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Xue Z, Ning D, Jia K, Liu H, Xiang Y, Cao J, Chen J, Zhong Y, Wang X, Zhang Z. Mechanism study of Dual-Emission ratiometric fluorescent pH-Sensitive carbon quantum dots and its application on mornitoring enzymatic catalysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 325:125048. [PMID: 39217959 DOI: 10.1016/j.saa.2024.125048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/10/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024]
Abstract
Carbon dots (CQD) have received significant attention as a novel ratiometric fluorescent pH nanoprobe, owing to their favorable optical properties and excellent biocompatibility. Despite their appealing features, the precise mechanism behind the pH-sensitive photoluminescence of CQDs remains to be fully understood. This study endeavors to unravel the mechanism underlying the pH-responsive ratiometric fluorescence in dual-emission CQDs, synthesized through a one-step hydrothermal method using o-phenylenediamine and oxalic acid as precursors. The resultant CQDs exhibit inherent dual-emission at wavelengths of 383 nm and 566 nm, with the ratiometric fluorescence response tailored by the ratio of precursors, providing a robust tool for pH sensing across a range of 2 to 6. Detailed characterizations, including chemical, morphological, and optical analyses, alongside theoretical insights from time-dependent density functional theory (TD-DFT), elucidate the mechanism underlying the pH-dependent luminescence, attributed to the electron cloud transmission between amide and adjacent carboxyl groups on the CQD surface. The superior performance of these CQDs in real-time pH monitoring is demonstrated through their application in glucose oxidase-catalyzed reactions, showcasing their potential as efficient, reliable nanoprobes for biomedical research and diagnostic applications.
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Affiliation(s)
- Zhiyu Xue
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - De Ning
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Kaihong Jia
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Hao Liu
- BOE Technology Group Co., Ltd, Beijing 100176, China
| | - Yong Xiang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China; Frontier Center of Energy Distribution and Integration, Tianfu Jiangxi Lab, Chengdu 641419, China
| | - Jinlong Cao
- State Key Laboratory of Polymer Materials Engineering, Polymer Research Institute of Sichuan University, Chengdu 610017, China
| | - Junxian Chen
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610093, China
| | - Yeshuang Zhong
- Department of Physics, School of Biology and Engineering, Guizhou Medical University, Guizhou 550031, China
| | - Xinyu Wang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Zhen Zhang
- Trauma Medical Center, Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China.
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2
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Tinker J, Anees P, Krishnan Y. Quantitative Chemical Imaging of Organelles. Acc Chem Res 2024; 57:1906-1917. [PMID: 38916405 DOI: 10.1021/acs.accounts.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
ConspectusDNA nanodevices are nanoscale assemblies, formed from a collection of synthetic DNA strands, that may perform artificial functions. The pioneering developments of a DNA cube by Nadrian Seeman in 1991 and a DNA nanomachine by Turberfield and Yurke in 2000 spawned an entire generation of DNA nanodevices ranging from minimalist to rococo architectures. Since our first demonstration in 2009 that a DNA nanodevice can function autonomously inside a living cell, it became clear that this molecular scaffold was well-placed to probe living systems. Its water solubility, biocompatibility, and engineerability to yield molecularly identical assemblies predisposed it to probe and program biology.Since DNA is a modular scaffold, one can integrate independent or interdependent functionalities onto a single assembly. Work from our group has established a new class of organelle-targeted, DNA-based fluorescent reporters. These reporters comprise three to four oligonucleotides that each display a specific motif or module with a specific function. Given the 1:1 stoichiometry of Watson-Crick-Franklin base pairing, all modules are present in a fixed ratio in every DNA nanodevice. These modules include an ion-sensitive dye or a detection module and a normalizing dye for ratiometry that along with detection module forms a "measuring module". The third module is an organelle-targeting module that engages a cognate protein so that the whole assembly is trafficked to the lumen of a target organelle. Together, these modules allow us to measure free ion concentrations with accuracies that were previously unattainable, in subcellular locations that were previously inaccessible, and at single organelle resolution. By revealing that organelles exist in different chemical states, DNA nanodevices are providing new insights into organelle biology. Further, the ability to deliver molecules with cell-type and organelle level precision in animal models is leading to biomedical applications.This Account outlines the development of DNA nanodevices as fluorescent reporters for chemically mapping or modulating organelle function in real time in living systems. We discuss the technical challenges of measuring ions within endomembrane organelles and show how the unique properties of DNA nanodevices enable organelle targeting and chemical mapping. Starting from the pioneering finding that an autonomous DNA nanodevice could map endolysosomal pH in cells, we chart the development of strategies to target organelles beyond the endolysosomal pathway and expanding chemical maps to include all the major ions in physiology, reactive species, enzyme activity, and voltage. We present a series of vignettes highlighting the new biology unlocked with each development, from the discovery of chemical heterogeneity in lysosomes to identifying the first protein importer of Ca2+ into lysosomes. Finally, we discuss the broader applicability of targeting DNA nanodevices organelle-specifically beyond just reporting ions, namely using DNA nanodevices to modulate organelle state, and thereby cell state, with potential therapeutic applications.
