In SituHybridization in Living Cells: Detection of RNA Molecules

1997 ◽  
Vol 231 (1) ◽  
pp. 226-233 ◽  
Author(s):  
S. Paillasson ◽  
M. Van De Corput ◽  
R.W. Dirks ◽  
H.J. Tanke ◽  
M. Robert-Nicoud ◽  
...  
Keyword(s):  
Living Cells ◽  
Rna Molecules ◽  
In Situhybridization

scholarly journals Fluctuating Diffusivity of RNA-Protein Particles: Analogy with Thermodynamics

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 333
Author(s):  
Yuichi Itto
Keyword(s):  
Internal Energy ◽  
Messenger Rna ◽  
Living Cells ◽  
Statistical Fluctuation ◽  
Rna Molecules ◽  
Average Value ◽  
Thermodynamic Entropy ◽  
Laws Of Thermodynamics ◽  
Protein Particles ◽  
Quantity Of Heat

A formal analogy of fluctuating diffusivity to thermodynamics is discussed for messenger RNA molecules fluorescently fused to a protein in living cells. Regarding the average value of the fluctuating diffusivity of such RNA-protein particles as the analog of the internal energy, the analogs of the quantity of heat and work are identified. The Clausius-like inequality is shown to hold for the entropy associated with diffusivity fluctuations, which plays a role analogous to the thermodynamic entropy, and the analog of the quantity of heat. The change of the statistical fluctuation distribution is also examined from a geometric perspective. The present discussions may contribute to a deeper understanding of the fluctuating diffusivity in view of the laws of thermodynamics.

scholarly journals Effects on protein synthesis of injecting synthetic polyribonucleotides into living cells

1974 ◽  
Vol 144 (1) ◽  
pp. 11-19 ◽  
Author(s):  
Hugh Woodland ◽  
Sarah E. Ayers
Keyword(s):  
Protein Synthesis ◽  
Xenopus Laevis ◽  
Potent Inhibitor ◽  
Living Cells ◽  
Initiation Factor ◽  
Rna Molecules ◽  
Endogenous Protein ◽  
Limited Supply ◽  
Inhibitor Of Protein Synthesis ◽  
Haemoglobin Synthesis

Micro-injection into the oocytes and eggs of Xenopus laevis was used to ascertain the effects of synthetic polyribonucleotides on protein synthesis in living cells. Poly(U) and poly(A) were not translated detectably, nor did they change the rate of endogenous protein synthesis. The same was true of poly(G,U), poly(A,G,U), poly(A,C,G,U), G-U-G-(U)n, A-(U)n and AUG. In contrast, A-U-G-(U)n was a potent inhibitor of protein synthesis in the cell. This might be because it is initiated normally but lacks a termination codon, or because it inhibits the translation of other molecules in some way not dependent on its normal initiation. Poly(G,U), poly(A,G,U) and poly(A,C,G,U) inhibited haemoglobin synthesis when they were injected into the oocyte with haemoglobin mRNA. The synthetic polyribonucleotides did not inhibit the translation of the natural mRNA when the two sorts of molecules were injected at different times. It is suggested that the synthetic RNA molecules compete with the natural mRNA for a pre-initiation factor in limited supply.

scholarly journals A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

2021 ◽  
Author(s):  
Tycho Marinus ◽  
Adam B Fessler ◽  
Craig A Ogle ◽  
Danny Incarnato
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Critical Role ◽  
Living Cells ◽  
Pathological Process ◽  
Rna Structures ◽  
Rna Molecules ◽  
Derived Data

Abstract Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.

scholarly journals A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

2020 ◽  
Author(s):  
Tycho Marinus ◽  
Adam B. Fessler ◽  
Craig A. Ogle ◽  
Danny Incarnato
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
Critical Role ◽  
Living Cells ◽  
Pathological Process ◽  
Rna Structures ◽  
Rna Molecules ◽  
Derived Data

ABSTRACTDue to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art SHAPE reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.

IMAGING RNA IN LIVING CELLS WITH MOLECULAR BEACONS: CURRENT PERSPECTIVES AND CHALLENGES

2009 ◽  
Vol 02 (04) ◽  
pp. 315-324 ◽  
Author(s):  
ANTONY K. CHEN ◽  
ANDREW TSOURKAS
Keyword(s):  
Gene Expression ◽  
Molecular Imaging ◽  
Cell Fate ◽  
Dna Microarrays ◽  
Living Cells ◽  
Molecular Beacons ◽  
Rna Molecules ◽  
Molecular Imaging Probes ◽  
Imaging Probes ◽  
Phenotype Diversity

There is a growing realization that cell-to-cell variations in gene expression have important biological consequences underlying phenotype diversity and cell fate. Although analytical tools for measuring gene expression, such as DNA microarrays, reverse-transcriptase PCR and in situ hybridization have been widely utilized to discover the role of genetic variations in governing cellular behavior, these methods are performed in cell lysates and/or on fixed cells, and therefore lack the ability to provide comprehensive spatial-dynamic information on gene expression. This has invoked the recent development of molecular imaging strategies capable of illuminating the distribution and dynamics of RNA molecules in living cells. In this review, we describe a class of molecular imaging probes known as molecular beacons (MBs), which have increasingly become the probe of choice for imaging RNA in living cells. In addition, we present the major challenges that can limit the ability of MBs to provide accurate measurements of RNA, and discuss efforts that have been made to overcome these challenges. It is envisioned that with continued refinement of the MB design, MBs will eventually become an indispensable tool for analyzing gene expression in biology and medicine.

