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DNA nanomachines: monitoring molecular encounter dynamics in live cell membranes

DNA nanomachines: monitoring molecular encounter dynamics in live cell membranes Downloaded from https://academic.oup.com/nsr/article/5/3/300/4081681 by DeepDyve user on 19 July 2022 RESEARCH HIGHLIGHTS CHEMISTRY DNA nanomachines: monitoring molecular encounter dynamics in live cell membranes 1,2 1,2,∗ Jiachao Xu and Xiaohong Fang The cell membrane features a variety of heterogeneous and dynamic compart- ments to regulate cell structure and func- tion. These compartments are generally classified into a relatively packed, lipid- ordered (L ) domain (10-200 nm) en- riched in saturated lipids and cholesterol, and a more fluid, liquid-disordered (L ) domain comprising mainly unsaturated lipids [1]. According to the lipid raft the- ory, L domains, which selectively recruit specific lipids and proteins, serve as criti- cal platforms for signal transduction and membrane protein trafficking [ 2]. There- fore, resolving the interplay and dynam- ics of lipids and proteins on the plasma membrane is of great importance to un- veil the properties and biological rele- vance of membrane domains. Despite accumulating knowledge from in vitro assays, the organization and dynamics of membrane domains in living cells are still elusive. Efforts have been made to use advanced microscopic techniques such as single-molecule tracking (SMT), super-resolution fluo- rescence imaging and Forster ¨ resonance energy transfer (FRET) for live-cell investigations [3]. For example, the application of SMT to evaluate the oligomerization, transient interaction, domain incorporation and diffusion of membrane components has been demonstrated. However, the limitations of these methods include complex in- strumentation and operation, inefficient Figure 1. Schematic illustration of the DNA nanomachine operation on live-cell membrane. After time resolution for transient interac- the addition of the initiator (I) strand to remove the block (B) strand from the anchor site S1, the tion at the μs level and/or inability of locomotion of the DNA walker strand (W) from anchor site S2 to S1 is monitored by detecting the simultaneously monitoring of the entire fluorescence signal decrease. Thus the collision of the two membrane components respectively plasma membrane [4]. conjugated with S1 and S2 is probed (from [5]). The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. All rights reserved. For permissions, plea se e-mail: journals.permissions@oup.com Downloaded from https://academic.oup.com/nsr/article/5/3/300/4081681 by DeepDyve user on 19 July 2022 RESEARCH HIGHLIGHTS Song and Ming 301 In recent work by the Tan group, a The authors used this method to study ther our understanding of membrane simple and elegant method was devel- three typical lipids on the plasma mem- functions, especially their differences in oped to probe the dynamics of mem- brane of Ramos cells: L lipid diacyllipids healthy and diseased states. brane lipids and proteins in living cells. (L), L lipid tocopherols (T) and This was achieved by taking advantage cholesterols (C). Their encounter rates, 1,2 1,2,∗ Jiachao Xu and Xiaohong Fang of emerging DNA nanomachine technol- encounter preference and percentage of Beijing National Laboratory for Molecular ogy. As shown in Fig. 1, they designed diffusion areas across the cell membrane Sciences, Key Laboratory of Molecular a DNA nanomachine operated with five have been calculated. The results suppor- Nanostructure and Nanotechnology, Institute of ssDNA probes: two anchor strands (S1, ted the lipid raft theory that the plasma Chemistry, Chinese Academy of Sciences, China S2) that linked to two target membrane membrane is heterogeneous and the University of Chinese Academy of Sciences, components (lipids in this case) and la- same lipids tend to confine in the same China beled with a quencher in one strand (S1), type of lipid domain. In addition, after Corresponding author. one walker strand (W) labeled with a flu- coupling the protein-specific aptamers E-mail: xfang@iccas.ac.cn orophore, one block strand (B) and one to the DNA nanomachine probes, initiator strand (I). In the absence of I, they applied the same method to in- S1 and S2 hybridized with B and W, re- vestigate the interaction of membrane REFERENCES spectively, at different locations on the proteins. 1. Sezgin E, Levental I and Mayor S et al. Nat Rev Mol cell surface; thus, the cell was fluorescent. The strategy developed by the Tan Cell Biol 2017; 18: 361–74. Running of the nanomachine was initi- group demonstrates a novel and prac- 2. Honigmann A, Mueller V and Ta H et al. Nat Com- ated with the addition of strand I, which tical way to study dynamic interactions mun 2014; 5: 5412. removed strand B from strand S1. There- of membrane components. Although it 3. Xia T, Li N and Fang XH. Annu Rev Phys Chem 2013; fore, when the two target components needs to be considered whether the dif- 64: 459–80. encountered, strand W was translocated fusion and encounter of native lipids or 4. Sezgin E and Schwille P. Cold Spring Harb Perspect from S2 to S1 for W/S1 hybridization proteins are affected by the DNA strand Biol 2011; 3: a009803. through a toehold-mediated DNA strand conjugation and strand displacement effi- 5. You M, Lyu Y and Han D et al. Nat Nanotechnol displacement, resulting in the quenching ciency, exploring the new DNA nanoma- 2017; 12: 453–9. of fluorescence. In this way, the transient chines to live-cell investigation is of great membrane encounter events were trans- interest. Future work would be expected duced to the cumulative fluorescence sig- to correlate the membrane encounter National Science Review nal change, which was easily measured by dynamics with important cellular pro- 5: 300–301, 2018 the commonly accessible flow cytometry cesses, such as membrane trafficking, cell doi: 10.1093/nsr/nwx091 or fluorescence microscopy [ 5]. signaling and cell polarization, to fur- Advance access publication 11 August 2017 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png National Science Review Oxford University Press

