1
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Jabak AA, Bryden N, Westerlund F, Lincoln P, McCauley MJ, Rouzina I, Williams MC, Paramanathan T. Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers. Biophys J 2022; 121:3745-3752. [PMID: 35470110 PMCID: PMC9617076 DOI: 10.1016/j.bpj.2022.04.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/27/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022] Open
Abstract
Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.
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Affiliation(s)
- Adam A Jabak
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Nicholas Bryden
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Thayaparan Paramanathan
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts.
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2
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Newton MD, Fairbanks SD, Thomas JA, Rueda DS. A Minimal Load‐and‐Lock Ru
II
Luminescent DNA Probe. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew D. Newton
- Department of Infectious Disease Faculty of Medicine Imperial College London London W12 0NN UK
- Single Molecule Imaging Group, MRC- London Institute of Medical Sciences London W12 0NN UK
| | - Simon D. Fairbanks
- Department of Chemistry University of Sheffield Sheffield S3 7HF UK
- Department of Molecular Biology and Biotechnology University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Jim A. Thomas
- Department of Chemistry University of Sheffield Sheffield S3 7HF UK
| | - David S. Rueda
- Department of Infectious Disease Faculty of Medicine Imperial College London London W12 0NN UK
- Single Molecule Imaging Group, MRC- London Institute of Medical Sciences London W12 0NN UK
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3
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Newton MD, Fairbanks SD, Thomas JA, Rueda DS. A Minimal Load-and-Lock Ru II Luminescent DNA Probe. Angew Chem Int Ed Engl 2021; 60:20952-20959. [PMID: 34378843 PMCID: PMC8518596 DOI: 10.1002/anie.202108077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/26/2022]
Abstract
Threading intercalators bind DNA with high affinities. Here, we describe single-molecule studies on a cell-permeant luminescent dinuclear ruthenium(II) complex that has been previously shown to thread only into short, unstable duplex structures. Using optical tweezers and confocal microscopy, we show that this complex threads and locks into force-extended duplex DNA in a two-step mechanism. Detailed kinetic studies reveal that an individual stereoisomer of the complex exhibits the highest binding affinity reported for such a mono-intercalator. This stereoisomer better preserves the biophysical properties of DNA than the widely used SYTOX Orange. Interestingly, threading into torsionally constrained DNA decreases dramatically, but is rescued on negatively supercoiled DNA. Given the "light-switch" properties of this complex on binding DNA, it can be readily used as a long-lived luminescent label for duplex or negatively supercoiled DNA through a unique "load-and-lock" protocol.
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Affiliation(s)
- Matthew D. Newton
- Department of Infectious DiseaseFaculty of MedicineImperial College LondonLondonW12 0NNUK
- Single Molecule Imaging Group, MRC-London Institute of Medical SciencesLondonW12 0NNUK
| | - Simon D. Fairbanks
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jim A. Thomas
- Department of ChemistryUniversity of SheffieldSheffieldS3 7HFUK
| | - David S. Rueda
- Department of Infectious DiseaseFaculty of MedicineImperial College LondonLondonW12 0NNUK
- Single Molecule Imaging Group, MRC-London Institute of Medical SciencesLondonW12 0NNUK
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4
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Feng B, Sundin E, Lincoln P, Mårtensson AKF. DNA threading intercalation of enantiopure [Ru(phen) 2bidppz] 2+ induced by hydrophobic catalysis. Phys Chem Chem Phys 2021; 23:2238-2244. [PMID: 33439155 DOI: 10.1039/d0cp00845a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The enantiomers of a novel mononuclear ruthenium(ii) complex [Ru(phen)2bidppz]2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
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Affiliation(s)
- Bobo Feng
- Department of Chemistry and Chemical Engineering, Kemigården 4, SE-412 96 Gothenburg, Sweden.
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5
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Li G, Zhu D, Wang X, Su Z, Bryce MR. Dinuclear metal complexes: multifunctional properties and applications. Chem Soc Rev 2020; 49:765-838. [DOI: 10.1039/c8cs00660a] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Dinuclear metal complexes have enabled breakthroughs in OLEDs, photocatalytic water splitting and CO2reduction, DSPEC, chemosensors, biosensors, PDT and smart materials.