scholarly journals Detection and quantification of single mRNA dynamics with the Riboglow fluorescent RNA tag

2019 ◽  
Author(s):  
Esther Braselmann ◽  
Timothy J. Stasevich ◽  
Kenneth Lyon ◽  
Robert T. Batey ◽  
Amy E. Palmer
Keyword(s):  
Single Molecule ◽  
Fluorescent Probes ◽  
Mammalian Cells ◽  
Fluorescent Antibody ◽  
Living Cells ◽  
Rna Molecules ◽  
Single Molecule Level ◽  
Rna Biology ◽  
Tagging System ◽  
Detection And Quantification

AbstractLabeling and tracking biomolecules with fluorescent probes on the single molecule level enables quantitative insights into their dynamics in living cells. We previously developed Riboglow, a platform to label RNAs in live mammalian cells, consisting of a short RNA tag and a small organic probe that increases fluorescence upon binding RNA. Here, we demonstrate that Riboglow is capable of detecting and tracking single RNA molecules. We benchmark RNA tracking by comparing results with the established MS2 RNA tagging system. To demonstrate versatility of Riboglow, we assay translation on the single molecule level, where the translated mRNA is tagged with Riboglow and the nascent polypeptide is labeled with a fluorescent antibody. The growing effort to investigate RNA biology on the single molecule level requires sophisticated and diverse fluorescent probes for multiplexed, multi-color labeling of biomolecules of interest, and we present Riboglow as a new member in this toolbox.

scholarly journals RNA at the surface of phase-separated condensates impacts their size and number

2021 ◽  
Author(s):  
Audrey Cochard ◽  
Marina Garcia-Jove Navarro ◽  
Shunnichi Kashida ◽  
Michel Kress ◽  
Dominique Weil ◽  
...  
Keyword(s):  
Surface Density ◽  
Protein Composition ◽  
Living Cells ◽  
Rna Molecules ◽  
Physical Constraints ◽  
P Bodies ◽  
Intracellular Organization ◽  
Condensate Formation ◽  
Size And Morphology ◽  
Liquid Liquid Phase Separation

Membrane-less organelles, by localizing and regulating complex biochemical reactions, are ubiquitous functional subunits of intracellular organization. They include a variety of nuclear and cytoplasmic ribonucleoprotein (RNP) condensates, such as nucleoli, P-bodies, germ granules and stress granules. While is it now recognized that specific RNA and protein families are critical for the biogenesis of RNP condensates, how these molecular constituents determine condensate size and morphology is unknown. To circumvent the biochemical complexity of endogenous RNP condensates, the use of programmable tools to reconstitute condensate formation with minimal constituents can be instrumental. Here we report a methodology to form RNA-containing condensates in living cells with controlled RNA and protein composition. Our bioengineered condensates are made of ArtiGranule scaffolds undergoing liquid-liquid phase separation in cells and programmed to specifically recruit a unique RNA species. We found that RNAs mainly localized on condensate surface, either as isolated RNA molecules or as a homogenous corona of RNA molecules around the condensate. This simplified system allowed us to demonstrate that the size of the condensates scales with RNA surface density, the higher the RNA density is, the smaller and more frequent the condensates are. Our observations suggest a mechanism based on physical constraints, provided by RNAs localized on condensate surface, that limit condensate growth and coalescence.

scholarly journals Harnessing biomolecular condensates in living cells

2019 ◽  
Vol 166 (1) ◽  
pp. 13-27 ◽  
Author(s):  
Hideki Nakamura ◽  
Robert DeRose ◽  
Takanari Inoue
Keyword(s):  
Living Cells ◽  
Technological Advance ◽  
Liquid Droplets ◽  
Molecular Tools ◽  
Rna Molecules ◽  
Cell Functions ◽  
Pathological Conditions ◽  
A Cell ◽  
Membrane Bound

Abstract As part of the ‘Central Dogma’ of molecular biology, the function of proteins and nucleic acids within a cell is determined by their primary sequence. Recent work, however, has shown that within living cells the role of many proteins and RNA molecules can be influenced by the physical state in which the molecule is found. Within living cells, both protein and RNA molecules are observed to condense into non-membrane-bound yet distinct structures such as liquid droplets, hydrogels and insoluble aggregates. These unique intracellular organizations, collectively termed biomolecular condensates, have been found to be vital in both normal and pathological conditions. Here, we review the latest studies that have developed molecular tools attempting to recreate artificial biomolecular condensates in living cells. We will describe their design principles, implementation and unique characteristics, along with limitations. We will also introduce how these tools can be used to probe and perturb normal and pathological cell functions, which will then be complemented with discussions of remaining areas for technological advance under this exciting theme.

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