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Affiliation(s)
- JoAnn Tinker
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517619, India
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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3
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Anees P, Saminathan A, Rozmus ER, Di A, Malik AB, Delisle BP, Krishnan Y. Detecting organelle-specific activity of potassium channels with a DNA nanodevice. Nat Biotechnol 2024; 42:1065-1074. [PMID: 37735264 PMCID: PMC11021130 DOI: 10.1038/s41587-023-01928-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
Cell surface potassium ion (K+) channels regulate nutrient transport, cell migration and intercellular communication by controlling K+ permeability and are thought to be active only at the plasma membrane. Although these channels transit the trans-Golgi network, early and recycling endosomes, whether they are active in these organelles is unknown. Here we describe a pH-correctable, ratiometric reporter for K+ called pHlicKer, use it to probe the compartment-specific activity of a prototypical voltage-gated K+ channel, Kv11.1, and show that this cell surface channel is active in organelles. Lumenal K+ in organelles increased in cells expressing wild-type Kv11.1 channels but not after treatment with current blockers. Mutant Kv11.1 channels, with impaired transport function, failed to increase K+ levels in recycling endosomes, an effect rescued by pharmacological correction. By providing a way to map the organelle-specific activity of K+ channels, pHlicKer technology could help identify new organellar K+ channels or channel modulators with nuanced functions.
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Affiliation(s)
- Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Center for Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Center for Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Ezekiel R Rozmus
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Anke Di
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Asrar B Malik
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Brian P Delisle
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA.
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Grossman Center for Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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4
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Liu X, Cao S, Gao Y, Luo S, Zhu Y, Wang L. Subcellular localization of DNA nanodevices and their applications. Chem Commun (Camb) 2023; 59:3957-3967. [PMID: 36883516 DOI: 10.1039/d2cc06017e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The application of nanodevices based on DNA self-assembly in the field of cell biology has made significant progress in the past decade. In this study, the development of DNA nanotechnology is briefly reviewed. The subcellular localization of DNA nanodevices, and their new progress and applications in the fields of biological detection, subcellular and organ pathology, biological imaging, and other fields are reviewed. The future of subcellular localization and biological applications of DNA nanodevices is also discussed.
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Affiliation(s)
- Xia Liu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Gao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. .,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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6
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Bhatia D, Wunder C, Johannes L. Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications. Chembiochem 2021; 22:763-778. [PMID: 32961015 DOI: 10.1002/cbic.202000372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/19/2020] [Indexed: 12/28/2022]
Abstract
The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.
