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Li S, Hu Y, Lin J, Schneiderman Z, Shao F, Wei L, Li A, Hsieh K, Kokkoli E, Curk T, Mao HQ, Wang TH. Single-Particle Spectroscopic Chromatography Reveals Heterogeneous RNA Loading and Size Correlations in Lipid Nanoparticles. ACS NANO 2024; 18:15729-15743. [PMID: 38839059 PMCID: PMC11191693 DOI: 10.1021/acsnano.4c02341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024]
Abstract
Lipid nanoparticles (LNP) have emerged as pivotal delivery vehicles for RNA therapeutics. Previous research and development usually assumed that LNPs are homogeneous in population, loading density, and composition. Such perspectives are difficult to examine due to the lack of suitable tools to characterize these physicochemical properties at the single-nanoparticle level. Here, we report an integrated spectroscopy-chromatography approach as a generalizable strategy to dissect the complexities of multicomponent LNP assembly. Our platform couples cylindrical illumination confocal spectroscopy (CICS) with single-nanoparticle free solution hydrodynamic separation (SN-FSHS) to simultaneously profile population identity, hydrodynamic size, RNA loading levels, and distributions of helper lipid and PEGylated lipid of LNPs at the single-particle level and in a high-throughput manner. Using a benchmark siRNA LNP formulation, we demonstrate the capability of this platform by distinguishing seven distinct LNP populations, quantitatively characterizing size distribution and RNA loading level in wide ranges, and more importantly, resolving composition-size correlations. This SN-FSHS-CICS analysis provides critical insights into a substantial degree of heterogeneity in the packing density of RNA in LNPs and size-dependent loading-size correlations, explained by kinetics-driven assembly mechanisms of RNA LNPs.
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Affiliation(s)
- Sixuan Li
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Yizong Hu
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Biomedical Engineering, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
- Translational
Tissue Engineering Center, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
| | - Jinghan Lin
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Translational
Tissue Engineering Center, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Zachary Schneiderman
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Fangchi Shao
- Department
of Biomedical Engineering, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
| | - Lai Wei
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Andrew Li
- Department
of Biomedical Engineering, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Efrosini Kokkoli
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tine Curk
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Hai-Quan Mao
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Biomedical Engineering, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
- Translational
Tissue Engineering Center, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department
of Mechanical Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Department
of Biomedical Engineering, Johns Hopkins
University School of Medicine, Baltimore, Maryland 21218, United States
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2
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Wang P, Fang X, Du R, Wang J, Liu M, Xu P, Li S, Zhang K, Ye S, You Q, Yang Y, Wang C. Principles of Amino Acid and Nucleotide Revealed by Binding Affinities between Homogeneous Oligopeptides and Single-stranded DNA Molecule s. Chembiochem 2022; 23:e202200048. [PMID: 35191574 DOI: 10.1002/cbic.202200048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Indexed: 11/11/2022]
Abstract
We have determined the binding strengths between nucleotides of adenine, thymine, guanine and cytosine in homogeneous single stranded DNAs and homo-octapeptides consisting of 20 common amino acids. We use a bead-based fluorescence assay for these measurements in which octapeptides are immobilized on the bead surface and ssDNAs are in solutions. The results provide a molecular basis for analyzing selectivity, specificity and polymorphisms of amino-acid-nucleotide interactions. Comparative analyses of the distribution of the binding energies reveal unique binding strengths patterns assignable to each pair of DNA nucleotide and amino acid originating from the chemical structures. Pronounced favorable (such as Arg-G , etc.) and unfavorable (such as Ile-T , etc.) binding interactions can be identified in selected groups of amino acid and nucleotide pairs that could provide basis to elucidate energetics of amino-acid-nucleotide interactions. Such interaction selectivity, specificity and polymorphism manifest the contributions from DNA backbone, DNA bases, as well as main chain and side chain of the amino acids.
