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Fluorescent Dynamic Covalent Polymers for DNA Complexation and Templated Assembly. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196648. [PMID: 36235185 PMCID: PMC9570939 DOI: 10.3390/molecules27196648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
Dynamic covalent polymers (DCPs) offer opportunities as adaptive materials of particular interest for targeting, sensing and delivery of biological molecules. In this view, combining cationic units and fluorescent units along DCP chains is attractive for achieving optical probes for the recognition and delivery of nucleic acids. Here, we report on the design of acylhydrazone-based DCPs combining cationic arginine units with π-conjugated fluorescent moieties based on thiophene-ethynyl-fluorene cores. Two types of fluorescent building blocks bearing neutral or cationic side groups on the fluorene moiety are considered in order to assess the role of the number of cationic units on complexation with DNA. The (chir)optical properties of the building blocks, the DCPs, and their complexes with several types of DNA are explored, providing details on the formation of supramolecular complexes and on their stability in aqueous solutions. The DNA-templated formation of DCPs is demonstrated, which provides new perspectives on the assembly of fluorescent DCP based on the nucleic acid structure.
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2
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Sato T, Sato Y, Nishizawa S. Spectroscopic, thermodynamic and kinetic analysis of selective triplex formation by peptide nucleic acid with double-stranded RNA over its DNA counterpart. Biopolymers 2021; 113:e23474. [PMID: 34478151 DOI: 10.1002/bip.23474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/11/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022]
Abstract
Unlike conventional triplex-forming oligonucleotide (TFO), triplex-forming peptide nucleic acid (PNA) can tightly bind with double-stranded RNA (dsRNA) than double-stranded DNA (dsDNA). Here, we performed spectroscopic, thermodynamic and kinetic experiments for triplex formation by PNA to examine different binding behaviors between PNA - dsRNA and PNA - dsDNA triplexes. We found 9-mer PNA (cytosine content of 66%) formed the thermally stable triplex with dsRNA compared to dsDNA over a wide range of pH (5.5-8.0), salt concentration (50-500 mM NaCl). Both the calorimetric binding constant and the association rate constant for dsRNA were larger than those for dsDNA, indicating the favorable association process for the PNA - dsRNA triplex formation. Comparison with the DNA/RNA heteroduplexes revealed that the DNA strand was detrimental to the triplex stability for PNA, a contrasting result for conventional TFO. The keys underlying the difference in the triplex formation of PNA with different duplexes appear to be the conformational adoptability and the geometric compatibility of PNA to fit the deep, narrow major groove of dsRNA and the helical rigidity difference of the duplexes. Our results emphasize the importance of both the sugar puckering of the duplex and the appropriate conformational flexibility of PNA for the triplex formation.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
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3
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Pratihar S, Suseela YV, Govindaraju T. Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery. ACS APPLIED BIO MATERIALS 2020; 3:6979-6991. [PMID: 35019357 DOI: 10.1021/acsabm.0c00870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Yelisetty Venkata Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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4
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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5
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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6
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Heat-shrinking DNA nanoparticles for in vivo gene delivery. Gene Ther 2020; 27:196-208. [PMID: 31900424 DOI: 10.1038/s41434-019-0117-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022]
Abstract
The particle size of a PEG-peptide DNA nanoparticle is a key determinant of biodistribution following i.v. dosing. DNA nanoparticles of <100 nm in diameter are sufficiently small to cross through fenestrated endothelial cells to target hepatocytes in the liver. In addition, DNA nanoparticles must be close to charge-neutral to avoid recognition and binding to scavenger receptors found on Kupffer cells and endothelial cells in the liver. In the present study, we demonstrate an approach to heat shrink DNA nanoparticles to reduce their size to <100 nm to target hepatocytes. An optimized protocol heated plasmid DNA at 100 °C for 10 min resulting in partial denaturation. The immediate addition of a polyacridine PEG-peptide followed by cooling to room temperature resulted in heat-shrunken DNA nanoparticles that were ~70 nm in diameter compared with 170 nm when heating was omitted. Heat shrinking resulted in the conversion of supercoiled DNA into open circular to remove strain during compaction. Heat-shrunken DNA nanoparticles were stable to freeze-drying and reconstitution in saline. Hydrodynamic dosing established that 70 nm heat-shrunken DNA nanoparticles efficiently expressed luciferase in mouse liver. Biodistribution studies revealed that 70 nm DNA nanoparticles are rapidly and transiently taken up by liver whereas 170 nm DNA nanoparticles avoid liver uptake due to their larger size. The results provide a new approach to decrease the size of polyacridine PEG-peptide DNA nanoparticles to allow penetration of the fenestrated endothelium of the liver for the purpose of transfecting hepatocytes in vivo.