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Affiliation(s)
- Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, 382330, Gandhinagar, India
| | - Christian Wunder
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
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7
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Saminathan A, Devany J, Veetil AT, Suresh B, Pillai KS, Schwake M, Krishnan Y. A DNA-based voltmeter for organelles. NATURE NANOTECHNOLOGY 2021; 16:96-103. [PMID: 33139937 PMCID: PMC8513801 DOI: 10.1038/s41565-020-00784-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/21/2020] [Indexed: 05/16/2023]
Abstract
The role of membrane potential in most intracellular organelles remains unexplored because of the lack of suitable tools. Here, we describe Voltair, a fluorescent DNA nanodevice that reports the absolute membrane potential and can be targeted to organelles in live cells. Voltair consists of a voltage-sensitive fluorophore and a reference fluorophore for ratiometry, and acts as an endocytic tracer. Using Voltair, we could measure the membrane potential of different organelles in situ in live cells. Voltair can potentially guide the rational design of biocompatible electronics and enhance our understanding of how membrane potential regulates organelle biology.
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Affiliation(s)
- Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - John Devany
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Aneesh Tazhe Veetil
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Bhavyashree Suresh
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | | | - Michael Schwake
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, Bielefeld, Germany
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
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8
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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9
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Jani MS, Zou J, Veetil AT, Krishnan Y. A DNA-based fluorescent probe maps NOS3 activity with subcellular spatial resolution. Nat Chem Biol 2020; 16:660-666. [PMID: 32152543 DOI: 10.1038/s41589-020-0491-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 12/05/2019] [Accepted: 02/04/2020] [Indexed: 12/15/2022]
Abstract
Nitric oxide synthase 3 (NOS3) produces the gasotransmitter nitric oxide (NO), which drives critical cellular signaling pathways by S-nitrosylating target proteins. Endogenous NOS3 resides at two distinct subcellular locations: the plasma membrane and the trans-Golgi network (TGN). However, NO generation arising from the activities of both these pools of NOS3 and its relative contribution to physiology or disease is not yet resolvable. We describe a fluorescent DNA-based probe technology, NOckout, that can be targeted either to the plasma membrane or the TGN, where it can quantitatively map the activities of endogenous NOS3 at these locations in live cells. We found that, although NOS3 at the Golgi is tenfold less active than at the plasma membrane, its activity is essential for the structural integrity of the Golgi. The newfound ability to spatially map NOS3 activity provides a platform to discover selective regulators of the distinct pools of NOS3.
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Affiliation(s)
- Maulik S Jani
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA
| | - Junyi Zou
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA
| | - Aneesh T Veetil
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA.
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10
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Zajac M, Chakraborty K, Saha S, Mahadevan V, Infield DT, Accardi A, Qiu Z, Krishnan Y. What biologists want from their chloride reporters – a conversation between chemists and biologists. J Cell Sci 2020; 133:133/2/jcs240390. [DOI: 10.1242/jcs.240390] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Impaired chloride transport affects diverse processes ranging from neuron excitability to water secretion, which underlie epilepsy and cystic fibrosis, respectively. The ability to image chloride fluxes with fluorescent probes has been essential for the investigation of the roles of chloride channels and transporters in health and disease. Therefore, developing effective fluorescent chloride reporters is critical to characterizing chloride transporters and discovering new ones. However, each chloride channel or transporter has a unique functional context that demands a suite of chloride probes with appropriate sensing characteristics. This Review seeks to juxtapose the biology of chloride transport with the chemistries underlying chloride sensors by exploring the various biological roles of chloride and highlighting the insights delivered by studies using chloride reporters. We then delineate the evolution of small-molecule sensors and genetically encoded chloride reporters. Finally, we analyze discussions with chloride biologists to identify the advantages and limitations of sensors in each biological context, as well as to recognize the key design challenges that must be overcome for developing the next generation of chloride sensors.
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Affiliation(s)
- Matthew Zajac
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Kasturi Chakraborty
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Sonali Saha
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Vivek Mahadevan
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Daniel T. Infield
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA 52242, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY 10065, USA
- Department of Biochemistry, Weill Cornell Medical School, New York, NY 10065, USA
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
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11
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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12
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Sharma S, Zajac M, Krishnan Y. A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. Chembiochem 2019; 21:157-162. [PMID: 31099939 DOI: 10.1002/cbic.201900259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Indexed: 12/12/2022]
Abstract
As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA-based sensor for cAMP. Herein, we describe a new, 31-base long single-stranded DNA aptamer for cAMP, denoted caDNApt-1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt-1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt-1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.
