1
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Song L, Wang Y, Guo Y, Bulale S, Zhou M, Yu F, He L. Engineering aptamers to enhance their interaction with protein target for selective inhibition of cell surface receptors. Int J Biol Macromol 2024; 278:134989. [PMID: 39181365 DOI: 10.1016/j.ijbiomac.2024.134989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/09/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Cell surface receptors play a key role in intracellular signaling, and their overexpression and activation are among the drivers of multiple diseases. Selective inhibition of cell surface receptors is important for regulating intracellular signaling pathways and cell behavior. Here, we design engineered aptamers to selectively inhibit receptor function. In this strategy, the aptamer specifically recognizing the extracellular structural domain of the EGFR, was conjugated to an adamantane moiety through linking arms of various lengths in order to obtain better performances toward EGFR. These interactions inhibit EGFR dimerization, thereby impeding the activation of downstream signaling pathways. It is shown that the adamantane-modified aptamers exhibit superior inhibition of downstream effector proteins relative to the unmodified aptamers. The optimal inhibitory effect was observed with a linker arm of 40 T-base in length. Notably, the best-performing adamantane-modified aptamer specifically binds to A549 cells with a dissociation constant (22.6 ± 4.5 nM) that is approximately 4-fold lower than that of the parent EGFR aptamer (94.4 ± 21.9 nM). We further combine the use of the adamantane-modified aptamer with that of genistein, a natural isoflavone compound with EGFR tyrosine kinase inhibition activity, to enhance the inhibitory effect on EGFR and its downstream signaling employing a synergistic action. This study is expected to provide a versatile approach for the improvement of existing aptamers obtaining increased selective inhibition of cell surface receptors.
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Affiliation(s)
- Lulu Song
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujing Guo
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shajidan Bulale
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Miaomiao Zhou
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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2
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Winer L, Motiei L, Margulies D. Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates. Bioconjug Chem 2023; 34:1509-1522. [PMID: 37556353 PMCID: PMC10515487 DOI: 10.1021/acs.bioconjchem.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/27/2023] [Indexed: 08/11/2023]
Abstract
The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.
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Affiliation(s)
- Lulu Winer
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - Leila Motiei
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - David Margulies
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
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3
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Maity D. Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches. Biophys Chem 2023; 297:107022. [PMID: 37058879 DOI: 10.1016/j.bpc.2023.107022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.
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Affiliation(s)
- Debabrata Maity
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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4
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Borum RM, Lin AE, Dong X, Kai M, Chen Y. DNA Origami Disguises Herpes Simplex Virus 1 Particles and Controls Their Virulence. Molecules 2022; 27:7162. [PMID: 36363990 PMCID: PMC9656247 DOI: 10.3390/molecules27217162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 01/25/2023] Open
Abstract
DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed "HSV1 pockets" to agglomerated "HSV1 sleeves". "Pockets" were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity.
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Affiliation(s)
- Raina M. Borum
- Department of NanoEngineering, University of California, San Diego, CA 92093, USA
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5
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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6
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Zhou Y, Jie K, Zhao R, Huang F. Supramolecular-Macrocycle-Based Crystalline Organic Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904824. [PMID: 31535778 DOI: 10.1002/adma.201904824] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Supramolecular macrocycles are well known as guest receptors in supramolecular chemistry, especially host-guest chemistry. In addition to their wide applications in host-guest chemistry and related areas, macrocycles have also been employed to construct crystalline organic materials (COMs) owing to their particular structures that combine both rigidity and adaptivity. There are two main types of supramolecular-macrocycle-based COMs: those constructed from macrocycles themselves and those prepared from macrocycles with other organic linkers. This review summarizes recent developments in supramolecular-macrocycle-based COMs, which are categorized by various types of macrocycles, including cyclodextrins, calixarenes, resorcinarenes, pyrogalloarenes, cucurbiturils, pillararenes, and others. Effort is made to focus on the structures of supramolecular-macrocycle-based COMs and their structure-function relationships. In addition, the application of supramolecular-macrocycle-based COMs in gas storage or separation, molecular separation, solid-state electrolytes, proton conduction, iodine capture, water or environmental treatment, etc., are also presented. Finally, perspectives and future challenges in the field of supramolecular-macrocycle-based COMs are discussed.