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7
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Mora AK, Basu A, Kalel R, Nath S. Polymer-assisted drug sequestration from plasma protein by a surfactant with curtailed denaturing capacity. Phys Chem Chem Phys 2019; 21:7127-7136. [PMID: 30887975 DOI: 10.1039/c8cp03576h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The capability of a surfactant to sequester a drug bound to plasma protein was investigated using steady-state and time-resolved spectroscopic techniques. Surfactants are known to denature protein, and hence are not suitable for the sequestration of a drug from protein. Herein, we show that the denaturing capacity of a surfactant is curtailed completely and its drug sequestration power is enhanced in the presence of biocompatible Pluronic micelles due to the formation of unique supramolecular assemblies. Further, our detailed studies indicate that the concentration of surfactant required for the sequestration of a drug is less than its critical micellar concentration (CMC). The extent of sequestration of drug by polymer-surfactant supramolecular assemblies can be tuned finely by controlling the concentration of surfactant. Detailed analysis showed that up to ∼85% sequestration of a drug from plasma protein could be achieved using a sub-CMC concentration of surfactant. Our results clearly show that controlled sequestration of a drug from plasma protein can be achieved with a reduction in the protein denaturing properties of surfactants.
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Affiliation(s)
- Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
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8
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Chen C, Wu Y, Li H. Fine-Tuning Aromatic Stacking and Single-Crystal Photoluminescence Through Coordination Chemistry. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chaoyuan Chen
- Key Laboratory of Cluster Science of Ministry of Education; School of Chemistry and Chemical Engineering; Beijing Institute of Technology; 100081 Beijing P. R. China
| | - Yilei Wu
- Department of Chemical Engineering; Stanford University; 443 Via Ortega 94305-4125 Stanford CA United States
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education; School of Chemistry and Chemical Engineering; Beijing Institute of Technology; 100081 Beijing P. R. China
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9
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Basak S, Léon JC, Ferranco A, Sharma R, Hebenbrock M, Lough A, Müller J, Kraatz HB. AgI
-Induced Switching of DNA Binding Modes via Formation of a Supramolecular Metallacycle. Chemistry 2018; 24:3729-3732. [DOI: 10.1002/chem.201800440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Shibaji Basak
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Annaleizle Ferranco
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Renu Sharma
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Alan Lough
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
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10
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Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure. Sci Rep 2018; 8:2666. [PMID: 29422637 PMCID: PMC5805748 DOI: 10.1038/s41598-018-20960-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.
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11
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Ikkanda BA, Iverson BL. Exploiting the interactions of aromatic units for folding and assembly in aqueous environments. Chem Commun (Camb) 2018; 52:7752-9. [PMID: 27080050 DOI: 10.1039/c6cc01861k] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A variety of non-covalent interactions (including hydrogen bonding, ionic interactions, metal coordination and desolvation/solvation) have been utilized to organize oligomers into well-defined structures. Herein is described a survey of aromatic foldamers that capitalize on electrostatic complementarity of substituted aromatic units to drive folding and assembly in aqueous environments. A brief description of recent advances in the understanding of aromatic interactions is provided, followed by examples of foldamers that exploit interactions between aromatic units to drive their assembly in predictable fashion. The history of our aromatic foldamers is traced from the first structure designed to fold into a pleated structure in an aqueous environment to a heteroduplex system more related to nucleic acids. Taken together, the results demonstrate that electrostatic complementarity of aromatic units provides a versatile framework for driving predictable folding and assembly in aqueous environments.
