Recent Advances in Liposome-Based Molecular Robots

A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a single micro compartment. Due to recent developments in microfluidic technologies, DNA nanotechnologies, synthetic biology, and molecular engineering, these individual parts have been developed, with the final picture beginning to come together. In this review, we describe recent developments of these sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots. First, we explain liposome generation for the compartments of molecular robots. Next, we discuss the emergence of robotics functions by using and functionalizing liposomal membranes. Then, we discuss actuators and intelligence via the encapsulation of chemicals into liposomes. Finally, the future vision and the challenges of molecular robots are described.

[1]  Norihisa Miki,et al.  Automated Parallel Recordings of Topologically Identified Single Ion Channels , 2013, Scientific Reports.

[2]  Kai Sundmacher,et al.  Light‐Driven ATP Regeneration in Diblock/Grafted Hybrid Vesicles , 2020, Chembiochem : a European journal of chemical biology.

[3]  Tomoko Emura,et al.  A Photocaged DNA Nanocapsule for Controlled Unlocking and Opening inside the Cell. , 2019, Bioconjugate chemistry.

[4]  D. Branton,et al.  Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. , 1999, Biophysical journal.

[5]  Bastiaan C. Buddingh,et al.  Artificial Cells: Synthetic Compartments with Life-like Functionality and Adaptivity , 2017, Accounts of chemical research.

[6]  Friedrich C Simmel,et al.  Molecular transport through large-diameter DNA nanopores , 2016, Nature Communications.

[7]  A. Meijering,et al.  Octanol-assisted liposome assembly on chip , 2016, Nature Communications.

[8]  Gevorg Grigoryan,et al.  De novo design of a transmembrane Zn2+-transporting four-helix bundle , 2014, Science.

[9]  Sanobar Khan,et al.  Durable proteo-hybrid vesicles for the extended functional lifetime of membrane proteins in bionanotechnology† †Electronic supplementary information (ESI) available: Additional supporting data and experimental methods. See DOI: 10.1039/c6cc04207d Click here for additional data file. , 2016, Chemical communications.

[10]  Stefan Howorka,et al.  A Temperature-Gated Nanovalve Self-Assembled from DNA to Control Molecular Transport across Membranes. , 2019, ACS nano.

[11]  D. Baker,et al.  Accurate computational design of multipass transmembrane proteins , 2018, Science.

[12]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Hui Li,et al.  Self-assembling subnanometer pores with unusual mass-transport properties , 2012, Nature Communications.

[14]  A. Abate,et al.  High-throughput injection with microfluidics using picoinjectors , 2010, Proceedings of the National Academy of Sciences.

[15]  Manouk Abkarian,et al.  Continuous droplet interface crossing encapsulation (cDICE) for high throughput monodisperse vesicle design , 2011 .

[16]  Noah Malmstadt,et al.  Microfluidic fabrication of asymmetric giant lipid vesicles. , 2011, ACS applied materials & interfaces.

[17]  Luke Theogarajan,et al.  Tailored Polymeric Membranes for Mycobacterium Smegmatis Porin A (MspA) Based Biosensors. , 2015, Journal of materials chemistry. B.

[18]  Ryuji Kawano,et al.  Amplification and Quantification of an Antisense Oligonucleotide from Target microRNA Using Programmable DNA and a Biological Nanopore. , 2017, Analytical chemistry.

[19]  Christine D. Keating,et al.  Complete Budding and Asymmetric Division of Primitive Model Cells To Produce Daughter Vesicles with Different Interior and Membrane Compositions , 2011, Journal of the American Chemical Society.

[20]  B. Paegel,et al.  Stepwise Synthesis of Giant Unilamellar Vesicles on a Microfluidic Assembly Line , 2011, Journal of the American Chemical Society.

[21]  Denis Wirtz,et al.  Water Permeation Drives Tumor Cell Migration in Confined Microenvironments , 2014, Cell.

[22]  Bert Poolman,et al.  A synthetic metabolic network for physicochemical homeostasis , 2019, Nature Communications.

[23]  A. Bangham,et al.  Diffusion of univalent ions across the lamellae of swollen phospholipids. , 1965, Journal of molecular biology.

[24]  Ryuji Kawano,et al.  Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots. , 2018, Chemphyschem : a European journal of chemical physics and physical chemistry.

[25]  Stefan Howorka,et al.  Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State , 2014, ACS nano.

[26]  Tomoko Emura,et al.  Supporting Information Single-Molecule Observation of the Photoregulated Conformational Dynamics of DNAOrigami Nanoscissors , 2017 .