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Affiliation(s)
- Suruchi Sharma
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India
| | - Matthew Zajac
- Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA
| | - Yamuna Krishnan
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India.,Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA.,Grossman Institute of Neuroscience, Quantitative Biology and, Human Behavior, University of Chicago, Chicago, IL, 60637, USA
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13
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Leung K, Chakraborty K, Saminathan A, Krishnan Y. A DNA nanomachine chemically resolves lysosomes in live cells. NATURE NANOTECHNOLOGY 2019; 14:176-183. [PMID: 30510277 PMCID: PMC6859053 DOI: 10.1038/s41565-018-0318-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/25/2018] [Indexed: 05/05/2023]
Abstract
Lysosomes are multifunctional, subcellular organelles with roles in plasma membrane repair, autophagy, pathogen degradation and nutrient sensing. Dysfunctional lysosomes underlie Alzheimer's disease, Parkinson's disease and rare lysosomal storage diseases, but their contributions to these pathophysiologies are unclear. Live imaging has revealed lysosome subpopulations with different physical characteristics including dynamics, morphology or cellular localization. Here, we chemically resolve lysosome subpopulations using a DNA-based combination reporter that quantitatively images pH and chloride simultaneously in the same lysosome while retaining single-lysosome information in live cells. We call this technology two-ion measurement or 2-IM. 2-IM of lysosomes in primary skin fibroblasts derived from healthy individuals shows two main lysosome populations, one of which is absent in primary cells derived from patients with Niemann-Pick disease. When patient cells are treated with relevant therapeutics, the second population re-emerges. Chemically resolving lysosomes by 2-IM could enable decoding the mechanistic underpinnings of lysosomal diseases, monitoring disease progression or evaluating therapeutic efficacy.
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Affiliation(s)
- KaHo Leung
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Kasturi Chakraborty
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Anand Saminathan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL, USA.
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14
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Lei Y, He X, Tang J, Shi H, He D, Yan L, Liu J, Zeng Y, Wang K. Ultra-pH-responsive split i-motif based aptamer anchoring strategy for specific activatable imaging of acidic tumor microenvironment. Chem Commun (Camb) 2018; 54:10288-10291. [DOI: 10.1039/c8cc04420a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Non-blocking split i-motif based aptamer anchoring strategy was developed as a general platform for sensing weakly acidic tumor microenvironment.
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Affiliation(s)
- Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Lv’an Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Yu Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
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15
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Kim SH, Kim KR, Ahn DR, Lee JE, Yang EG, Kim SY. Reversible Regulation of Enzyme Activity by pH-Responsive Encapsulation in DNA Nanocages. ACS NANO 2017; 11:9352-9359. [PMID: 28846390 DOI: 10.1021/acsnano.7b04766] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Reversible regulation of enzyme activity by chemical and physical stimuli is often achieved by incorporating stimuli-responsive domains in the enzyme of interest. However, this method is suitable for a limited number of enzymes with well-defined structural and conformational changes. In this study, we present a method to encapsulate enzymes in a DNA cage that could transform its conformation depending on the pH, allowing reversible control of the accessibility of the enzyme to the surrounding environment. This enabled us to regulate various properties of the enzyme, such as its resistance to protease-dependent degradation, binding affinity to the corresponding antibody, and most importantly, enzyme activity. Considering that the size and pH responsiveness of the DNA cage can be easily adjusted by the DNA length and sequence, our method provides a broad-impact platform for controlling enzyme functions without modifying the enzyme of interest.
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Affiliation(s)
- Seong Ho Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
| | - Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
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16
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Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem 2017; 85:349-73. [PMID: 27294440 DOI: 10.1146/annurev-biochem-060815-014244] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.
