Imaging Membrane Order and Dynamic Interactions in Living Cells with a DNA Zipper Probe

2021 ◽  
Author(s):  
Yousef Bagheri ◽  
Ahsan Ausaf Ali ◽  
Puspam Keshri ◽  
James Chambers ◽  
Anne Gershenson ◽  
...  
Author(s):  
Yousef Bagheri ◽  
Ahsan Ausaf Ali ◽  
Puspam Keshri ◽  
James Chambers ◽  
Anne Gershenson ◽  
...  

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1701
Author(s):  
Teresa R. Wagner ◽  
Ulrich Rothbauer

In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Shipeng Shao ◽  
Hongchen Zhang ◽  
Yong Zeng ◽  
Yongliang Li ◽  
Chaoying Sun ◽  
...  

AbstractProtein-protein interactions (PPIs) are critical for cellular activity regulation. Visualization of PPIs using bimolecular fluorescence complementation (BiFC) techniques helps to understand how PPIs implement their functions. However, current BiFC is based on fluorescent proteins and the brightness and photostability are suboptimal for single molecule tracking experiments, resulting in either low spatiotemporal resolution or incapability of tracking for extended time course. Here, we developed the TagBiFC technique based on split HaloTag, a self-labeling tag that could conjugate an organic dye molecule and thus offered better brightness and photostability than fluorescent proteins for PPI visualization inside living cells. Through screening and optimization, we demonstrated that the reconstituted HaloTag exhibited higher localization precision and longer tracking length than previous methods. Using TagBiFC, we reveal that the dynamic interactions of transcription factor dimers with chromatin DNA are distinct and closely related to their dimeric states, indicating a general regulatory mechanism for these kinds of transcription factors. In addition, we also demonstrated the advantageous applications of TagBiFC in single nucleosome imaging, light-burden imaging of single mRNA, low background imaging of cellular structures. We believe these superior properties of our TagBiFC system will have broad applications in the studies of single molecule imaging inside living cells.


Methods ◽  
2014 ◽  
Vol 65 (3) ◽  
pp. 359-366 ◽  
Author(s):  
José Rino ◽  
Robert M. Martin ◽  
Teresa Carvalho ◽  
Maria Carmo-Fonseca

2004 ◽  
Vol 165 (3) ◽  
pp. 305-311 ◽  
Author(s):  
Maddalena de Virgilio ◽  
William B. Kiosses ◽  
Sanford J. Shattil

Stable platelet aggregation, adhesion, and spreading during hemostasis are promoted by outside-in αIIbβ3 signals that feature rapid activation of c-Src and Syk, delayed activation of FAK, and cytoskeletal reorganization. To evaluate these αIIbβ3–tyrosine kinase interactions at nanometer proximity in living cells, we monitored bioluminescence resonance energy transfer between GFP and Renilla luciferase chimeras and bimolecular fluorescence complementation between YFP half-molecule chimeras. These techniques revealed that αIIbβ3 interacts with c-Src at the periphery of nonadherent CHO cells. After plating cells on fibrinogen, complexes of αIIbβ3–c-Src, αIIbβ3–Syk, and c-Src–Syk are observed in membrane ruffles and focal complexes, and the interactions involving Syk require Src activity. In contrast, FAK interacts with αIIbβ3 and c-Src, but not with Syk, in focal complexes and adhesions. All of these interactions require the integrin β3 cytoplasmic tail. Thus, αIIbβ3 interacts proximally, if not directly, with tyrosine kinases in a coordinated, selective, and dynamic manner during sequential phases of αIIbβ3 signaling to the actin cytoskeleton.