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Affiliation(s)
- Guangfu Li
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Dongxia Zhu
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Xinlong Wang
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
| | - Zhongmin Su
- Department of Chemistry
- Northeast Normal University
- Changchun
- P. R. China
- School of Chemistry and Environmental Engineering
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6
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Jia F, Hébraud P, Han K, Wang J, Liang X, Liu B. Flexibility and thermal dynamic stability increase of dsDNA induced by Ru(bpy) 2dppz 2+ based on AFM and HRM technique. BMC Chem 2019; 13:68. [PMID: 31384815 PMCID: PMC6661754 DOI: 10.1186/s13065-019-0584-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/02/2019] [Indexed: 01/05/2023] Open
Abstract
Ru(bpy)2dppz2+ has been widely used as a probe for exploring the structure of double-stranded DNA (dsDNA). The flexibility change of DNA helix is important in many of its biological functions but not well understood. Here, flexibility change of dsDNA helix caused by intercalation with Ru(bpy)2dppz2+ was investigated using the atomic force microscopy. At first, the interactions between ruthenium complex and dsDNA helix were characterized and the binding site size (p = 2.87 bp) and binding constant (Ka = 5.9 * 107 M−1) were determined by the relative extension of DNA helix using the equation of McGhee and von Hippel. By measuring intercalator-induced DNA elongation and the mean square of end-to-end distance at different molar ratios of Ru(bpy)2dppz2+ to dsDNA, the changes of persistence length under different ruthenium concentrations were determined by the worm-like chain model. We found that the persistence length of dsDNA decreased with increasing Ru(bpy)2dppz2+ concentration, demonstrating that the flexibility of dsDNA obviously enhanced due to the intercalation. Especially, the persistence length changed greatly from 54 to 34 nm on changing the molar ratio of ruthenium to dsDNA from 0 to 0.2. We speculated that the intercalation of dsDNA with Ru(bpy)2dppz2+ resulted in local deformation or bending of the DNA duplex. In addition, the thermal dynamic stability of DNA helix was measured with high resolution melting method which revealed the increase in thermal dynamic stability of DNA helix due to the ruthenium intercalation.
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Affiliation(s)
- Fuchao Jia
- 1Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo, 255000 China
| | - Pascal Hébraud
- 2Institut de Physique et Chimie des Matériaux de Strasbourg/Centre National de la Recherche Scientifique, University of Strasbourg, 67034 Strasbourg, France
| | - Kezhen Han
- 1Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo, 255000 China
| | - Jing Wang
- 3College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Xingguo Liang
- 3College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Bo Liu
- 1Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo, 255000 China
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7
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Almaqwashi AA, Zhou W, Naufer MN, Riddell IA, Yilmaz ÖH, Lippard SJ, Williams MC. DNA Intercalation Facilitates Efficient DNA-Targeted Covalent Binding of Phenanthriplatin. J Am Chem Soc 2019; 141:1537-1545. [PMID: 30599508 DOI: 10.1021/jacs.8b10252] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phenanthriplatin, a monofunctional anticancer agent derived from cisplatin, shows significantly more rapid DNA covalent-binding activity compared to its parent complex. To understand the underlying molecular mechanism, we used single-molecule studies with optical tweezers to probe the kinetics of DNA-phenanthriplatin binding as well as DNA binding to several control complexes. The time-dependent extensions of single λ-DNA molecules were monitored at constant applied forces and compound concentrations, followed by rinsing with a compound-free solution. DNA-phenanthriplatin association consisted of fast and reversible DNA lengthening with time constant τ ≈ 10 s, followed by slow and irreversible DNA elongation that reached equilibrium in ∼30 min. In contrast, only reversible fast DNA elongation occured for its stereoisomer trans-phenanthriplatin, suggesting that the distinct two-rate kinetics of phenanthriplatin is sensitive to the geometric conformation of the complex. Furthermore, no DNA unwinding was observed for pyriplatin, in which the phenanthridine ligand of phenanthriplatin is replaced by the smaller pyridine molecule, indicating that the size of the aromatic group is responsible for the rapid DNA elongation. These findings suggest that the mechanism of binding of phenanthriplatin to DNA involves rapid, partial intercalation of the phenanthridine ring followed by slower substitution of the adjacent chloride ligand by, most likely, the N7 atom of a purine base. The cis isomer affords the proper stereochemistry at the metal center to facilitate essentially irreversible DNA covalent binding, a geometric advantage not afforded by trans-phenanthriplatin. This study demonstrates that reversible DNA intercalation provides a robust transition state that is efficiently converted to an irreversible DNA-Pt bound state.