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Affiliation(s)
- Yujuan Zhou
- State Key Laboratory of Chemical Engineering, Department of Chemistry, Center for Chemistry of High-Performance & Novel Materials, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kecheng Jie
- State Key Laboratory of Chemical Engineering, Department of Chemistry, Center for Chemistry of High-Performance & Novel Materials, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Run Zhao
- State Key Laboratory of Chemical Engineering, Department of Chemistry, Center for Chemistry of High-Performance & Novel Materials, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering, Department of Chemistry, Center for Chemistry of High-Performance & Novel Materials, Zhejiang University, Hangzhou, 310027, P. R. China
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7
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Lahav-Mankovski N, Prasad PK, Oppenheimer-Low N, Raviv G, Dadosh T, Unger T, Salame TM, Motiei L, Margulies D. Decorating bacteria with self-assembled synthetic receptors. Nat Commun 2020; 11:1299. [PMID: 32157077 PMCID: PMC7064574 DOI: 10.1038/s41467-020-14336-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
The responses of cells to their surroundings are mediated by the binding of cell surface proteins (CSPs) to extracellular signals. Such processes are regulated via dynamic changes in the structure, composition, and expression levels of CSPs. In this study, we demonstrate the possibility of decorating bacteria with artificial, self-assembled receptors that imitate the dynamic features of CSPs. We show that the local concentration of these receptors on the bacterial membrane and their structure can be reversibly controlled using suitable chemical signals, in a way that resembles changes that occur with CSP expression levels or posttranslational modifications (PTMs), respectively. We also show that these modifications can endow the bacteria with programmable properties, akin to the way CSP responses can induce cellular functions. By programming the bacteria to glow, adhere to surfaces, or interact with proteins or mammalian cells, we demonstrate the potential to tailor such biomimetic systems for specific applications. Cell surface proteins mediate the interactions between cells and their extracellular environment. Here the authors design synthetic biomemetic receptor-like sensors that facilitate programmable interactions between bacteria and their target.
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Affiliation(s)
- Naama Lahav-Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Pragati Kishore Prasad
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noa Oppenheimer-Low
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Gal Raviv
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tamar Unger
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tomer Meir Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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8
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Chen K, Fu T, Sun W, Huang Q, Zhang P, Zhao Z, Zhang X, Tan W. DNA-supramolecule conjugates in theranostics. Theranostics 2019; 9:3262-3279. [PMID: 31244953 PMCID: PMC6567960 DOI: 10.7150/thno.31885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to develop various molecular probes, drug delivery carriers and theranostic systems for cancer diagnosis and therapy. In addition, supramolecular chemistry, also termed "chemistry beyond the molecule", is a promising research field that aims to develop functional chemical systems by bringing discrete molecular components together in a manner that invokes noncovalent intermolecular forces, such as hydrophobic interaction, hydrogen bonding, metal coordination, and shape or size matching. Thus, DNA-supramolecule conjugates (DSCs) combine accurate recognition, programmability and addressability of DNA with the greater toolbox of supramolecular chemistry. This review discusses the applications of DSCs in sensing, protein activity regulation, cell behavior manipulation, and biomedicine.