DNA nanomachines: monitoring molecular encounter dynamics in live cell membranes

Xu, Jiachao; Fang, Xiaohong
National Science Review , Volume 5 (3) – May 1, 2018
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Oxford University Press
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Copyright © 2022 China Science Publishing & Media Ltd. (Science Press)
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2095-5138
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2053-714X
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10.1093/nsr/nwx091
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Abstract

Downloaded from https://academic.oup.com/nsr/article/5/3/300/4081681 by DeepDyve user on 19 July 2022 RESEARCH HIGHLIGHTS CHEMISTRY DNA nanomachines: monitoring molecular encounter dynamics in live cell membranes 1,2 1,2,∗ Jiachao Xu and Xiaohong Fang The cell membrane features a variety of heterogeneous and dynamic compart- ments to regulate cell structure and func- tion. These compartments are generally classified into a relatively packed, lipid- ordered (L ) domain (10-200 nm) en- riched in saturated lipids and cholesterol, and a more fluid, liquid-disordered (L ) domain comprising mainly unsaturated lipids [1]. According to the lipid raft the- ory, L domains, which selectively recruit specific lipids and proteins, serve as criti- cal platforms for signal transduction and membrane protein trafficking [ 2]. There- fore, resolving the interplay and dynam- ics of lipids and proteins on the plasma membrane is of great importance to un- veil the properties and biological rele- vance of membrane domains. Despite accumulating knowledge from in vitro assays, the organization and dynamics of membrane domains in living cells are still elusive. Efforts have been made to use advanced microscopic techniques such as single-molecule tracking (SMT), super-resolution fluo- rescence imaging and Forster ¨ resonance energy transfer (FRET) for live-cell investigations [3]. For example, the application of SMT to evaluate the oligomerization, transient interaction, domain incorporation and diffusion of membrane components has been demonstrated. However, the limitations of these methods include complex in- strumentation and operation, inefficient Figure 1. Schematic illustration of the DNA nanomachine operation on live-cell membrane. After time resolution for transient interac- the addition of the initiator (I) strand to remove the block (B) strand from the anchor site S1, the tion at the μs level and/or inability of locomotion of the DNA walker strand (W) from anchor site S2 to S1 is monitored by detecting the simultaneously monitoring of the entire fluorescence signal decrease. Thus the collision of the two membrane components respectively plasma membrane [4]. conjugated with S1 and S2 is probed (from [5]). The Author(s) 2017. