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Jäck N, Hemming A, Hartmann L. Synthesis of Dual-Responsive Amphiphilic Glycomacromolecules: Controlled Release of Glycan Ligands via pH and UV Stimuli. Macromol Rapid Commun 2024:e2400439. [PMID: 39037337 DOI: 10.1002/marc.202400439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/25/2024] [Indexed: 07/23/2024]
Abstract
This work presents a versatile strategy for the synthesis of dual stimuli-responsive amphiphilic glycomacromolecules with tailored release properties. Amphiphilic precision glycomacromolecules (APGs) derived from tailor-made building blocks using solid phase polymer synthesis form glycofunctionalized micelles, a versatile class of materials with applications in drug delivery, as antiinfection agents as well as simple cell mimetics. In this work, this concept is extended by integrating cleavable building blocks into APGs now allowing stimuli-responsive release of glycan ligands or destruction of the micelles. This study incorporates a newly designed acid-labile building block, 4-(4-(((((9H-fluoren-9-yl)methoxy)carbonyl)amino)methyl)-1,3-dioxolan-2-yl)benzoic acid (DBA), suitable also for other types of solid phase or amide chemistry, and an established UV-cleavable 2-nitrobenzyl linker (PL). The results demonstrate that both linkers can be cleaved independently and thus allow dual stimuli-responsive release from the APG micelles. By choosing the APG design e.g., placing the cleavable linkers between glycomacromolecular blocks presenting different types of carbohydrates, they can tune APG and micellar stability as well as the interaction and cluster formation with a carbohydrate-recognizing lectin. Such dual-responsive glycofunctionalized micelles have wide potential for use in drug delivery applications or for the development as anti-adhesion agents in antiviral and antibacterial treatments.
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Affiliation(s)
- Nicholas Jäck
- Institute of Macromolecular Chemistry, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg, Germany
| | - Arne Hemming
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Laura Hartmann
- Institute of Macromolecular Chemistry, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg, Germany
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2
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Xuan J, Wang Z, Huang Y, Liu Y, Han Y, Li M, Xiao M. DNA response element-based smart drug delivery systems for precise drug release. Biomater Sci 2024; 12:3550-3564. [PMID: 38832670 DOI: 10.1039/d4bm00138a] [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: 06/05/2024]
Abstract
Smart drug delivery systems (DDSs) that respond to, interact with, or are actuated by biological signals or pathological abnormalities (e.g., the tumor microenvironment) for controllable drug release are appealing therapeutic platforms for cancer treatment. Owing to their inherent self-assembled nature, nucleic acids have emerged as programmable materials for the development of multifunctional structures. In response to external environmental stimuli, DNA response elements can serve as switches to trigger conformational changes in DNA structures. Their stimulus-responsive properties make them promising candidates for constructing smart DDSs, and advancements in DNA response element-based DDSs in the field of biomedicine have been made. This review summarizes different types of DNA response elements, including DNA aptamers, DNAzymes, disulfide bond-modified DNA, pH-responsive DNA motifs, and photocleavable DNA building blocks, and highlights the advancements in DNA response element-based smart DDSs for precise drug release. Finally, future challenges and perspectives in this field are discussed.
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Affiliation(s)
- Jinnan Xuan
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
- 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.
| | - Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Yuting Huang
- Department of Radiotherapy, Chaohu Hospital of Anhui Medical University, 64 Chaohu North Road, Chaohu 238000, P. R. China
| | - Yisi Liu
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
| | - Yuqiang Han
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
| | - Man Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - 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.
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3
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Talbot H, Halvorsen K, Chandrasekaran AR. Encoding, Decoding, and Rendering Information in DNA Nanoswitch Libraries. ACS Synth Biol 2023; 12:978-983. [PMID: 36541933 PMCID: PMC10121895 DOI: 10.1021/acssynbio.2c00649] [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] [Indexed: 12/24/2022]
Abstract
DNA-based construction allows the creation of molecular devices that are useful in information storage and processing. Here, we combine the programmability of DNA nanoswitches and stimuli-responsive conformational changes to demonstrate information encoding and graphical readout using gel electrophoresis. We encoded information as 5-bit binary codes for alphanumeric characters using a combination of DNA and RNA inputs that can be decoded using molecular stimuli such as a ribonuclease. We also show that a similar strategy can be used for graphical visual readout of alphabets on an agarose gel, information that is encoded by nucleic acids and decoded by a ribonuclease. Our method of information encoding and processing could be combined with DNA actuation for molecular computation and diagnostics that require a nonarbitrary visual readout.
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Affiliation(s)
- Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
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4
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Trinh T, Thompson IAP, Clark F, Remington JM, Eisenstein M, Li J, Soh HT. A Photoresponsive Intramolecular Triplex Motif That Enables Rapid and Reversible Control of Aptamer Binding Activity. ACS NANO 2022; 16:14549-14557. [PMID: 36094303 DOI: 10.1021/acsnano.2c05010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA switches that can change conformation in response to certain wavelengths of light could enable rapid and noninvasive control of chemical processes for a wide range of applications. However, most current photoresponsive DNA switches are limited by either irreversible switching or reversible switching with impractically slow kinetics. Here, we report the design of an intramolecular triplex photoswitch (TPS) design based on single-stranded DNA that undergoes rapid and reversible photoswitching between folded and unfolded states through isomerization of internal azobenzene modifications. After optimizing the performance of our photoswitch design, we used molecular dynamics simulations to reveal how individual azobenzenes contribute to the stabilization or destabilization of the triplex depending on their photoisomerization state. By coupling our TPS to an existing aptamer, we can reversibly modulate its binding affinity with less than 15 s of UV light exposure. We further demonstrate reproducible shifting in affinity over multiple cycles of UV and blue light irradiation without substantial photobleaching.