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Affiliation(s)
- Kun Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Weidi Sun
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Qin Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Pengge Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai (P. R. China)
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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9
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Unger-Angel L, Motiei L, Margulies D. Molecular Logic as a Means to Assess Therapeutic Antidotes. Front Chem 2019; 7:243. [PMID: 31106191 PMCID: PMC6499185 DOI: 10.3389/fchem.2019.00243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
An emerging direction in the area of molecular logic and computation is developing molecular-scale devices that can operate in complex biological environments, such as within living cells, which are beyond the reach of conventional electronic devices. Herein we demonstrate, at the proof-of-principle level, how concepts applied in the field of molecular logic gates can be used to convert a simple fluorescent switch (YES gate), which lights up in the presence of glutathione s-transferase (GST), into a medicinally relevant INHIBIT gate that responds to both GST and beta-cyclodextrin (β-CD) as input signals. We show that the optical responses generated by this device indicate the ability to use it as an enzyme inhibitor, and more importantly, the ability to use β-CD as an "antidote" that prevents GST inhibition. The relevance of this system to biomedical applications is demonstrated by using the INHIBIT gate and β-CD to regulate the growth of breast cancer cells, highlighting the possibility of applying supramolecular inputs, commonly used to control the fluorescence of molecular logic gates, as antidotes that reverse the toxic effect of chemotherapy agents. We also show that the effect of β-CD can be prevented by introducing 1-adamantanecarboxylic acid (Ad-COOH) as an additional input signal, indicating the potential of obtaining precise, temporal control over enzyme activity and anticancer drug function.
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Affiliation(s)
| | | | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
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10
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Dubel N, Liese S, Scherz F, Seitz O. Untersuchungen zu Grenzen der Bivalenz mit DNA-basierter räumlicher Rasterung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Natali Dubel
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Susanne Liese
- Institut für Theoretische Physik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Deutschland
| | - Franziska Scherz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Oliver Seitz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
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11
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Dubel N, Liese S, Scherz F, Seitz O. Exploring the Limits of Bivalency by DNA-Based Spatial Screening. Angew Chem Int Ed Engl 2018; 58:907-911. [DOI: 10.1002/anie.201810996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Natali Dubel
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Susanne Liese
- Institute for Theoretical Physics; Free University Berlin; Arnimallee 14 14195 Berlin Germany
| | - Franziska Scherz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Oliver Seitz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
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12
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Zhou X, Pathak P, Jayawickramarajah J. Design, synthesis, and applications of DNA-macrocyclic host conjugates. Chem Commun (Camb) 2018; 54:11668-11680. [PMID: 30255866 DOI: 10.1039/c8cc06716c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With this Feature Article we review, for the first time, the development of DNA-host conjugates-a nascent yet rapidly growing research focus within the ambit of DNA supramolecular chemistry. Synthetic hosts (such as cyclodextrins, cucurbiturils, and calixarenes) are well-suited to be partnered with DNA, since DNA assembly and host-guest binding both thrive in aqueous media, are largely orthogonal, and exhibit controllable and input-responsive properties. The covalent braiding of these two supramolecular synthons thus leads to advanced self-assemblies and nanostructures with exciting function that range from drug delivery agents to input-triggered switches. The latter class of DNA-host conjugates have been demonstrated to precisely control protein activity, and have also been used as modulable catalysts and versatile biosensors.
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Affiliation(s)
- X Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, USA.
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13
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Wang S, Wang J, Xu G, Wei L, Fu B, Wu L, Song Y, Yang X, Li C, Liu S, Zhou X. The Cucurbit[7]Uril-Based Supramolecular Chemistry for Reversible B/Z-DNA Transition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800231. [PMID: 30027051 PMCID: PMC6051393 DOI: 10.1002/advs.201800231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/07/2018] [Indexed: 06/08/2023]
Abstract
As a left-handed helical structure, Z-DNA is biologically active and it may be correlated with transcription and genome stability. Until recently, it remained a significant challenge to control the B/Z-DNA transition under physiological conditions. The current study represents the first to reversibly control B/Z-DNA transition using cucurbit[7]uril-based supramolecular approach. It is demonstrated that cucurbit[7]uril can encapsulate the central butanediamine moiety [HN(CH2)4NH] and reverses Z-DNA caused by spermine back to B-DNA. The subsequent treatment with 1-adamantanamine disassembles the cucurbit[7]uril/spermine complex and readily induces reconversion of B- into Z-DNA. The DNA conformational change is unequivocally demonstrated using different independent methods. Direct evidence for supramolecular interactions involved in DNA conformational changes is further provided. These findings can therefore open a new route to control DNA helical structure in a reversible way.