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd. All rights reserved. For permissions, plea se e-mail: journals.permissions@oup.com Downloaded from https://academic.oup.com/nsr/article/5/3/300/4081681 by DeepDyve user on 19 July 2022 RESEARCH HIGHLIGHTS Song and Ming 301 In recent work by the Tan group, a The authors used this method to study ther our understanding of membrane simple and elegant method was devel- three typical lipids on the plasma mem- functions, especially their differences in oped to probe the dynamics of mem- brane of Ramos cells: L lipid diacyllipids healthy and diseased states. brane lipids and proteins in living cells. (L), L lipid tocopherols (T) and This was achieved by taking advantage cholesterols (C). Their encounter rates, 1,2 1,2,∗ Jiachao Xu and Xiaohong Fang of emerging DNA nanomachine technol- encounter preference and percentage of Beijing National Laboratory for Molecular ogy. As shown in Fig. 1, they designed diffusion areas across the cell membrane Sciences, Key Laboratory of Molecular a DNA nanomachine operated with five have been calculated. The results suppor- Nanostructure and Nanotechnology, Institute of ssDNA probes: two anchor strands (S1, ted the lipid raft theory that the plasma Chemistry, Chinese Academy of Sciences, China S2) that linked to two target membrane membrane is heterogeneous and the University of Chinese Academy of Sciences, components (lipids in this case) and la- same lipids tend to confine in the same China beled with a quencher in one strand (S1), type of lipid domain. In addition, after Corresponding author. one walker strand (W) labeled with a flu- coupling the protein-specific aptamers E-mail: xfang@iccas.ac.cn orophore, one block strand (B) and one to the DNA nanomachine probes, initiator strand (I). In the absence of I, they applied the same method to in- S1 and S2 hybridized with B and W, re- vestigate the interaction of membrane REFERENCES spectively, at different locations on the proteins. 1. Sezgin E, Levental I and Mayor S et al. Nat Rev Mol cell surface; thus, the cell was fluorescent. The strategy developed by the Tan Cell Biol 2017; 18: 361–74. Running of the nanomachine was initi- group demonstrates a novel and prac- 2. Honigmann A, Mueller V and Ta H et al. Nat Com- ated with the addition of strand I, which tical way to study dynamic interactions mun 2014; 5: 5412. removed strand B from strand S1. There- of membrane components. Although it 3. Xia T, Li N and Fang XH. Annu Rev Phys Chem 2013; fore, when the two target components needs to be considered whether the dif- 64: 459–80. encountered, strand W was translocated fusion and encounter of native lipids or 4. Sezgin E and Schwille P. Cold Spring Harb Perspect from S2 to S1 for W/S1 hybridization proteins are affected by the DNA strand Biol 2011; 3: a009803. through a toehold-mediated DNA strand conjugation and strand displacement effi- 5. You M, Lyu Y and Han D et al. Nat Nanotechnol displacement, resulting in the quenching ciency, exploring the new DNA nanoma- 2017; 12: 453–9. of fluorescence. In this way, the transient chines to live-cell investigation is of great membrane encounter events were trans- interest. Future work would be expected duced to the cumulative fluorescence sig- to correlate the membrane encounter National Science Review nal change, which was easily measured by dynamics with important cellular pro- 5: 300–301, 2018 the commonly accessible flow cytometry cesses, such as membrane trafficking, cell doi: 10.1093/nsr/nwx091 or fluorescence microscopy [ 5]. signaling and cell polarization, to fur- Advance access publication 11 August 2017

Journal

National Science Review – Oxford University Press

Published: May 1, 2018

References