4-hydroxyphenyl)-5-[5-(4-methylpiperazine-1-yl) benzimidazo-2-yl]-benzimidazole (H-258)- calf thymus (CT) DNA complexes at various [H-258]/[DNA bp] ratios were performed to elucidate the binding of H-258 with DNA. Upon binding to double-stranded CT DNA (CT ds DNA) at a [H-258]/[DNA bp] ratio of 0.05 the relative fluorescence quantum yield, Phi(f), of H-258 increases from 0.02 to 0.58. The fluorescence decay can be fitted almost by a mono-exponential model with a lifetime of approximately 3.6 ns. This indicates that H-258 binds almost quantitatively in the minor groove of DNA at low [H-258]/[DNA bp] ratios. With increasing [H-258]/[DNA bp] ratios, e.g. 0.15 and 0.20, the fluorescence quantum yield of H-258 decreases to 0.28 and 0.19, respectively. Fitting of the fluorescence decays measured for higher [H-258]/[DNA bp] ratios reveals the presence of additional shorter fluorescence lifetime components in the range of 0.5-2.0 ns. Our results suggest that H-258 partially intercalates in G:C sequences at higher [H-258]/[DNA bp] ratios reflected by a lifetime component of 1.5-2 ns. In addition, stacking or adsorption of H-258 molecules on DNA occurs at higher [H-258]/[DNA bp] ratios. These molecules exhibit a short fluorescence lifetime of approximately 500 ps and are more exposed to the aqueous environment. Fluorescence transients of the intensity and lifetime of single H-258 CT ds DNA demonstrate that weakly (unspecific) bound H-258 molecules exhibit a shorter fluorescence lifetime and a strongly reduced photostability.
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Affiliation(s)
- Amitava Adhikary
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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Breusegem SY, Clegg RM, Loontiens FG. Base-sequence specificity of Hoechst 33258 and DAPI binding to five (A/T)4 DNA sites with kinetic evidence for more than one high-affinity Hoechst 33258-AATT complex. J Mol Biol 2002; 315:1049-61. [PMID: 11827475 DOI: 10.1006/jmbi.2001.5301] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding of Hoechst 33258 and DAPI to five different (A/T)4 sequences in a stable DNA hairpin was studied exploiting the substantial increase in dye fluorescence upon binding. The two dyes have comparable affinities for the AATT site (e.g. association constant K(a)=5.5 x 10(8) M(-1) for DAPI), and their affinities decrease in the series AATT >> TAAT approximately equal to ATAT > TATA approximately equal to TTAA. The extreme values of K(a) differ by a factor of 200 for Hoechst 33258 but only 30 for DAPI. The binding kinetics of Hoechst 33258 were measured by stopped-flow under pseudo-first order conditions with an (A/T)4 site in excess. The lower-resolution experiments can be well represented by single exponential processes, corresponding to a single-step binding mechanism. The calculated association-rate parameters for the five (A/T)4 sites are similar (2.46 x 10(8) M(-1) s(-1) to 0.86 x 10(8) M(-1) s(-1)) and nearly diffusion-controlled, while the dissociation-rate parameters vary from 0.42 s(-1) to 96 s(-1). Thus the association constants are kinetically controlled and are close to their equilibrium-determined values. However, when obtained with increased signal-to-noise ratio, the kinetic traces for Hoechst 33258 binding at the AATT site reveal two components. The concentration dependencies of the two time constants and amplitudes are consistent with two different kinetically equivalent two-step models. In the first model, fast bimolecular binding is followed by an isomerization of the initial complex. In the second model, two single-step associations form two complexes that mutually exclude each other. For both models the four reaction-rate parameters are calculated. Finally, specific dissociation kinetics, using poly[d(A-5BrU)], show that the kinetics are even more complex than either two-step model. We correlate our results with the different binding orientations and locations of Hoechst 33258 in the DNA minor groove found in several structural studies in the literature.