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Affiliation(s)
- B A Ikkanda
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, TX 78712, USA.
| | - B L Iverson
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, TX 78712, USA.
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12
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Pramanik B, Ahmed S, Roy R, Das BK, Singha N, Das D. A DNA-NDI Hybrid to Efficiently Detect Histone in Parts per Trillion (ppt) Level. ChemistrySelect 2017. [DOI: 10.1002/slct.201701888] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bapan Pramanik
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Sahnawaz Ahmed
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Rupam Roy
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Basab K. Das
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Nilotpal Singha
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Debapratim Das
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
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13
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Single molecule high-throughput footprinting of small and large DNA ligands. Nat Commun 2017; 8:304. [PMID: 28824174 PMCID: PMC5563512 DOI: 10.1038/s41467-017-00379-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 06/20/2017] [Indexed: 02/04/2023] Open
Abstract
Most DNA processes are governed by molecular interactions that take place in a sequence-specific manner. Determining the sequence selectivity of DNA ligands is still a challenge, particularly for small drugs where labeling or sequencing methods do not perform well. Here, we present a fast and accurate method based on parallelized single molecule magnetic tweezers to detect the sequence selectivity and characterize the thermodynamics and kinetics of binding in a single assay. Mechanical manipulation of DNA hairpins with an engineered sequence is used to detect ligand binding as blocking events during DNA unzipping, allowing determination of ligand selectivity both for small drugs and large proteins with nearly base-pair resolution in an unbiased fashion. The assay allows investigation of subtle details such as the effect of flanking sequences or binding cooperativity. Unzipping assays on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allows determination of the ligand mechanical footprint, recognition site, and binding orientation. Mapping the sequence specificity of DNA ligands remains a challenge, particularly for small drugs. Here the authors develop a parallelized single molecule magnetic tweezers approach using engineered DNA hairpins that can detect sequence selectivity, thermodynamics and kinetics of binding for small drugs and large proteins.
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14
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Keshri SK, Kumar S, Mandal K, Mukhopadhyay P. Ambient Water-Stable Dianionic Electron Donors: Intramolecular Noncovalent Conduits Assist Charge Delocalization. Chemistry 2017; 23:11802-11809. [DOI: 10.1002/chem.201701868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Sudhir Kumar Keshri
- Supramolecular and Material Chemistry Lab; School of Physical Sciences; Jawaharlal Nehru University; New Delhi 110067 India
| | - Sharvan Kumar
- Supramolecular and Material Chemistry Lab; School of Physical Sciences; Jawaharlal Nehru University; New Delhi 110067 India
| | - Kalyanashis Mandal
- Supramolecular and Material Chemistry Lab; School of Physical Sciences; Jawaharlal Nehru University; New Delhi 110067 India
| | - Pritam Mukhopadhyay
- Supramolecular and Material Chemistry Lab; School of Physical Sciences; Jawaharlal Nehru University; New Delhi 110067 India
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15
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Kalel R, Mora AK, Patro BS, Palit DK, Nath S. Synergistic enhancement in the drug sequestration power and reduction in the cytotoxicity of surfactants. Phys Chem Chem Phys 2017; 19:25446-25455. [DOI: 10.1039/c7cp05042a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Surfactants in supramolecular assemblies show a significant increase in their drug sequestration power with a remarkably reduced cytotoxicity.