Author(s):  
M. S. Cooper

Movements of exocytic and endocytic vesicles within cells are controlled in part by active transport along microtubules. The forces generated by microtubule-based transport are also known to strongly influence the distribution and shapes of membranous organelles, such as mitochondria and the endoplasmic reticulum. The ability to observe such dynamic interactions between cytoskeletal elements and fluorescently-labelled intracellular membranes in living cells has been improved recently by the advent of scanning laser confocal microscopy. Here we describe the use of this technique to study activities of the Golgi apparatus in living cells.Vesicular traffic, diffusive transport and morphological dynamics within the Golgi apparatus of cultured rat hippocampal astrocytes were imaged with a Bio-Rad MRC-500 scanning laser confocal microscope. Golgi elements were labelled with NBD-ceramide, a molecule which serves as a vital stain for the trans-most cisternae of Golgi stacks. Single scans of the specimen, obtained with the laser microscope's slow scan rate (4 sec/image), were stored sequentially on an optical memory disk recorder.


Author(s):  
R. Y. Tsien ◽  
A. Minta ◽  
M. Poenie ◽  
J.P.Y. Kao ◽  
A. Harootunian

Recent technical advances now enable the continuous imaging of important ionic signals inside individual living cells with micron spatial resolution and subsecond time resolution. This methodology relies on the molecular engineering of indicator dyes whose fluorescence is strong and highly sensitive to ions such as Ca2+, H+, or Na+, or Mg2+. The Ca2+ indicators, exemplified by fura-2 and indo-1, derive their high affinity (Kd near 200 nM) and selectivity for Ca2+ to a versatile tetracarboxylate binding site3 modeled on and isosteric with the well known chelator EGTA. The most commonly used pH indicators are fluorescein dyes (such as BCECF) modified to adjust their pKa's and improve their retention inside cells. Na+ indicators are crown ethers with cavity sizes chosen to select Na+ over K+: Mg2+ indicators use tricarboxylate binding sites truncated from those of the Ca2+ chelators, resulting in a more compact arrangement of carboxylates to suit the smaller ion.


Author(s):  
K. Jacobson ◽  
A. Ishihara ◽  
B. Holifield ◽  
F. Zhang

Our laboratory is concerned with understanding the dynamic structure of the plasma membrane with particular reference to the movement of membrane constituents during cell locomotion. In addition to the standard tools of molecular cell biology, we employ both fluorescence recovery after photo- bleaching (FRAP) and digitized fluorescence microscopy (DFM) to investigate individual cells. FRAP allows the measurement of translational mobility of membrane and cytoplasmic molecules in small regions of single, living cells. DFM is really a new form of light microscopy in that the distribution of individual classes of ions, molecules, and macromolecules can be followed in single, living cells. By employing fluorescent antibodies to defined antigens or fluorescent analogs of cellular constituents as well as ultrasensitive, electronic image detectors and video image averaging to improve signal to noise, fluorescent images of living cells can be acquired over an extended period without significant fading and loss of cell viability.


Author(s):  
D. L. Taylor

Cells function through the complex temporal and spatial interplay of ions, metabolites, macromolecules and macromolecular assemblies. Biochemical approaches allow the investigator to define the components and the solution chemical reactions that might be involved in cellular functions. Static structural methods can yield information concerning the 2- and 3-D organization of known and unknown cellular constituents. Genetic and molecular techniques are powerful approaches that can alter specific functions through the manipulation of gene products and thus identify necessary components and sequences of molecular events. However, full knowledge of the mechanism of particular cell functions will require direct measurement of the interplay of cellular constituents. Therefore, there has been a need to develop methods that can yield chemical and molecular information in time and space in living cells, while allowing the integration of information from biochemical, molecular and genetic approaches at the cellular level.


Author(s):  
Shinya Inoué

This paper reports progress of our effort to rapidly capture, and display in time-lapsed mode, the 3-dimensional dynamic architecture of active living cells and developing embryos at the highest resolution of the light microscope. Our approach entails: (A) real-time video tape recording of through-focal, ultrathin optical sections of live cells at the highest resolution of the light microscope; (B) repeat of A at time-lapsed intervals; (C) once each time-lapsed interval, an image at home focus is recorded onto Optical Disk Memory Recorder (OMDR); (D) periods of interest are selected using the OMDR and video tape records; (E) selected stacks of optical sections are converted into plane projections representing different view angles (±4 degrees for stereo view, additional angles when revolving stereos are desired); (F) analysis using A - D.


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