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Affiliation(s)
- Shao‐Ru Wang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Jia‐Qi Wang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Guo‐Hua Xu
- Key Laboratory of Magnetic Resonance in Biological SystemsState Key Laboratory of Magnetic Resonance and Atomic and Molecular PhysicsWuhan Institute of Physics and MathematicsChinese Academy of SciencesWuhan430071HubeiChina
| | - Lai Wei
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Bo‐Shi Fu
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Ling‐Yu Wu
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Yan‐Yan Song
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
| | - Xi‐Ran Yang
- College of Chemical Engineering and TechnologyWuhan University of Science and TechnologyWuhan430081HubeiChina
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological SystemsState Key Laboratory of Magnetic Resonance and Atomic and Molecular PhysicsWuhan Institute of Physics and MathematicsChinese Academy of SciencesWuhan430071HubeiChina
| | - Si‐Min Liu
- College of Chemical Engineering and TechnologyWuhan University of Science and TechnologyWuhan430081HubeiChina
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhan430072HubeiChina
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14
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Chabba S, Vashishat R, Mahajan RK. Characterization of interactions between β-lactoglobulin with surface active ionic liquids in aqueous medium. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Rudra S, Jana A, Sepay N, Patel BK, Mahapatra A. Characterization of the binding of strychnine with bovine β-lactoglobulin and human lysozyme using spectroscopic, kinetic and molecular docking analysis. NEW J CHEM 2018. [DOI: 10.1039/c8nj00810h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The binding interaction of a well known alkaloid strychnine (STN) with the mammalian milk protein β-lactoglobulin and human lysozyme has been explored by using several spectroscopic techniques along with computational studies.
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Affiliation(s)
- Suparna Rudra
- Department of Chemistry
- Jadavpur University
- Kolkata 700032
- India
| | - Abhisek Jana
- Department of Chemistry
- Jadavpur University
- Kolkata 700032
- India
| | - Nayim Sepay
- Department of Chemistry
- Jadavpur University
- Kolkata 700032
- India
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16
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Zhou X, Su X, Pathak P, Vik R, Vinciguerra B, Isaacs L, Jayawickramarajah J. Host-Guest Tethered DNA Transducer: ATP Fueled Release of a Protein Inhibitor from Cucurbit[7]uril. J Am Chem Soc 2017; 139:13916-13921. [PMID: 28882044 DOI: 10.1021/jacs.7b07977] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Host-guest complexes are emerging as powerful components in functional systems with applications ranging from materials to biomedicine. In particular, CB7 based host-guest complexes have received much attention for the controlled release of drugs due to the remarkable ability of CB7 toward binding input molecules in water with high affinity leading to displacement of CB7 from included pharmacophores (or from drug loaded porous particles). However, the release of bound guests from CB7 in response to endogenous biological molecules remains limited since the input biomolecule needs to have the appropriate chemical structure to bind tightly into the CB7 cavity. Herein we describe a synthetic transducer based on self-assembling DNA-small molecule chimeras (DCs) that is capable of converting a chosen biological input, adenosine triphosphate (ATP; that does not directly bind to the CB7 host), into functional displacement of a protein inhibitor that is bound within the CB7 host. Our system-which features the first example of a covalent CB-DNA conjugate-is highly modular and can be adapted to enable responsiveness to other biologically/clinically relevant stimuli via its split DNA aptamer architecture.