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Affiliation(s)
- Rahul Kalel
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Aruna K. Mora
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Birija S. Patro
- Homi Bhabha National Institute
- Training School Complex
- Anushaktinagar
- Mumbai 400094
- India
| | - Dipak K. Palit
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Sukhendu Nath
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
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16
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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17
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Imidazolyl-Naphthalenediimide-Based Threading Intercalators of DNA. Chembiochem 2016; 17:2162-2171. [DOI: 10.1002/cbic.201600478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Indexed: 12/22/2022]
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18
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Dana S, Keshri SK, Shukla J, Vikramdeo KS, Mondal N, Mukhopadhyay P, Dhar SK. Design, Synthesis and Evaluation of Bifunctional Acridinine-Naphthalenediimide Redox-Active Conjugates as Antimalarials. ACS OMEGA 2016; 1:318-333. [PMID: 30023479 PMCID: PMC6044610 DOI: 10.1021/acsomega.6b00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 06/30/2016] [Indexed: 06/08/2023]
Abstract
A novel class of bifunctional molecules was synthesized integrating acridine (Ac) and redox-active naphthalenediimide (NDI) scaffolds directly and through a flexible linker (en). We evaluated in vitro antiplasmodial activity, physicochemical properties, and a possible mode of action. Theoretical studies suggested electronic segmentation between the electron-rich Ac and electron-deficient NDI scaffolds. Orthogonal Ac-NDI molecules showed activities in the micromolar to submicromolar range against a chloroquine (CQ)-sensitive strain of human malaria pathogen Plasmodium falciparum (maximum activity, IC50: 0.419 μM). The flexible Ac-en-NDI molecules were most potent and showed activity in the nanomolar range against both CQ-sensitive (with most effective compounds, IC50: 3.65 and 4.33 nM) as well as CQ-resistant (with most effective compounds, IC50: 52.20 and 28.53 nM) strains of P. falciparum. Significantly, with CQ-resistant strains, the activity of the most effective compounds was 1 order of magnitude better than that of standard drug CQ. Ac-en-NDI-conjugated molecules were significantly more potent than the individual NDI and Ac-based molecules. The structure-activity relationship (SAR) suggests that the flexible spacer (en) linking the Ac and NDI scaffolds plays a vital role in exhibiting improved potency. None of the molecules triggered hemolysis in culture, and the most potent compounds did not show cytotoxicity in vitro against mammalian fibroblast NIH3T3 cells at their respective IC50 values. The other significant outcome of this work is that some of the investigated molecules have the potential to affect multiple processes in the parasite including the hemozoin formation in digestive vacuoles (DVs), mitochondrial membrane potential, and the redox homeostasis of the parasite.
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Affiliation(s)
- Srikanta Dana
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New
Mehrauli Road, 110067 New Delhi, India
| | - Sudhir Kumar Keshri
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
| | - Jyoti Shukla
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
| | - Kunwar Somesh Vikramdeo
- School
of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
| | - Neelima Mondal
- School
of Life Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
| | - Pritam Mukhopadhyay
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Mehrauli Road, 110067 New Delhi, India
| | - Suman Kumar Dhar
- Special
Centre for Molecular Medicine, Jawaharlal
Nehru University, New
Mehrauli Road, 110067 New Delhi, India
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19
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Al Kobaisi M, Bhosale SV, Latham K, Raynor AM, Bhosale SV. Functional Naphthalene Diimides: Synthesis, Properties, and Applications. Chem Rev 2016; 116:11685-11796. [DOI: 10.1021/acs.chemrev.6b00160] [Citation(s) in RCA: 557] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohammad Al Kobaisi
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sidhanath V. Bhosale
- Polymers
and Functional Materials Division, CSIR-Indian Institute of Chemical Technology
, Hyderabad, Telangana-500007, India
| | - Kay Latham
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Aaron M. Raynor
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sheshanath V. Bhosale
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
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20
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Burmistrova A, Fresch B, Sluysmans D, De Pauw E, Remacle F, Duwez AS. Force measurements reveal how small binders perturb the dissociation mechanisms of DNA duplex sequences. NANOSCALE 2016; 8:11718-11726. [PMID: 27221618 DOI: 10.1039/c6nr02201d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The force-driven separation of double-stranded DNA is crucial to the accomplishment of cellular processes like genome transactions. Ligands binding to short DNA sequences can have a local stabilizing or destabilizing effect and thus severely affect these processes. Although the design of ligands that bind to specific sequences is a field of intense research with promising biomedical applications, so far, their effect on the force-induced strand separation has remained elusive. Here, by means of AFM-based single molecule force spectroscopy, we show the co-existence of two different mechanisms for the separation of a short DNA duplex and demonstrate how they are perturbed by small binders. With the support of Molecular Dynamics simulations, we evidence that above a critical pulling rate one of the dissociation pathways becomes dominant, with a dramatic effect on the rupture forces. Around the critical threshold, we observe a drop of the most probable rupture forces for ligand-stabilized duplexes. Our results offer a deep understanding of how a stable DNA-ligand complex behaves under force-driven strand separation.