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Affiliation(s)
- Sophia Y Breusegem
- Laboratory for Biochemistry Department of Biochemistry Physiology and Microbiology, Ghent University, Gent, B-9000, Belgium
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Breusegem SY, Loontiens FG, Regenfuss P, Clegg RM. Kinetics of binding of Hoechst dyes to DNA studied by stopped-flow fluorescence techniques. Methods Enzymol 2001; 340:212-33. [PMID: 11494850 DOI: 10.1016/s0076-6879(01)40424-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- S Y Breusegem
- Laboratory for Fluorescence Dynamics, Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
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Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Significance of ligand tails for interaction with the minor groove of B-DNA. Biophys J 2001; 81:1588-99. [PMID: 11509372 PMCID: PMC1301637 DOI: 10.1016/s0006-3495(01)75813-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Minor groove binding ligands are of great interest due to their extraordinary importance as transcription controlling drugs. We performed three molecular dynamics simulations of the unbound d(CGCGAATTCGCG)(2) dodecamer and its complexes with Hoechst33258 and Netropsin. The structural behavior of the piperazine tail of Hoechst33258, which has already been shown to be a contributor in sequence-specific recognition, was analyzed. The simulations also reveal that the tails of the ligands are able to influence the width of the minor groove. The groove width is even sensitive for conformational transitions of these tails, indicating a high adaptability of the minor groove. Furthermore, the ligands also exert an influence on the B(I)/B(II) backbone conformational substate behavior. All together these results are important for the understanding of the binding process of sequence-specific ligands.
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Affiliation(s)
- B Wellenzohn
- Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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Breusegem SY, Sadat-Ebrahimi SE, Douglas KT, Clegg RM, Loontiens FG. Increased stability and lifetime of the complex formed between DNA and meta-phenyl-substituted Hoechst dyes as studied by fluorescence titrations and stopped-flow kinetics. J Mol Biol 2001; 308:649-63. [PMID: 11350167 DOI: 10.1006/jmbi.2001.4615] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The large increase in fluorescence upon binding of five para- and meta-phenyl substituted hydroxy and methoxy derivatives of the Hoechst dye with poly[d(A-T)], d(CGCGAATTCGCG)2, and its corresponding T4-looped 28-mer hairpin was used to monitor the binding by equilibrium titrations and by stopped-flow kinetics. The affinity increases in the same order for the three DNAs: p-OH<m-OCH3, p-OH<m-OH<m-OH, p-OCH3<bis-m-OH. The association constants K(a) are three to 11 times larger for the AATT site than for poly[d(A-T)]. The AATT site binds m-OH Hoechst with K(a)=3.8 x 10(9 )M(-1) and bis-m-OH Hoechst with K(a)=1.9 x 10(10 )M(-1), which are seven and 37 times higher than p-OH Hoechst (Hoechst 33258), respectively. The high K(a )values determined at equilibrium agree with the kinetically defined association constants K(kin)=k(on)/k(off). The association-rate parameters k(on) were obtained by stopped-flow kinetics and the dissociation-rate parameters k(off) by dissociation kinetics using poly[d(A-5BrU)]. For binding to the AATT site, k(on) values are similar and nearly diffusion-controlled (2.0 x 10(8) M(-1) x s(-1) to 2.9 x 10(8) M(-1) x s(-1)), while k(off) values (0.42 s(-1) to 0.012 s(-1)) depend on the phenyl substitution and determine the affinity. At the AATT site, the longest-living complex is formed when the dye carries a bis-m-OH phenyl group that probably integrates in a hydrogen-bonding network of water molecules. With poly(dA).poly(dT), poly[d(A-T)] and poly[d(A-5BrU)], k(on) (between 6.1 x 10(7) M(-1) x s(-1) and 5.2 x 10(8) M(-1) x s(-1)) depends on the DNA.
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Affiliation(s)
- S Y Breusegem
- Laboratory for Biochemistry Department of Biochemistry Physiology and Microbiology Faculty of Sciences, Ghent University, Ledeganckstraat, Gent, B-9000, Belgium
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