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Affiliation(s)
- Xiao Zhou
- Department of Chemistry, Tulane University , 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiaoye Su
- Department of Chemistry, Tulane University , 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University , 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Ryan Vik
- Department of Chemistry, Tulane University , 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Brittany Vinciguerra
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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17
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Abstract
Biotin/(strept)avidin self-assembly is a powerful platform for nanoscale fabrication and capture with many different applications in science, medicine, and nanotechnology. However, biotin/(strept)avidin self-assembly has several well-recognized drawbacks that limit performance in certain technical areas and there is a need for synthetic mimics that can either become superior replacements or operational partners with bio-orthogonal recognition properties. The goal of this tutorial review is to describe the recent progress in making high affinity synthetic association partners that operate in water or biological media. The review starts with a background summary of biotin/(strept)avidin self-assembly and the current design rules for creating synthetic mimics. A series of case studies are presented that describe recent success using synthetic derivatives of cyclodextrins, cucurbiturils, and various organic cyclophanes such as calixarenes, deep cavitands, pillararenes, and tetralactams. In some cases, two complementary partners associate to produce a nanoscale complex and in other cases a ditopic host molecule is used to link two partners. The article concludes with a short discussion of future directions and likely challenges.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Soumen K. Samanta
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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18
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Peri-Naor R, Motiei L, Margulies D. Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy. J Vis Exp 2016. [PMID: 27768030 DOI: 10.3791/54396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Signal transduction pathways, which control the response of cells to various environmental signals, are mediated by the function of signaling proteins that interact with each other and activate one other with high specificity. Synthetic agents that mimic the function of these proteins might therefore be used to generate unnatural signal transduction steps and consequently, alter the cell's function. We present guidelines for designing 'chemical transducers' that can induce artificial communication between native proteins. In addition, we present detailed protocols for synthesizing and testing a specific 'transducer', which can induce communication between two unrelated proteins: platelet-derived growth-factor (PDGF) and glutathione-S-transferase (GST). The way by which this unnatural PDGF-GST communication could be used to control the cleavage of an anticancer prodrug is also presented, indicating the potential for using such systems in 'artificial signal transduction therapy'. This work is intended to facilitate developing additional 'transducers' of this class, which may be used to mediate intracellular protein-protein communication and consequently, to induce artificial cell signaling pathways.
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Affiliation(s)
- Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science;
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19
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Shi ZQ, Cai YT, Deng J, Zhao WF, Zhao CS. Host-Guest Self-Assembly Toward Reversible Thermoresponsive Switching for Bacteria Killing and Detachment. ACS APPLIED MATERIALS & INTERFACES 2016; 8:23523-23532. [PMID: 27552087 DOI: 10.1021/acsami.6b07397] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A facile method to construct reversible thermoresponsive switching for bacteria killing and detachment was currently developed by host-guest self-assembly of β-cyclodextrin (β-CD) and adamantane (Ad). Ad-terminated poly(N-isopropylacrylamide) (Ad-PNIPAM) and Ad-terminated poly[2-(methacryloyloxy)ethyl]trimethylammonium chloride (Ad-PMT) were synthesized via atom transfer radical polymerization, and then assembled onto the surface of β-CD grafted silicon wafer (SW-CD) by simply immersing SW-CD into a mixed solution of Ad-PNIPAM and Ad-PMT, thus forming a thermoresponsive surface (SW-PNIPAM/PMT). Atomic force microscopy (AFM), X-ray photoelectron spectrometry (XPS), and water contact angle (WCA) analysis were used to characterize the surface of SW-PNIPAM/PMT. The thermoresponsive bacteria killing and detachment switch of the SW-PNIPAM/PMT was investigated against Staphyloccocus aureus. The microbiological experiments confirmed the efficient bacteria killing and detachment switch across the lower critical solution temperature (LCST) of PNIPAM. Above the LCST, the Ad-PNIPAM chains on the SW-PNIPAM/PMT surface were collapsed to expose Ad-PMT chains, and then the exposed Ad-PMT would kill the attached bacteria. While below the LCST, the previously collapsed Ad-PNIPAM chains became more hydrophilic and swelled to cover the Ad-PMT chains, leading to the detachment of bacterial debris. Besides, the proposed method to fabricate stimuli-responsive surfaces with reversible switches for bacteria killing and detachment is facile and efficient, which creates a new route to extend the application of such smart surfaces in the fields requiring long-term antimicrobial treatment.