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Affiliation(s)
| | - Barbara Fresch
- University of Liege, Department of Chemistry, Sart-Tilman B6, 4000 Liege, Belgium.
| | - Damien Sluysmans
- University of Liege, Department of Chemistry, Sart-Tilman B6, 4000 Liege, Belgium.
| | - Edwin De Pauw
- University of Liege, Department of Chemistry, Sart-Tilman B6, 4000 Liege, Belgium.
| | - Françoise Remacle
- University of Liege, Department of Chemistry, Sart-Tilman B6, 4000 Liege, Belgium.
| | - Anne-Sophie Duwez
- University of Liege, Department of Chemistry, Sart-Tilman B6, 4000 Liege, Belgium.
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21
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Banerjee T, Banerjee S, Sett S, Ghosh S, Rakshit T, Mukhopadhyay R. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy. PLoS One 2016; 11:e0154666. [PMID: 27183010 PMCID: PMC4868319 DOI: 10.1371/journal.pone.0154666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.
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Affiliation(s)
- T. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - T. Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - R. Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
- * E-mail:
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22
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Takai A, Sakamaki D, Seki S, Matsushita Y, Takeuchi M. Ferrocene‐Substituted Naphthalenediimide with Broad Absorption and Electron‐Transport Properties in the Segregated‐Stack Structure. Chemistry 2016; 22:7385-8. [DOI: 10.1002/chem.201600196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Atsuro Takai
- International Center for Young Scientists and Molecular Design & Function Group National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Daisuke Sakamaki
- Department of Molecular Engineering Kyoto University, Nishikyo-ku Kyoto 615-8510 Japan
| | - Shu Seki
- Department of Molecular Engineering Kyoto University, Nishikyo-ku Kyoto 615-8510 Japan
| | - Yoshitaka Matsushita
- Materials Analysis Station National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
| | - Masayuki Takeuchi
- International Center for Young Scientists and Molecular Design & Function Group National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba Ibaraki 305-0047 Japan
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23
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Mora AK, Singh PK, Nath S. Controlled Sequestration of DNA Intercalated Drug by Polymer–Surfactant Supramolecular Assemblies. J Phys Chem B 2016; 120:4143-51. [DOI: 10.1021/acs.jpcb.5b12689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aruna K. Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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24
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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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25
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Choi JS, Han SH, Kim H, Lim YB. Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs. Bioconjug Chem 2016; 27:799-808. [PMID: 26886413 DOI: 10.1021/acs.bioconjchem.6b00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although there has been substantial advancement in the development of nanostructures, the development of self-assembled nanostructures that can selectively recognize multivalent targets has been very difficult. Here we show the proof of concept that topology-controlled peptide nanoassemblies can selectively recognize and detect a multivalent RNA target. We compared the differential behaviors of peptides in a linear or cyclic topology in terms of peptide-gold nanoparticle hybrid nanostructure formation, conformational stabilization, monovalent and multivalent RNA binding in vitro, and multivalent RNA recognition in live cells. When the topology-dependent selectivity amplification of the cyclic peptide hybrids is combined with the noninvasive nature of dark-field microscopy, the cellular localization of the viral Rev response element (RRE) RNA can be monitored in situ. Because intracellular interactions are often mediated by overlapping binding partners with weak affinity, the topology-controlled peptide assemblies can provide a versatile means to convert weak ligands into multivalent ligands with high affinity and selectivity.
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Affiliation(s)
- Jun Shik Choi
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - Hyoseok Kim
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - Yong-Beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
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26
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Mao Y, Liu K, Chen L, Cao X, Yi T. A Programmed DNA Marker Based on Bis(4‐ethynyl‐1,8‐naphthalimide) and Three‐Methane‐Bridged Thiazole Orange. Chemistry 2015; 21:16623-30. [DOI: 10.1002/chem.201502874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Yueyuan Mao
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Keyin Liu
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Liang Chen
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Xinhua Cao
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Tao Yi
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
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27
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Islam MM, Fujii S, Sato S, Okauchi T, Takenaka S. Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs. Bioorg Med Chem 2015; 23:4769-4776. [PMID: 26081762 DOI: 10.1016/j.bmc.2015.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/22/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
Abstract
Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2.