[27]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[28]  H. Sugiyama,et al.  Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures , 2015, Nature Communications.

[29]  Satoshi Kobayashi,et al.  Molecular Robotics: A New Paradigm for Artifacts , 2012, New Generation Computing.

[30]  Hirokazu Hotani,et al.  Giant liposomes: from membrane dynamics to cell morphogenesis , 1999 .

[31]  Sophie Pautot,et al.  Engineering asymmetric vesicles , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[33]  Maaruthy Yelleswarapu,et al.  Monodisperse Uni- and Multicompartment Liposomes. , 2016, Journal of the American Chemical Society.

[34]  Akira Kakugo,et al.  Stabilization of microtubules by encapsulation of the GFP using a Tau-derived peptide. , 2019, Chemical communications.

[35]  T. G. Martin,et al.  Synthetic Lipid Membrane Channels Formed by Designed DNA Nanostructures , 2012, Science.

[36]  K. Shoji,et al.  Biological Nanopore Probe: Probing of Viscous Solutions in a Confined Nanospace. , 2020, The journal of physical chemistry. B.

[37]  Eberhard Bodenschatz,et al.  Supplementary Information for Sequential bottom-up assembly of mechanically stabilized synthetic cells by microfluidics , 2017 .

[38]  Cheng Zhang,et al.  DNA nanotechnology assisted nanopore-based analysis , 2020, Nucleic acids research.

[39]  Petra Schwille,et al.  Shaping Giant Membrane Vesicles in 3D-Printed Protein Hydrogel Cages. , 2020, Small.

[40]  Hyo-Jick Choi,et al.  Artificial organelle: ATP synthesis from cellular mimetic polymersomes. , 2005, Nano letters.

[41]  Luis E Contreras-Llano,et al.  Minimizing Context Dependency of Gene Networks Using Artificial Cells. , 2018, ACS applied materials & interfaces.

[42]  Ho Cheung Shum,et al.  Multicompartment polymersomes from double emulsions. , 2011, Angewandte Chemie.

[43]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

[44]  Yaakov Benenson,et al.  Biocomputers: from test tubes to live cells. , 2009, Molecular bioSystems.

[45]  Friedrich C. Simmel,et al.  Membrane-Assisted Growth of DNA Origami Nanostructure Arrays , 2015, ACS nano.

[46]  Hiroyuki Kitahata,et al.  Chemically artificial rovers based on self-propelled droplets in micrometer-scale environment , 2020 .

[47]  Kan Shoji,et al.  Microfluidic Formation of Double-Stacked Planar Bilayer Lipid Membranes by Controlling the Water-Oil Interface , 2018, Micromachines.

[48]  Masahito Hayashi,et al.  Repetitive stretching of giant liposomes utilizing the nematic alignment of confined actin , 2018 .

[49]  D. Deamer,et al.  Sequence-dependent gating of an ion channel by DNA hairpin molecules , 2006, Nucleic acids research.

[50]  David A. Weitz,et al.  Production of Unilamellar Vesicles Using an Inverted Emulsion , 2003 .

[51]  Shoji Takeuchi,et al.  Metal-Organic Cuboctahedra for Synthetic Ion Channels with Multiple Conductance States , 2017 .

[52]  Werner Tjarks,et al.  A novel pH-sensitive liposome formulation containing oleyl alcohol. , 2002, Biochimica et biophysica acta.

[53]  Jejoong Yoo,et al.  Large-Conductance Transmembrane Porin Made from DNA Origami , 2016, ACS nano.

[54]  Akihito Uemura,et al.  Light-induced propulsion of a giant liposome driven by peptide nanofibre growth , 2018, Scientific Reports.

[55]  Satoshi Murata,et al.  On DNA-Based Gellular Automata , 2014, UCNC.

[56]  Luke Theogarajan,et al.  Microfluidic block copolymer membrane arrays for nanopore DNA sequencing , 2019, Applied Physics Letters.

[57]  N J Brooks,et al.  Preparation and mechanical characterisation of giant unilamellar vesicles by a microfluidic method. , 2015, Lab on a chip.

[58]  Hyunuk Kim,et al.  Synthetic ion channel based on metal-organic polyhedra. , 2008, Angewandte Chemie.

[59]  Stephen Mann,et al.  Chemical Signaling and Functional Activation in Colloidosome-Based Protocells. , 2016, Small.