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Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Aneesh T Veetil
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York 10065;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , , .,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637
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17
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Hung LY, Wang CH, Fu CY, Gopinathan P, Lee GB. Microfluidics in the selection of affinity reagents for the detection of cancer: paving a way towards future diagnostics. LAB ON A CHIP 2016; 16:2759-74. [PMID: 27381813 DOI: 10.1039/c6lc00662k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Microfluidic technologies have miniaturized a variety of biomedical applications, and these chip-based systems have several significant advantages over their large-scale counterparts. Recently, this technology has been used for automating labor-intensive and time-consuming screening processes, whereby affinity reagents, including aptamers, peptides, antibodies, polysaccharides, glycoproteins, and a variety of small molecules, are used to probe for molecular biomarkers. When compared to conventional methods, the microfluidic approaches are faster, more compact, require considerably smaller quantities of samples and reagents, and can be automated. Furthermore, they allow for more precise control of reaction conditions (e.g., pH, temperature, and shearing forces) such that more efficient screening can be performed. A variety of affinity reagents for targeting cancer cells or cancer biomarkers are now available and will likely replace conventional antibodies. In this review article, the selection of affinity reagents for cancer cells or cancer biomarkers on microfluidic platforms is reviewed with the aim of highlighting the utility of such approaches in cancer diagnostics.
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MESH Headings
- Animals
- Antibodies, Immobilized/chemistry
- Antibodies, Immobilized/metabolism
- Antibodies, Neoplasm/chemistry
- Antibodies, Neoplasm/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cells, Cultured
- Coculture Techniques
- Humans
- Immobilized Nucleic Acids/chemistry
- Immobilized Nucleic Acids/metabolism
- Immobilized Proteins/metabolism
- Lab-On-A-Chip Devices/trends
- Leukocytes/cytology
- Leukocytes/metabolism
- Ligands
- Mice
- Neoplasms/blood
- Neoplasms/diagnosis
- Neoplasms/metabolism
- Neoplasms/pathology
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/metabolism
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Affiliation(s)
- Lien-Yu Hung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
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18
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Cell Penetrating Peptide Conjugated Chitosan for Enhanced Delivery of Nucleic Acid. Int J Mol Sci 2015; 16:28912-30. [PMID: 26690119 PMCID: PMC4691089 DOI: 10.3390/ijms161226142] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/25/2015] [Accepted: 11/27/2015] [Indexed: 01/05/2023] Open
Abstract
Gene therapy is an emerging therapeutic strategy for the cure or treatment of a spectrum of genetic disorders. Nevertheless, advances in gene therapy are immensely reliant upon design of an efficient gene carrier that can deliver genetic cargoes into the desired cell populations. Among various nonviral gene delivery systems, chitosan-based carriers have gained increasing attention because of their high cationic charge density, excellent biocompatibility, nearly nonexistent cytotoxicity, negligible immune response, and ideal ability to undergo chemical conjugation. However, a major shortcoming of chitosan-based carriers is their poor cellular uptake, leading to inadequate transfection efficiency. The intrinsic feature of cell penetrating peptides (CPPs) for transporting diverse cargoes into multiple cell and tissue types in a safe manner suggests that they can be conjugated to chitosan for improving its transfection efficiency. In this review, we briefly discuss CPPs and their classification, and also the major mechanisms contributing to the cellular uptake of CPPs and cargo conjugates. We also discuss immense improvements for the delivery of nucleic acids using CPP-conjugated chitosan-based carriers with special emphasis on plasmid DNA and small interfering RNA.