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Affiliation(s)
- Md Monirul Islam
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Satoshi Fujii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
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28
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Camunas-Soler J, Manosas M, Frutos S, Tulla-Puche J, Albericio F, Ritort F. Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline. Nucleic Acids Res 2015; 43:2767-79. [PMID: 25690887 PMCID: PMC4357703 DOI: 10.1093/nar/gkv087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bis-intercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel single-molecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.
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Affiliation(s)
- Joan Camunas-Soler
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Silvia Frutos
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
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29
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Pandeeswar M, Govindaraju T. Bioinspired Nanoarchitectonics of Naphthalene Diimide to Access 2D Sheets of Tunable Size, Shape, and Optoelectronic Properties. J Inorg Organomet Polym Mater 2014. [DOI: 10.1007/s10904-014-0144-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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30
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Avinash MB, Govindaraju T. Nanoarchitectonics of biomolecular assemblies for functional applications. NANOSCALE 2014; 6:13348-69. [PMID: 25287110 DOI: 10.1039/c4nr04340e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit (NCU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P. O., Bangalore 560064, India.
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31
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Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Nucleic Acids Res 2014; 42:11634-41. [PMID: 25245944 PMCID: PMC4191423 DOI: 10.1093/nar/gku859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Thayaparan Paramanathan
- Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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32
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Kumar S, Ajayakumar MR, Hundal G, Mukhopadhyay P. Extraordinary Stability of Naphthalenediimide Radical Ion and Its Ultra-Electron-Deficient Precursor: Strategic Role of the Phosphonium Group. J Am Chem Soc 2014; 136:12004-10. [DOI: 10.1021/ja504903j] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sharvan Kumar
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - M. R. Ajayakumar
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Geeta Hundal
- Department
of Chemistry, X-Ray Crystallography Laboratory, Guru Nanak Dev University, Amritsar-143005, India
| | - Pritam Mukhopadhyay
- Supramolecular
and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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33
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Zheng W, Vargiu AV, Vargiu AV, Rohrdanz MA, Carloni P, Clementi C. Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile. J Chem Phys 2014; 139:145102. [PMID: 24116648 DOI: 10.1063/1.4824106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the molecular mechanism by which probes and chemotherapeutic agents bind to nucleic acids is a fundamental issue in modern drug design. From a computational perspective, valuable insights are gained by the estimation of free energy landscapes as a function of some collective variables (CVs), which are associated with the molecular recognition event. Unfortunately the choice of CVs is highly non-trivial because of DNA's high flexibility and the presence of multiple association-dissociation events at different locations and/or sliding within the grooves. Here we have applied a modified version of Locally-Scaled Diffusion Map (LSDMap), a nonlinear dimensionality reduction technique for decoupling multiple-timescale dynamics in macromolecular systems, to a metadynamics-based free energy landscape calculated using a set of intuitive CVs. We investigated the binding of the organic drug anthramycin to a DNA 14-mer duplex. By performing an extensive set of metadynamics simulations, we observed sliding of anthramycin along the full-length DNA minor groove, as well as several detachments from multiple sites, including the one identified by X-ray crystallography. As in the case of equilibrium processes, the LSDMap analysis is able to extract the most relevant collective motions, which are associated with the slow processes within the system, i.e., ligand diffusion along the minor groove and dissociation from it. Thus, LSDMap in combination with metadynamics (and possibly every equivalent method) emerges as a powerful method to describe the energetics of ligand binding to DNA without resorting to intuitive ad hoc reaction coordinates.