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Affiliation(s)
- Ali A Almaqwashi
- Physics Department , King Abdulaziz University , Rabigh 21911 , Saudi Arabia
| | - Wen Zhou
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - M Nabuan Naufer
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Imogen A Riddell
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry , The University of Manchester , Manchester M13 9PL , United Kingdom
| | - Ömer H Yilmaz
- David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Stephen J Lippard
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Mark C Williams
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
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8
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Ypsilantis K, Plakatouras JC, Manos MJ, Kourtellaris A, Markopoulos G, Kolettas E, Garoufis A. Stepwise synthesis, characterization, DNA binding properties and cytotoxicity of diruthenium oligopyridine compounds conjugated with peptides. Dalton Trans 2018; 47:3549-3567. [PMID: 29436543 DOI: 10.1039/c7dt04639a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although the interactions of oligopyridine ruthenium complexes with DNA have been widely studied, the biological activity of similar diruthenium oligopyridine complexes conjugated with peptides has not been investigated. Herein, we report the stepwise synthesis and characterization of diruthenium complexes with the general formula [(La)Ru(tppz)Ru(Lb)]n+ (tppz = 2,3,5,6-tetra(2-pyridyl)pyrazine, La = 2,2':6',2''-terpyridine or 4-phenyl-2,2':6',2''-terpyridine and Lb = 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Gly3-LysCONH2) (5), (6), n = 5; 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Lys1-Lys2CONH2) (7), (8), n = 6; 2,2':6',2''-terpyridine-4'-CO(Ahx-Lys1Lys2CONH2) (9), (10), n = 5, Ahx = 6-aminohexanoic acid). The compounds [(trpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (2)(PF6)4, [(ptrpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (3)(PF6)4 and [(ptrpy)Ru(tppz)Ru(trpy)](PF6)4, (4)(PF6)4 were also characterized by single crystal X-ray methods. Moreover, the interactions of the chloride salts (5), (6) and (4) with the self-complementary dodecanucleotide duplex d(5'-CGCGAATTCGCG-3')2 were studied by NMR spectroscopic techniques. The results show that complex (4) binds in the central part of the oligonucleotide, from the minor groove through the ligand ptrpy, while the ligand trpy, which was located on the other side of the diruthenium core, does not contribute to the binding. Complex (5) binds similarly, through the ligand ptrpy. However, the induced upfield shifts of the ptrpy proton signals are significantly lower than the corresponding ones in the case of (4), indicating much lower binding affinity. This is clear evidence that the tethered peptide Gly1-Gly2-Gly3-Lys1CONH2 hinders the complex binding, even though it contains groups that are able to assist it (e.g., the positively charged amino group of lysine, the peptidic backbone, the terminal amide). Complex (6) shows a non-specific binding, interacting through electrostatic forces. The chloride salts of (4), (5) and (6) had insignificant effects on the cell cycle distribution and marginal cytotoxicity (IC50 > 750 μM) against human lung cancer cell lines H1299 and H1437, indicating that their binding to the oligonucleotide is not a sufficient condition for their cytotoxicity.
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Affiliation(s)
- Konstantinos Ypsilantis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, Ioannina 45110, Greece.
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9
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Clark AG, Naufer MN, Westerlund F, Lincoln P, Rouzina I, Paramanathan T, Williams MC. Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation. Biochemistry 2018; 57:614-619. [PMID: 29243480 DOI: 10.1021/acs.biochem.7b01036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Δ,Δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Δ,Δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Δ,Δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Δ,Δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.