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Affiliation(s)
- Zhen-Qiang Shi
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University , Chengdu 610065, China
| | - Yu-Ting Cai
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University , Chengdu 610065, China
| | - Jie Deng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University , Chengdu 610065, China
| | - Wei-Feng Zhao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University , Chengdu 610065, China
| | - Chang-Sheng Zhao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University , Chengdu 610065, China
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20
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Su X, Zhou X, Zhang N, Zhu M, Zhang H, Jayawickramarajah J. A stable bidentate protein binder achieved via DNA self-assembly driven ligand migration. Chem Commun (Camb) 2016. [PMID: 26225890 DOI: 10.1039/c5cc03213j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein we disclose the development of two complementary single stranded DNA-small molecule chimeras (DCs) that by themselves only bind weakly to a protein target (human serum albumin; HSA). However, upon self-assembly, the DC duplex facilitates a ligand migration reaction leading to a covalently fastened high-affinity, bidentate, protein-binder that resides at the terminus of only one of the DC strands. Due to this specific localization, the bidentate projection remains intact—and thus the system continues to strongly bind HSA—even under conditions that denature and degrade the DNA scaffolds.
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Affiliation(s)
- Xiaoye Su
- Department of Chemistry, Tulane University, Louisiana 70118, USA.
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21
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Chen J, Gao C, Mallik AK, Qiu H. A WS2 nanosheet-based nanosensor for the ultrasensitive detection of small molecule–protein interaction via terminal protection of small molecule-linked DNA and Nt.BstNBI-assisted recycling amplification. J Mater Chem B 2016; 4:5161-5166. [DOI: 10.1039/c6tb00881j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel, ultrasensitive and specific fluorescent nanosensor for the detection of small molecule–protein interaction based on the terminal protection of small molecule-linked DNA and Nt.BstNBI-assisted recycling amplification was reported.
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Affiliation(s)
- Jia Chen
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Cunji Gao
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Abul K. Mallik
- Department of Applied Chemistry and Chemical Engineering
- University of Dhaka
- Dhaka-1000
- Bangladesh
| | - Hongdeng Qiu
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
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22
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Chu X, Battle CH, Zhang N, Aryal GH, Mottamal M, Jayawickramarajah J. Bile Acid Conjugated DNA Chimera that Conditionally Inhibits Carbonic Anhydrase-II in the Presence of MicroRNA-21. Bioconjug Chem 2015; 26:1606-12. [PMID: 26191606 DOI: 10.1021/acs.bioconjchem.5b00231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In order to tackle the issue of systemic toxicity in chemotherapy, there is a need to develop novel mechanisms for the activation of protein inhibitors using biomarkers overexpressed in cancer cells. Many current strategies focus on using cancer associated enzymes as a triggering agent for prodrugs. Herein, we detail an alternative approach that harnesses a microRNA (miR-21) that is overexpressed in cancers as the trigger that activates an inhibitor of human carbonic anhydrase-II (hCA-II). Specifically, we have developed a DNA-small molecule chimera (DC) composed of an hCA-II binding lithocholic acid amide (LAA) headgroup that can transition from a rigid duplex state (that does not bind appreciably to hCA) to a single-stranded conformation via a miR-21 trigger. The activated single-stranded DC can project the LAA headgroup into the hCA-II active site and is a robust hCA-II inhibitor (K(i) of 3.12 μM). This work may spur research into developing new classes of cancer selective protein inhibitors.
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Affiliation(s)
- Xiaozhu Chu
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Cooper H Battle
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Nan Zhang
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Gyan H Aryal
- †Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Madhusoodanan Mottamal
- ‡RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, Louisiana 70125, United States
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23
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Ghosh N, Mondal R, Mukherjee S. Inverse Temperature Dependence in Static Quenching versus Calorimetric Exploration: Binding Interaction of Chloramphenicol to β-Lactoglobulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8074-8080. [PMID: 26145148 DOI: 10.1021/acs.langmuir.5b02103] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The binding interaction between the whey protein bovine β-lactoglobulin (βLG) with the well-known antibiotic chloramphenicol (Clp) is explored by monitoring the intrinsic fluorescence of βLG. Steady-state and time-resolved fluorescence spectral data reveal that quenching of βLG fluorescence proceeds through ground state complex formation, i.e., static quenching mechanism. However, the drug-protein binding constant is found to vary proportionately with temperature. This anomalous result is explained on the basis of the Arrhenius theory which states that the rate constant varies proportionally with temperature. Thermodynamic parameters like ΔH, ΔS, ΔG, and the stoichiometry for the binding interaction have been estimated by isothermal titration calorimetric (ITC) study. Thermodynamic data show that the binding phenomenon is mainly an entropy driven process suggesting the major role of hydrophobic interaction forces in the Clp-βLG binding. Constant pressure heat capacity change (ΔCp) has been calculated from enthalpy of binding at different temperatures which reveals that hydrophobic interaction is the major operating force. The inverse temperature dependence in static quenching is however resolved from ITC data which show that the binding constant regularly decreases with increase in temperature. The modification of native protein conformation due to binding of drug has been monitored by circular dichroism (CD) spectroscopy. The probable binding location of Clp inside βLG is explored from AutoDock based blind docking simulation.