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Affiliation(s)
- Wenwei Zheng
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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34
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Zhao Y, Beuchat C, Domoto Y, Gajewy J, Wilson A, Mareda J, Sakai N, Matile S. Anion−π Catalysis. J Am Chem Soc 2014; 136:2101-11. [DOI: 10.1021/ja412290r] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yingjie Zhao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - César Beuchat
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Yuya Domoto
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jadwiga Gajewy
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Adam Wilson
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jiri Mareda
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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35
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Lyall CL, Shotton CC, Pérez-Salvia M, Dan Pantoş G, Lewis SE. Direct core functionalisation of naphthalenediimides by iridium catalysed C–H borylation. Chem Commun (Camb) 2014; 50:13837-40. [DOI: 10.1039/c4cc06522k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the first boron-substituted naphthalenediimides (NDIs), prepared by iridium catalysed C–H activation. Both mono- and diborylated products are available, which have been further elaborated by Suzuki–Miyaura coupling.
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Pal S, Hatai J, Samanta M, Shaurya A, Bandyopadhyay S. A highly selective chemodosimeter for fast detection and intracellular imaging of Hg2+ions based on a dithiocarbamate–isothiocyanate conversion in aqueous ethanol. Org Biomol Chem 2014; 12:1072-8. [DOI: 10.1039/c3ob42108b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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37
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Liu K, Zheng X, Samuel AZ, Ramkumar SG, Ghosh S, Tan X, Wang D, Shuai Z, Ramakrishnan S, Liu D, Zhang X. Stretching single polymer chains of donor-acceptor foldamers: toward the quantitative study on the extent of folding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14438-14443. [PMID: 24168699 DOI: 10.1021/la403709u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Single-molecule force spectroscopy has proven to be an efficient tool for the quantitative characterization of flexible foldamers on the single-molecule level in this study. The extent of folding has been estimated quantitatively for the first time to the best of our knowledge, which is crucial for a better understanding of the "folding-process" on single-molecule level. Therefore, this study may provide a guidance to regulate folding for realizing rational control over the functions of bulk materials.
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Affiliation(s)
- Kai Liu
- Key Lab of Organic Optoelectronics & Molecular Engineering Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
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Manchineella S, Prathyusha V, Priyakumar UD, Govindaraju T. Solvent‐Induced Helical Assembly and Reversible Chiroptical Switching of Chiral Cyclic‐Dipeptide‐Functionalized Naphthalenediimides. Chemistry 2013; 19:16615-24. [DOI: 10.1002/chem.201303123] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Shivaprasad Manchineella
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India), Fax: (+91) 80‐2208‐2627
| | - V. Prathyusha
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032 (India)
| | - U. Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032 (India)
| | - T. Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064 (India), Fax: (+91) 80‐2208‐2627
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Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Avinash MB, Sandeepa KV, Govindaraju T. Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor-acceptor-donor triads. Beilstein J Org Chem 2013; 9:1565-71. [PMID: 23946856 PMCID: PMC3740681 DOI: 10.3762/bjoc.9.178] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/08/2013] [Indexed: 12/15/2022] Open
Abstract
Amino acid interlinked pyrene and naphthalenediimide (NDI) based novel donor–acceptor–donor (D-A-D) triads are designed to exploit their topological symmetry and complementary π-character for facile charge-transfer complexation. Consequently, free-floating high-aspect-ratio supercoiled nanofibres and hierarchical helical bundles of triads are realized by modulating the chemical functionality of interlinking amino acids.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064, India. ; Tel: +91 80 2208 2969
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Avinash MB, Samanta PK, Sandeepa KV, Pati SK, Govindaraju T. Molecular Architectonics of Stereochemically Constrained π-Complementary Functional Modules. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300677] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Haghighat Jahromi A, Honda M, Zimmerman SC, Spies M. Single-molecule study of the CUG repeat-MBNL1 interaction and its inhibition by small molecules. Nucleic Acids Res 2013; 41:6687-97. [PMID: 23661680 PMCID: PMC3711446 DOI: 10.1093/nar/gkt330] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Effective drug discovery and optimization can be accelerated by techniques capable of deconvoluting the complexities often present in targeted biological systems. We report a single-molecule approach to study the binding of an alternative splicing regulator, muscleblind-like 1 protein (MBNL1), to (CUG)n = 4,6 and the effect of small molecules on this interaction. Expanded CUG repeats (CUG(exp)) are the causative agent of myotonic dystrophy type 1 by sequestering MBNL1. MBNL1 is able to bind to the (CUG)n-inhibitor complex, indicating that the inhibition is not a straightforward competitive process. A simple ligand, highly selective for CUG(exp), was used to design a new dimeric ligand that binds to (CUG)n almost 50-fold more tightly and is more effective in destabilizing MBNL1-(CUG)4. The single-molecule method and the analysis framework might be extended to the study of other biomolecular interactions.