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19
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Saha S, Prakash V, Halder S, Chakraborty K, Krishnan Y. A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells. NATURE NANOTECHNOLOGY 2015; 10:645-51. [PMID: 26098226 DOI: 10.1038/nnano.2015.130] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 05/22/2015] [Indexed: 05/24/2023]
Abstract
The concentration of chloride ions in the cytoplasm and subcellular organelles of living cells spans a wide range (5-130 mM), and is tightly regulated by intracellular chloride channels or transporters. Chloride-sensitive protein reporters have been used to study the role of these chloride regulators, but they are limited to a small range of chloride concentrations and are pH-sensitive. Here, we show that a DNA nanodevice can precisely measure the activity and location of subcellular chloride channels and transporters in living cells in a pH-independent manner. The DNA nanodevice, called Clensor, is composed of sensing, normalizing and targeting modules, and is designed to localize within organelles along the endolysosomal pathway. It allows fluorescent, ratiometric sensing of chloride ions across the entire physiological regime. We used Clensor to quantitate the resting chloride concentration in the lumen of acidic organelles in Drosophila melanogaster. We showed that lumenal lysosomal chloride, which is implicated in various lysosomal storage diseases, is regulated by the intracellular chloride transporter DmClC-b.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, India
| | - Ved Prakash
- Department of Chemistry, University of Chicago, 929E, 57th Street, E305A, GCIS, Chicago, Illinois 60637, USA
| | - Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, India
| | - Kasturi Chakraborty
- Department of Chemistry, University of Chicago, 929E, 57th Street, E305A, GCIS, Chicago, Illinois 60637, USA
| | - Yamuna Krishnan
- 1] National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, India [2] Department of Chemistry, University of Chicago, 929E, 57th Street, E305A, GCIS, Chicago, Illinois 60637, USA
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20
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Lannes L, Halder S, Krishnan Y, Schwalbe H. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem 2015; 16:1647-56. [PMID: 26032298 DOI: 10.1002/cbic.201500182] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/19/2022]
Abstract
Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.
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Affiliation(s)
- Laurie Lannes
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany)
| | - Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India)
| | - Yamuna Krishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).,Department of Chemistry, University of Chicago, E305, GCIS, 929 E, 57th Street, Chicago, IL 60637 (USA)
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany).
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21
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Goltry S, Hallstrom N, Clark T, Kuang W, Lee J, Jorcyk C, Knowlton WB, Yurke B, Hughes WL, Graugnard E. DNA topology influences molecular machine lifetime in human serum. NANOSCALE 2015; 7:10382-90. [PMID: 25959862 PMCID: PMC4457601 DOI: 10.1039/c5nr02283e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/27/2015] [Indexed: 05/28/2023]
Abstract
DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology-programmable molecular shape-plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation.
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Affiliation(s)
- Sara Goltry
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Natalya Hallstrom
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Tyler Clark
- Department of Physics , Boise State University , Boise , Idaho 83725 , USA
- Department of Mathematics , Boise State University , Boise , Idaho 83725 , USA
| | - Wan Kuang
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - Jeunghoon Lee
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Chemistry & Biochemistry , Boise State University , Boise , Idaho 83725 , USA
| | - Cheryl Jorcyk
- Department of Biological Sciences , Boise State University , Boise , Idaho 83725 , USA
| | - William B. Knowlton
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - Bernard Yurke
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - William L. Hughes
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Elton Graugnard
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
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22
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Halder S, Krishnan Y. Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. NANOSCALE 2015; 7:10008-10012. [PMID: 25990365 DOI: 10.1039/c5nr01158b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Here we tune the pH sensitivity of a DNA-based conformational switch, called the I-switch, to yield a set of fluorescent pH sensitive nanodevices with a collective, expanded pH sensing regime from 5.3 to 7.5. The expanded pH regime of this new family of I-switches originates from a dramatic improvement in the overall percentage signal change in response to pH of these nanodevices.