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Affiliation(s)
- Narayani Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Indore By-Pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Ramakanta Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Indore By-Pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Indore By-Pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
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24
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Peri-Naor R, Ilani T, Motiei L, Margulies D. Protein-Protein Communication and Enzyme Activation Mediated by a Synthetic Chemical Transducer. J Am Chem Soc 2015; 137:9507-10. [PMID: 25955617 DOI: 10.1021/jacs.5b01123] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design and function of a synthetic "chemical transducer" that can generate an unnatural communication channel between two proteins is described. Specifically, we show how this transducer enables platelet-derived growth factor to trigger (in vitro) the catalytic activity of glutathione-s-transferase (GST), which is not its natural enzyme partner. GST activity can be further controlled by adding specific oligonucleotides that switch the enzymatic reaction on and off. We also demonstrate that a molecular machine, which can regulate the function of an enzyme, could be used to change the way a prodrug is activated in a "programmable" manner.
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Affiliation(s)
- Ronny Peri-Naor
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Ilani
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leila Motiei
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Margulies
- †Departments of Organic Chemistry and ‡Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Shi X, Zhan W, Chen G, Yu Q, Liu Q, Du H, Cao L, Liu X, Yuan L, Chen H. Regulation of Protein Binding Capability of Surfaces via Host-Guest Interactions: Effects of Localized and Average Ligand Density. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6172-6178. [PMID: 25986051 DOI: 10.1021/acs.langmuir.5b01380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The protein binding capability of biomaterial surfaces can significantly affect subsequent biological responses, and appropriate ligand presentation is often required to guarantee the best functions. Herein, a new facile method for regulating this capability by varying the localized and average ligand density is presented. Binding between lysine and plasminogen relevant to a fibrinolysis system was chosen as a model. We integrated different lysine-modified β-cyclodextrin (β-CD) derivatives onto bioinert copolymer brushes via host-guest interactions. The localized and average lysine density can be conveniently modulated by changing the lysine valency on β-CD scaffolds and by diluting lysine-persubstituted β-CD with pure β-CD, respectively. Both the plasminogen adsorption and the plasminogen binding affinity were enhanced by lysine-persubstituted β-CD compared with those of lysine-monosubstituted β-CD, which is possibly due to the higher localized lysine density and the multivalent binding of plasminogen on lysine-persubstituted β-CD surfaces. With a change in the ratio of lysine-persubstituted β-CD to β-CD, the average lysine density can be tuned, leading to the linear regulation of the adsorption of plasminogen on surfaces.