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Affiliation(s)
- Pengyu Wang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Xiaocui Fang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Rong Du
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Jiali Wang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Mingpeng Liu
- Tsinghua University, Department of Chemistry, CHINA
| | - Peng Xu
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Shiqi Li
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Kaiyue Zhang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Siyuan Ye
- Tsinghua University, Department of Chemistry, CHINA
| | - Qing You
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Yanlian Yang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Chen Wang
- National Center for NanoScience and Technology, China(NCNST), Beijing, CHINA
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3
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Zhou Y, Guo G, Wang X. Development of
Ultranarrow‐Bore
Open Tubular High Efficiency Liquid Chromatography. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yingyan Zhou
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
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4
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Wang Y, Zhou Y, Zhang D, Wang X, Liu S. Extension of hydrodynamic chromatography to DNA fragment sizing and quantitation. Heliyon 2021; 7:e07904. [PMID: 34522803 PMCID: PMC8427238 DOI: 10.1016/j.heliyon.2021.e07904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/12/2021] [Accepted: 08/27/2021] [Indexed: 01/10/2023] Open
Abstract
Hydrodynamic chromatography (HDC) is a technique originally developed for separating particles. We have recently extended it to DNA fragment sizing and quantitation. In this review, we focus on this extension. After we briefly introduce the history of HDC, we present the evolution of open tubular HDC for DNA fragment sizing. We cover both the theoretical aspect and the experimental implementation of this technique. We describe various approaches to execute the separation, discuss its representative applications and provide a future perspective of this technique in the conclusion section of this review.
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Affiliation(s)
- Yanan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Yingyan Zhou
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Dongtang Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, PR China
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
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5
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Hong T, Zheng R, Qiu L, Zhou S, Chao H, Li Y, Rui W, Cui P, Ni X, Tan S, Jiang P, Wang J. Fluorescence coupled capillary electrophoresis as a strategy for tetrahedron DNA analysis. Talanta 2021; 228:122225. [PMID: 33773730 DOI: 10.1016/j.talanta.2021.122225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 10/22/2022]
Abstract
A strategy based on fluorescence coupled capillary electrophoresis (CE-FL) was developed for analyzing tetrahedron DNA (TD) and TD-doxorubicin (DOX) conjugate. Capillary gel electrophoresis exhibited desirable performance for separating TD and DNA strands. Under the optimized conditions, satisfactory repeatability concerning run-to-run and interday repeatability was obtained, and relative standard deviation value of resolution (n = 6) was 0.64%. Furthermore, the combination of CE and fluorescence detection provided a sensitive platform for quantifying TD concentration and calculating the damage degree of TD. The electrophoretograms indicated that CE-FL was a suitable TD assay method with high specificity and sensitivity. In addition, the application of CE-FL for TD fluorescence resonance energy transfer (FRET) research was also explored. Two types of DNA strands were utilized to interfere the formation of TD. The impact of partially complementary chain and completely complementary chain on FRET signal was explored, and the influence mechanism was discussed. After applying CE-FL for characterizing TD, we also combine CE and FRET to analyze TD-DOX conjugate. CE presented a favourable technique to monitor DOX loading and releasing processes. These noteworthy results offered a stepping stone for DNA nanomaterials assay by using CE-FL.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Ronghui Zheng
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Lin Qiu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Shuwen Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Hufei Chao
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Ying Li
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Wen Rui
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Pengfei Cui
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Xinye Ni
- The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, PR China.
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China; Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu, 213100, China.
| | - Pengju Jiang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China.
| | - Jianhao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China; Changzhou Le Sun Pharmaceuticals Co., Ltd., Changzhou, Jiangsu, 213125, China; Jiangsu Yue Zhi Biopharmaceutical Co., Ltd., Changzhou, Jiangsu, 213125, China.
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6
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Hong T, Qiu L, Zhou S, Cai Z, Cui P, Zheng R, Wang J, Tan S, Jiang P. How does DNA 'meet' capillary-based microsystems? Analyst 2021; 146:48-63. [PMID: 33211035 DOI: 10.1039/d0an01336f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
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7
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Diffraction-based label-free photothermal detector for separation analyses in a nanocapillary. J Chromatogr A 2021; 1648:462214. [PMID: 34004365 DOI: 10.1016/j.chroma.2021.462214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 11/23/2022]
Abstract
Miniaturization of column diameter in liquid chromatography is one of the major trends in separation sciences toward single-cell proteomics and metabolomics. Micro/nanoscale open tubular (OT) capillaries are promising tools for efficient separation analyses of the ultra-small volume of samples. However, highly sensitive and label-free on-column detection is still challenging for such ultra-small capillaries. In this study, we developed a photothermal detector using optical diffraction phenomena by a single nanocapillary. Our detection method realized concentration determination of unlabeled sample solutions in a nanocapillary with 460 nm inner diameter. The calculated limit of detection was 0.12 µM, which corresponds to 16 molecules in a detection volume of 0.23 fL. Furthermore, normal-phase chromatography was performed on a 12 cm long nanocapillary, and femtoliter sample injection, efficient separation, and label-free detection of dye molecules were demonstrated. Our photothermal detector will be widely used as a universal tool for chemical/biological analyses using capillaries with micro/nanoscale diameters.