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Affiliation(s)
- Andrew G Clark
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - M Nabuan Naufer
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Thayaparan Paramanathan
- Department of Physics, Bridgewater State University , Bridgewater, Massachusetts 02325, United States
| | - Mark C Williams
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
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10
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Chung WJ, Cui Y, Chen CS, Wei WH, Chang RS, Shu WY, Hsu IC. Freezing shortens the lifetime of DNA molecules under tension. J Biol Phys 2017; 43:511-524. [PMID: 28887655 PMCID: PMC5696304 DOI: 10.1007/s10867-017-9466-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/16/2017] [Indexed: 12/24/2022] Open
Abstract
DNA samples are commonly frozen for storage. However, freezing can compromise the integrity of DNA molecules. Considering the wide applications of DNA molecules in nanotechnology, changes to DNA integrity at the molecular level may cause undesirable outcomes. However, the effects of freezing on DNA integrity have not been fully explored. To investigate the impact of freezing on DNA integrity, samples of frozen and non-frozen bacteriophage lambda DNA were studied using optical tweezers. Tension (5–35 pN) was applied to DNA molecules to mimic mechanical interactions between DNA and other biomolecules. The integrity of the DNA molecules was evaluated by measuring the time taken for single DNA molecules to break under tension. Mean lifetimes were determined by maximum likelihood estimates and variances were obtained through bootstrapping simulations. Under 5 pN of force, the mean lifetime of frozen samples is 44.3 min with 95% confidence interval (CI) between 36.7 min and 53.6 min while the mean lifetime of non-frozen samples is 133.2 min (95% CI: 97.8–190.1 min). Under 15 pN of force, the mean lifetimes are 10.8 min (95% CI: 7.6–12.6 min) and 78.5 min (95% CI: 58.1–108.9 min). The lifetimes of frozen DNA molecules are significantly reduced, implying that freezing compromises DNA integrity. Moreover, we found that the reduced DNA structural integrity cannot be restored using regular ligation process. These results indicate that freezing can alter the structural integrity of the DNA molecules.
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Affiliation(s)
- Wei-Ju Chung
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Yujia Cui
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
| | - Chi-Shuo Chen
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Wesley H Wei
- Department of Computer Science, Tufts University, 419 Boston Avenue, Medford, MA, 02155, USA
| | - Rong-Shing Chang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Wun-Yi Shu
- Institute of Statistics, National Tsing Hua University, 101, Section 2, Kuang-Fu road, Hsinchu, 30013, Taiwan
| | - Ian C Hsu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
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11
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Saeed HK, Saeed IQ, Buurma NJ, Thomas JA. The Structure of Linkers Affects the DNA Binding Properties of Tethered Dinuclear Ruthenium(II) Metallo-Intercalators. Chemistry 2017; 23:5467-5477. [PMID: 28072487 DOI: 10.1002/chem.201605750] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Indexed: 12/12/2022]
Abstract
With the long-term aim of enhancing the binding properties of dinuclear RuII -based DNA light-switch complexes, a series of eight structurally related mono- and dinuclear systems are reported in which the linker of the bridging ligand has been modulated. These tethered systems have been designed to explore issues of steric demand at the binding site and the thermodynamic cost of entropy loss upon binding. Detailed spectroscopic and isothermal titration calorimetry (ITC) studies on the new complexes reveal that one of the linkers produces a dinuclear system that binds to duplex DNA with an affinity (Kb >107 m-1 ) that is higher than its corresponding monometallic complex and is the highest affinity for a non-threading bis-intercalating metal complex. These studies confirm that the tether has a major effect on the binding properties of dinuclear complexes containing intercalating units and establishes key design rules for the construction of dinuclear complexes with enhanced DNA binding characteristics.
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Affiliation(s)
- Hiwa K Saeed
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Ibrahim Q Saeed
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Main Building Park Place, Cardiff, CF10 3AT, UK
| | - Niklaas J Buurma
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Main Building Park Place, Cardiff, CF10 3AT, UK
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
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12
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DNA intercalation optimized by two-step molecular lock mechanism. Sci Rep 2016; 6:37993. [PMID: 27917863 PMCID: PMC5137138 DOI: 10.1038/srep37993] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/03/2016] [Indexed: 11/25/2022] Open
Abstract
The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety. During this process, DNA undergoes significant structural rearrangements, first lengthening before relaxing to a shorter DNA-ligand complex in the intermediate state to form a molecular lock. To reach the final bound state, the molecular length must increase again as the ligand threads between disrupted DNA base pairs. This unusual binding mechanism results in an unprecedented optimized combination of high DNA binding affinity and slow kinetics, suggesting a new paradigm for rational design of DNA intercalators.
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13
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Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC. Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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