[60]  Thomas Lars Andresen,et al.  Membrane fusion of pH-sensitive liposomes – a quantitative study using giant unilamellar vesicles , 2011 .

[61]  Chunhai Fan,et al.  Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells. , 2017, ACS nano.

[62]  Daniel A. Hammer,et al.  Molecular Weight Dependence of Polymersome Membrane Structure, Elasticity, and Stability , 2002 .

[63]  Robert Blumenthal,et al.  Light-sensitive lipid-based nanoparticles for drug delivery: design principles and future considerations for biological applications , 2010, Molecular membrane biology.

[64]  R N Zare,et al.  Rapid preparation of giant unilamellar vesicles. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Kensuke Kurihara,et al.  Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA. , 2011, Nature chemistry.

[66]  Tomoaki Matsuura,et al.  Programmable Artificial Cells Using Histamine-Responsive Synthetic Riboswitch. , 2019, Journal of the American Chemical Society.

[67]  J. Szostak,et al.  Coupled Growth and Division of Model Protocell Membranes , 2009, Journal of the American Chemical Society.

[68]  Ho Cheung Shum,et al.  Fabrication of polymersomes using double-emulsion templates in glass-coated stamped microfluidic devices. , 2010, Small.

[69]  Satoshi Murata,et al.  Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles. , 2019, Chemical communications.

[70]  M Montal,et al.  Formation of bimolecular membranes from lipid monolayers and a study of their electrical properties. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[71]  Satoshi Murata,et al.  Programmable reactions and diffusion using DNA for pattern formation in hydrogel medium , 2019, Molecular Systems Design & Engineering.

[72]  D. Branton,et al.  Rapid nanopore discrimination between single polynucleotide molecules. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[73]  Wei Li,et al.  A photosensitive liposome with NIR light triggered doxorubicin release as a combined photodynamic‐chemo therapy system , 2018, Journal of controlled release : official journal of the Controlled Release Society.

[74]  Daeyeon Lee,et al.  Double emulsion templated monodisperse phospholipid vesicles. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[75]  Akihiko Konagaya,et al.  Artificial Smooth Muscle Model Composed of Hierarchically Ordered Microtubule Asters Mediated by DNA Origami Nanostructures. , 2019, Nano letters.

[76]  Henry Hess,et al.  DNA-assisted swarm control in a biomolecular motor system , 2018, Nature Communications.

[77]  Ulrich Koert,et al.  Synthetic ion channels. , 2004, Bioorganic & medicinal chemistry.

[78]  Masahiro Takinoue,et al.  Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System. , 2017, ACS synthetic biology.

[79]  Kan Shoji,et al.  Recessed Ag/AgCl Microelectrode-Supported Lipid Bilayer for Nanopore Sensing. , 2020, Analytical chemistry.

[80]  M. Niederweis,et al.  Single-molecule DNA detection with an engineered MspA protein nanopore , 2008, Proceedings of the National Academy of Sciences.

[81]  Kei Fujiwara,et al.  Generation of giant unilamellar liposomes containing biomacromolecules at physiological intracellular concentrations using hypertonic conditions. , 2014, ACS synthetic biology.

[82]  M. Yamamura,et al.  Leak-free million-fold DNA amplification with locked nucleic acid and targeted hybridization in one pot. , 2019, Organic & biomolecular chemistry.

[83]  Edward S Boyden,et al.  Engineering genetic circuit interactions within and between synthetic minimal cells , 2016, Nature chemistry.

[84]  Sean Conlan,et al.  Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter , 1999, Nature.

[85]  Kei Fujiwara,et al.  Droplet‐Shooting and Size‐Filtration (DSSF) Method for Synthesis of Cell‐Sized Liposomes with Controlled Lipid Compositions , 2015, Chembiochem : a European journal of chemical biology.

[86]  Shoji Takeuchi,et al.  Cell-sized asymmetric lipid vesicles facilitate the investigation of asymmetric membranes. , 2016, Nature chemistry.

[87]  Satoshi Kobayashi,et al.  Molecular robots with sensors and intelligence. , 2014, Accounts of chemical research.

[88]  Kan Shoji,et al.  Osmotic-engine-driven liposomes in microfluidic channels. , 2019, Lab on a chip.

[89]  Norihisa Miki,et al.  Droplet-based lipid bilayer system integrated with microfluidic channels for solution exchange. , 2013, Lab on a chip.

[90]  M. Yatvin,et al.  pH-sensitive liposomes: possible clinical implications. , 1980, Science.

[91]  J. Gouaux,et al.  Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore , 1996, Science.