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8
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Li S, Li A, Hsieh K, Friedrich SM, Wang TH. Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations. Anal Chem 2020; 92:6150-6157. [PMID: 32249576 PMCID: PMC7360426 DOI: 10.1021/acs.analchem.0c00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advances in microanalytical and microfluidic technologies have enabled rapid and amplification-free detection of DNA with a high signal-to-noise ratio. The low sample volume, however, poses a limit in the DNA detection sensitivity, which can be challenging for analyzing rare DNA in physiological samples. One way to improve the sensitivity is to concentrate the DNA in the sample prior to the analysis. The most common DNA concentration techniques are based on electrokinetics, which require an external electric field and generally become ineffective in high ionic concentration conditions. In this work, we present a facile method termed high-salt molecular rheotaxis (HiSMRT) to concentrate and recover DNA from samples with physiologically relevant ionic concentrations without any external electric field. HiSMRT requires only pressure-driven flow and ion concentration gradient to induce a stable local electric field and achieve DNA concentration, making it impervious to high ionic concentrations. We demonstrate that HiSMRT performs robustly at ionic concentrations equivalent to 2%-20% of the ionic concentration in blood serum. HiSMRT can concentrate DNA by up to 960-fold and recover an average of 96.4% of the DNA fragments from 2.0 to 23 kbp uniformly. The concentration process using HiSMRT takes as little as 7.5 min. Moreover, we show that this technique can be easily integrated to perform DNA concentration, size separation, and single-molecule detection all in one platform. We anticipate that this technique will be applicable to a wide range of biological samples and will help to improve the sensitivity of nucleic acid detection for low-abundance DNA biomarkers.
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9
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Zhao S, Wu M, Yang S, Wu Y, Gu Y, Chen C, Ye J, Xie Z, Tian Z, Bachman H, Huang PH, Xia J, Zhang P, Zhang H, Huang TJ. A disposable acoustofluidic chip for nano/microparticle separation using unidirectional acoustic transducers. LAB ON A CHIP 2020; 20:1298-1308. [PMID: 32195522 PMCID: PMC7199844 DOI: 10.1039/d0lc00106f] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Separation of nano/microparticles based on surface acoustic waves (SAWs) has shown great promise for biological, chemical, and medical applications ranging from sample purification to cancer diagnosis. However, the permanent bonding of a microchannel onto relatively expensive piezoelectric substrates and excitation transducers renders the SAW separation devices non-disposable. This limitation not only requires cumbersome cleaning and increased labor and material costs, but also leads to cross-contamination, preventing their implementation in many biological, chemical, and medical applications. Here, we demonstrate a high-performance, disposable acoustofluidic platform for nano/microparticle separation. Leveraging unidirectional interdigital transducers (IDTs), a hybrid channel design with hard/soft materials, and tilted-angle standing SAWs (taSSAWs), our disposable acoustofluidic devices achieve acoustic radiation forces comparable to those generated by existing permanently bonded, non-disposable devices. Our disposable devices can separate not only microparticles but also nanoparticles. Moreover, they can differentiate bacteria from human red blood cells (RBCs) with a purity of up to 96%. Altogether, we developed a unidirectional IDT-based, disposable acoustofluidic platform for micro/nanoparticle separation that can achieve high separation efficiency, versatility, and biocompatibility.
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Affiliation(s)
- Shuaiguo Zhao
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA.
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10
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Abstract
Nano liquid chromatography (nanoLC), with columns having an inner diameter (ID) of ≤100 μm, can provide enhanced sensitivity and enable analysis of limited samples.
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Affiliation(s)
- Steven Ray Wilson
- Department of Chemistry
- University of Oslo
- Oslo
- Norway
- Hybrid Technology Hub-Centre of Excellence
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