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Affiliation(s)
- Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560 065, India
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23
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Chen Y, Xiang Y, Yuan R, Chai Y. A restriction enzyme-powered autonomous DNA walking machine: its application for a highly sensitive electrochemiluminescence assay of DNA. NANOSCALE 2015; 7:981-986. [PMID: 25465224 DOI: 10.1039/c4nr05387g] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The construction of a restriction enzyme (Nt.AlwI)-powered DNA walking machine and its application for highly sensitive detection of DNA are described. DNA nanostructure tracks containing four overhang sequences with electrochemiluminescence (ECL) labels and complementary to the walker (target DNA) are self-assembled on the sensing electrode. The walker hybridizes with the complementary sequences on the tracks and forms specific recognition sites for Nt.AlwI, which cleaves the overhang sequences, releases the ECL labels and enables directional movement of the walker along the tracks. The formation of the nanostructure tracks and the Nt.AlwI-assisted cleavage of the overhang sequences in the presence of the walker are verified by using polyacrylamide gel electrophoresis analysis and cyclic voltammetry. The successive movement of the walker on the nanostructure tracks leads to continuous removal of massive ECL labels from the sensing electrode, which results in a significantly amplified suppression of the ECL emission for highly sensitive detection of sequence-specific DNA down to 0.19 pM. Results show that this DNA walking machine can also offer single-base mismatch discrimination capability. The successful application of the DNA walking machine for sequence-specific DNA detection can thus offer new opportunities for molecular machines in biosensing applications.
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Affiliation(s)
- Ying Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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24
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Sharma S, Zaveri A, Visweswariah SS, Krishnan Y. A fluorescent nucleic acid nanodevice quantitatively images elevated cyclic adenosine monophosphate in membrane-bound compartments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4276-80. [PMID: 25044725 DOI: 10.1002/smll.201400833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/03/2014] [Indexed: 05/09/2023]
Abstract
cAMPhor: In the presence of cAMP, cAMPhor folds into a structure that binds DFHBI (green), increasing its fluorescence, while Alexa 647 (red) functions as a normalizing dye. It can thus be used to spatially image cAMP quantitatively in membrane-bound compartments.
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Affiliation(s)
- Suruchi Sharma
- Department Biophysics and Biochemistry, National Centre for Biological Sciences, UAS-GKVK, Bellary Road, Bangalore-, 560065, India
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25
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Soshee A, Zürcher S, Spencer ND, Halperin A, Nizak C. General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules 2013; 15:113-21. [PMID: 24328191 DOI: 10.1021/bm401360y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent reports on the hitherto underestimated antigenicity of poly(ethylene glycol) (PEG), which is widely used for pharmaceutical applications, highlight the need for efficient testing of polymer antigenicity and for a better understanding of its molecular origins. With this goal in mind, we have used the phage-display technique to screen large, recombinant antibody repertoires of human origin in vitro for antibodies that bind poly(vinylpyrrolidone) (PVP). PVP is a neutral synthetic polymer of industrial and clinical interest that is also a well-known model antigen in animal studies, thus allowing the comparison of in vitro and in vivo responses. We have identified 44 distinct antibodies that bind specifically to PVP. Competitive binding assays show that the PVP-antibody binding constant is proportional to the polymerization degree of PVP and that specific binding is detected down to the vinylpyrrolidone (VP) monomer level. Statistical analysis of anti-PVP antibody sequences identifies an amino-acid motif that is shared by many phage-display-selected anti-PVP antibodies that are similar to a previously described natural anti-PVP antibody. This suggests a role for this motif in specific antibody/PVP interactions. Interestingly, sequence analysis also suggests that only a single antibody chain containing this shared motif is responsible for antibody binding to PVP, as confirmed upon systematic deletion of either antibody chain for 90% of selected anti-PVP antibodies. Overall, a large number of antibodies in the human repertoires we have screened bind specifically to PVP through a small number of shared amino acid motifs, and preliminary comparison points to significant correlations between the sequences of phage-display-selected anti-PVP antibodies and their natural counterparts isolated from immunized mice in previous studies. This study pioneers the use of antibody phage-display to explore the antigenicity of biotechnologically relevant polymers. It also paves the way for a fast, cost-effective, and systematic in vitro analysis, thus reducing the need for animal immunization experiments. Moreover, identifying the encoding DNA sequence of polymer-binding antibodies via phage-display enables future applications of a molecular biology approach to protein-polymer conjugation, based on protein-antibody fusion.
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Affiliation(s)
- Anandakumar Soshee
- Laboratory of Interdisciplinary Physics, UMR5588 Grenoble Université 1/CNRS , Grenoble, France
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