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Affiliation(s)
- Amin Haghighat Jahromi
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
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Avinash MB, Govindaraju T. Extremely Slow Dynamics of an Abiotic Helical Assembly: Unusual Relevance to the Secondary Structure of Proteins. J Phys Chem Lett 2013; 4:583-8. [PMID: 26281870 DOI: 10.1021/jz4001642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Serendipitously, we found that isoleucine methylester functionalized perylenediimide 1 undergoes an extremely slow supramolecular helical assembly over a day's time. Surprisingly, heating led to irreversible chiral denaturation. However, reversible helical assembly could be achieved only in the presence of nondenatured aggregates of 1, which act as seeds. The intriguing functional relevance deduced from 1 was employed to draw parallels with the secondary structure of proteins, envisaging its plausible implications.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bangalore 560064, India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P.O., Bangalore 560064, India
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Gonzalez O, Petkevičiūtė D, Maddocks JH. A sequence-dependent rigid-base model of DNA. J Chem Phys 2013; 138:055102. [DOI: 10.1063/1.4789411] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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45
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Banerjee S, Veale EB, Phelan CM, Murphy SA, Tocci GM, Gillespie LJ, Frimannsson DO, Kelly JM, Gunnlaugsson T. Recent advances in the development of 1,8-naphthalimide based DNA targeting binders, anticancer and fluorescent cellular imaging agents. Chem Soc Rev 2013; 42:1601-18. [DOI: 10.1039/c2cs35467e] [Citation(s) in RCA: 492] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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46
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Sasikala WD, Mukherjee A. Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy. Phys Chem Chem Phys 2013; 15:6446-55. [DOI: 10.1039/c3cp50501d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Narayanaswamy N, Avinash MB, Govindaraju T. Exploring hydrogen bonding and weak aromatic interactions induced assembly of adenine and thymine functionalised naphthalenediimides. NEW J CHEM 2013. [DOI: 10.1039/c3nj00060e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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48
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Pandeeswar M, Govindaraju T. Green-fluorescent naphthalene diimide: conducting layered hierarchical 2D nanosheets and reversible probe for detection of aromatic solvents. RSC Adv 2013. [DOI: 10.1039/c3ra41701h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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49
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Ajayakumar MR, Asthana D, Mukhopadhyay P. Core-Modified Naphthalenediimides Generate Persistent Radical Anion and Cation: New Panchromatic NIR Probes. Org Lett 2012; 14:4822-5. [DOI: 10.1021/ol302140x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- M. R. Ajayakumar
- Supramolecular and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| | - Deepak Asthana
- Supramolecular and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| | - Pritam Mukhopadhyay
- Supramolecular and Material Chemistry Lab, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Avinash MB, Govindaraju T. Amino acid derivatized arylenediimides: a versatile modular approach for functional molecular materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:3905-22. [PMID: 22714652 DOI: 10.1002/adma.201201544] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Indexed: 05/05/2023]
Abstract
Nature's elegant molecular designs and their assemblies with specific structure-property correlations have inspired researchers to design and develop bio-mimics for advanced functional applications. To realize such advanced molecular materials, naturally evolved amino acids are arguably the ideal auxiliaries due to their remarkable molecular/chiral recognition and distinctive sequence specific self-assembling properties. Over the years, this modular approach of derivatizing naphthalenediimides (NDIs) and perylenediimides (PDIs) with amino acids and peptides have resulted in several hitherto unknown molecular assemblies with phenomenal impact on their performance. Derivatization with versatile arylenediimides is especially interesting due to their wide spread applications in fields ranging from biomedicine to electronics. Herein some of these seminal reports of this rapidly emerging field and the design principles embraced are discussed.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
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