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Affiliation(s)
- Xiujuan Shi
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Wenjun Zhan
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Gaojian Chen
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
- ‡Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, P. R. China
| | - Qian Yu
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Qi Liu
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Hui Du
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Limin Cao
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Xiaoli Liu
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Lin Yuan
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Hong Chen
- †College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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26
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Paul BK, Ghosh N, Mukherjee S. Binding interaction of a prospective chemotherapeutic antibacterial drug with β-lactoglobulin: results and challenges. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:5921-9. [PMID: 24807302 DOI: 10.1021/la501252x] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This Article reports a detailed characterization of the binding interaction of a potential chemotherapeutic antibacterial drug, norfloxacin (NOF), with the mammalian milk protein β-lactoglobulin (βLG). The thermodynamic parameters, ΔH, ΔS, and ΔG, for the binding phenomenon as-evaluated on the basis of van't Hoff relationship reveal the predominance of electrostatic/ionic interactions underlying the binding process. However, the drug-induced quenching of the intrinsic tryptophanyl fluorescence of the protein exhibits intriguing characteristics on Stern-Volmer analysis (displays an upward curvature instead of conforming to a linear regression). Thus, an extensive time-resolved fluorescence spectroscopic characterization of the quenching process has been undertaken in conjugation with temperature-dependent fluorescence quenching studies to unveil the actual quenching mechanism. The invariance of the fluorescence decay behavior of βLG as a function of the quencher (here NOF) concentration coupled with the commensurate dependence of the drug-protein binding constant (K) on temperature, the drug-induced fluorescence quenching of βLG is argued to proceed through static mechanism. This postulate is aided further support from absorption, fluorescence, and circular dichroism (CD) spectral studies. The present study also throws light on the important issue of drug-induced modification in the native protein conformation on the lexicon of CD, excitation-emission matrix spectroscopic techniques. Concurrently, the drug-protein interaction kinetics and the energy of activation of the process are also explored from stopped-flow fluorescence technique. The probable binding locus of NOF in βLG is investigated from AutoDock-based blind docking simulation.
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Affiliation(s)
- Bijan K Paul
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Indore By-Pass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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27
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Mosquera J, Sánchez MI, Vázquez ME, Mascareñas JL. Ruthenium bipyridyl complexes as photocleavable dimerizers: deactivation of DNA-binding peptides using visible light. Chem Commun (Camb) 2014; 50:10975-8. [DOI: 10.1039/c4cc04512b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Turning off DNA binding by visible light.
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Affiliation(s)
- Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Campus Vida
- Universidade de Santiago de Compostela
- , Spain
| | - Mateo I. Sánchez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Campus Vida
- Universidade de Santiago de Compostela
- , Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Campus Vida
- Universidade de Santiago de Compostela
- , Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Campus Vida
- Universidade de Santiago de Compostela
- , Spain
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28
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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29
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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30
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Cao Y, Zhu S, Yu J, Zhu X, Yin Y, Li G. Protein Detection Based on Small Molecule-Linked DNA. Anal Chem 2012; 84:4314-20. [DOI: 10.1021/ac203401h] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ya Cao
- Laboratory of Biosensing Technology,
School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Sha Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jiacui Yu
- Laboratory of Biosensing Technology,
School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xuejun Zhu
- Department of Biochemistry and
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Genxi Li
- Laboratory of Biosensing Technology,
School of Life Sciences, Shanghai University, Shanghai 200444, China
- Department of Biochemistry and
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
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31
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Ihara T, Wasano T, Nakatake R, Arslan P, Futamura A, Jyo A. Electrochemical signal modulation in homogeneous solutions using the formation of an inclusion complex between ferrocene and β-cyclodextrin on a DNA scaffold. Chem Commun (Camb) 2011; 47:12388-90. [PMID: 22012412 DOI: 10.1039/c1cc15365j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Two DNA conjugates modified with ferrocene and β-cyclodextrin were prepared as a pair of probes that work cooperatively for DNA sensing, in which the electrochemical signal of ferrocene on one probe was significantly "quenched" by the formation of an inclusion complex with β-cyclodextrin of the other probe on the DNA templates.
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Affiliation(s)
- Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Kumamoto University, Kumamoto 860-8555, Japan.
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Affiliation(s)
- Jarl Ivar van der Vlugt
- Supramolecular & Homogeneous Catalysis, van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands, Fax: +31‐20‐5255604
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Yi JW, Park J, Kim KS, Kim BH. pH-Responsive self-duplex of PyA-substituted oligodeoxyadenylate in graphene oxide solution as a molecular switch. Org Biomol Chem 2011; 9:7434-8. [DOI: 10.1039/c1ob06037f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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