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Affiliation(s)
- Tuan Trinh
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Ian Andrew Paul Thompson
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Finley Clark
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Jacob M Remington
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hyongsok Tom Soh
- Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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5
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Mangubat-Medina AE, Ball ZT. Triggering biological processes: methods and applications of photocaged peptides and proteins. Chem Soc Rev 2021; 50:10403-10421. [PMID: 34320043 DOI: 10.1039/d0cs01434f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been a significant push in recent years to deploy fundamental knowledge and methods of photochemistry toward biological ends. Photoreactive groups have enabled chemists to activate biological function using the concept of photocaging. By granting spatiotemporal control over protein activation, these photocaging methods are fundamental in understanding biological processes. Peptides and proteins are an important group of photocaging targets that present conceptual and technical challenges, requiring precise chemoselectivity in complex polyfunctional environments. This review focuses on recent advances in photocaging techniques and methodologies, as well as their use in living systems. Photocaging methods include genetic and chemical approaches that require a deep understanding of structure-function relationships based on subtle changes in primary structure. Successful implementation of these ideas can shed light on important spatiotemporal aspects of living systems.
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Affiliation(s)
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
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6
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Forrest NT, Vilcapoma J, Alejos K, Halvorsen K, Chandrasekaran AR. Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues. Biochemistry 2021; 60:250-253. [PMID: 33464826 DOI: 10.1021/acs.biochem.0c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanoscale devices that can respond to external stimuli have potential applications in drug delivery, biosensing, and molecular computation. Construction using DNA has provided many such devices that can respond to cues such as nucleic acids, proteins, pH, light, or temperature. However, simultaneous control of molecular devices is still limited. Here, we present orthogonal control of DNA nanoswitches using physical (light) and biochemical (enzyme and nucleic acid) triggers. Each one of these triggers controls the reconfiguration of specific nanoswitches from locked to open states within a mixture and can be used in parallel to control a combination of nanoswitches. Such dynamic control over nanoscale devices allows the incorporation of tunable portions within larger structures as well as spatiotemporal control of DNA nanostructures.
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Affiliation(s)
- Nathan T Forrest
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Kristina Alejos
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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7
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Abstract
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
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Affiliation(s)
- Arun Richard Chandrasekaran
- grid.265850.c0000 0001 2151 7947The RNA Institute, University at Albany, State University of New York, Albany, NY USA
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8
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Chandrasekaran AR, Trivedi R, Halvorsen K. Ribonuclease-Responsive DNA Nanoswitches. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100117. [PMID: 32803173 PMCID: PMC7425801 DOI: 10.1016/j.xcrp.2020.100117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA has been used in the construction of dynamic DNA devices that can reconfigure in the presence of external stimuli. These nanodevices have found uses in fields ranging from biomedical to materials science applications. Here, we report a DNA nanoswitch that can be reconfigured using ribonucleases (RNases) and explore two applications: biosensing and molecular computing. For biosensing, we show the detection of RNase H and other RNases in relevant biological fluids and temperatures, as well as inhibition by the known enzyme inhibitor kanamycin. For molecular computing, we show that RNases can be used to enable erasing, write protection, and erase-rewrite functionality for information-encoding DNA nanoswitches. The simplistic mix-and-read nature of the ribonuclease-activated DNA nanoswitches could facilitate their use in assays for identifying RNase contamination in biological samples or for the screening and characterization of RNase inhibitors.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Twitter: @arunrichardc
| | - Ruju Trivedi
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Twitter: @HalvorsenLab
- Lead Contact
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9
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Abstract
DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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10
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Punnoose JA, Halvorsen K, Chandrasekaran AR. DNA nanotechnology in the undergraduate laboratory: Analysis of molecular topology using DNA nanoswitches. JOURNAL OF CHEMICAL EDUCATION 2020; 97:1448-1453. [PMID: 33814597 PMCID: PMC8015199 DOI: 10.1021/acs.jchemed.9b01185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
There is a disconnect between the cutting-edge research done in academic labs, such as nanotechnology, and what is taught in undergraduate labs. In the current undergraduate curriculum, very few students get a chance to do hands-on experiments in nanotechnology-related experiments most of which are through selective undergraduate research programs. In most cases, complicated synthesis procedures, expensive reagents, and requirement of specific instrumentation prevent broad adaptation of nanotechnology-based experiments to laboratory courses. DNA, being a nanoscale molecule, has recently been used in bottom-up nanotechnology with applications in sensing, nano-robotics, and computing. In this article, we propose a simple experiment involving the synthesis of a DNA nanoswitch that can change its shape from a linear "off" state to a looped "on" state in the presence of a target DNA molecule. The experiment also demonstrates the programmable topology of the looped state of the nanoswitch and its effect on gel migration. The experiment is easy to adapt in an undergraduate laboratory, requires only agarose gel electrophoresis, a minimal set-up cost for materials, and can be completed in a 3-hour time frame.
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Affiliation(s)
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 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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Chandrasekaran AR. Detecting miRNAs Using DNA Nanoswitches. Trends Biochem Sci 2019; 44:819-820. [DOI: 10.1016/j.tibs.2019.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 11/27/2022]
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13
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Valsangkar VA, Chandrasekaran AR, Zhuo L, Mao S, Lee GW, Kizer M, Wang X, Halvorsen K, Sheng J. Click and photo-release dual-functional nucleic acid nanostructures. Chem Commun (Camb) 2019; 55:9709-9712. [PMID: 31353371 PMCID: PMC6687541 DOI: 10.1039/c9cc03806j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.
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Affiliation(s)
- Vibhav A Valsangkar
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | | | - Lifeng Zhuo
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Goh Woon Lee
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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