[92]  Shoji Takeuchi,et al.  Lipid bilayer formation by contacting monolayers in a microfluidic device for membrane protein analysis. , 2006, Analytical chemistry.

[93]  Esther Amstad,et al.  Ultrathin Shell Double Emulsion Templated Giant Unilamellar Lipid Vesicles with Controlled Microdomain Formation Microfl Uidics , 2022 .

[94]  N J Brooks,et al.  Studying the effects of asymmetry on the bending rigidity of lipid membranes formed by microfluidics. , 2016, Chemical communications.

[95]  Akihiko Konagaya,et al.  Sensing surface mechanical deformation using active probes driven by motor proteins , 2016, Nature Communications.

[96]  Petra Schwille,et al.  Switchable domain partitioning and diffusion of DNA origami rods on membranes. , 2013, Faraday discussions.

[97]  Yuki Kazayama,et al.  Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure. , 2016, Langmuir : the ACS journal of surfaces and colloids.

[98]  Norihisa Miki,et al.  A Portable Lipid Bilayer System for Environmental Sensing with a Transmembrane Protein , 2014, PloS one.

[99]  Daniel A. Hammer,et al.  Molecular Weight Dependence of Polymersome Membrane Elasticity and Stability , 2001 .

[100]  D. O. Rudin,et al.  Reconstitution of Cell Membrane Structure in vitro and its Transformation into an Excitable System , 1962, Nature.

[101]  H. Itoh,et al.  Preparation of giant liposomes in physiological conditions and their characterization under an optical microscope. , 1996, Biophysical journal.

[102]  V. Noireaux,et al.  An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. , 2012, ACS synthetic biology.

[103]  Yoshie Harada,et al.  Construction of integrated gene logic-chip , 2018, Nature Nanotechnology.

[104]  Kan Shoji,et al.  Correction to Spatially Resolved Chemical Detection with a Nanoneedle-Probe-Supported Biological Nanopore. , 2019, ACS nano.

[105]  Francis C. Szoka,et al.  pH-Sensitive Liposomes , 1994 .

[106]  Shoji Takeuchi,et al.  Formation of giant lipid vesiclelike compartments from a planar lipid membrane by a pulsed jet flow. , 2007, Journal of the American Chemical Society.

[107]  Ryuji Kawano,et al.  DNA Logic Operation with Nanopore Decoding To Recognize MicroRNA Patterns in Small Cell Lung Cancer. , 2018, Analytical chemistry.

[108]  David J. Galas,et al.  Isothermal reactions for the amplification of oligonucleotides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[109]  S. Howorka,et al.  Self-assembled DNA nanopores that span lipid bilayers. , 2013, Nano letters.

[110]  Jeffery T. Davis,et al.  A unimolecular G-quadruplex that functions as a synthetic transmembrane Na+ transporter. , 2006, Journal of the American Chemical Society.

[111]  S. Howorka,et al.  A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. , 2016, Nature nanotechnology.

[112]  K. Takiguchi,et al.  Morphogenesis of liposomes encapsulating actin depends on the type of actin-crosslinking. , 1999, Journal of molecular biology.

[113]  Kan Shoji,et al.  Spatially Resolved Chemical Detection with a Nanoneedle-Probe-Supported Biological Nanopore. , 2019, ACS nano.

[114]  Petra Schwille,et al.  Amphipathic DNA origami nanoparticles to scaffold and deform lipid membrane vesicles. , 2015, Angewandte Chemie.

[115]  Qiang He,et al.  Recent Progress on Bioinspired Self-Propelled Micro/Nanomotors via Controlled Molecular Self-Assembly. , 2016, Small.

[116]  Raphaël Trouillon,et al.  A functioning artificial secretory cell , 2012, Scientific Reports.

[117]  Marlies Nijemeisland,et al.  Reversibly Triggered Protein-Ligand Assemblies in Giant Vesicles. , 2015, Angewandte Chemie.

[118]  Yusuke Sato,et al.  Micrometer-sized molecular robot changes its shape in response to signal molecules , 2017, Science Robotics.

[119]  Satoshi Murata,et al.  DNA cytoskeleton for stabilizing artificial cells , 2017, Proceedings of the National Academy of Sciences.

[120]  Xiaoyuan Chen,et al.  Artificial cells: from basic science to applications , 2016, Materials today.

[121]  Norihisa Miki,et al.  Droplet split-and-contact method for high-throughput transmembrane electrical recording. , 2013, Analytical chemistry.