Genetic Exchange Leading to Self-Assembling RNA Species upon Encapsulation in Artificial Protocells

The encapsulation of information-bearing macromolecules inside protocells is a critical step in scenarios for the origins of life on the Earth as well as for the construction of artificial living systems. For these protocells to emulate life, they must be able to transmit genetic information to other cells. We have used a water-in-oil emulsion system to simulate the compartmentalization of catalytic RNA molecules. By exploiting RNA-directed recombination reactions previously developed in our laboratory, including a ribozyme self-assembly pathway, we demonstrate that it is possible for information to be exchanged among protocells. This can happen either indirectly by the passage of divalent cations through the inter-protocellular medium (oil), or by the direct interaction of two or more protocells that allows RNA molecules to be exchanged. The degree of agitation affects the ability of such exchange. The consequences of these results include the implications that prototypical living systems can transmit information among compartments, and that the environment can regulate the extent of this crosstalk.

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Spatial RNA proximities reveal a bipartite nuclear transcriptome and territories of differential density and transcription elongation rates

10.1101/196147 ◽

2017 ◽

Cited By ~ 1

Author(s):

Jörg Morf ◽

Steven W. Wingett ◽

Irene Farabella ◽

Jonathan Cairns ◽

Mayra Furlan-Magaril ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Rna Seq ◽

Cell Nuclei ◽

Oil Emulsion ◽

Rna Molecules ◽

Emulsion Droplets ◽

Differential Density ◽

Genomic Regions ◽

Water In Oil Emulsion ◽

Nascent Transcripts

AbstractSpatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which enriches for nascent transcripts, and identifies contact preferences for individual RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA-barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing. We show a bipartite organization of the nuclear transcriptome in which compartments of different RNA density correlate with transcript families, tissue specificity and extent of alternative splicing. Integration of proximity measurements at the DNA and NA level identify transcriptionally active genomic regions with increased nucleic acid density and faster RNA polymerase II elongation located close to compact chromatin.

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Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

10.1101/551994 ◽

2019 ◽

Author(s):

Naoto Hori ◽

Natalia A. Denesyuk ◽

D. Thirumalai

Keyword(s):

Self Assembly ◽

Divalent Cations ◽

Coarse Grained ◽

Nucleotide Position ◽

Structural Elements ◽

Rna Molecules ◽

Low Concentrations ◽

Monovalent Ions ◽

Tertiary Interactions ◽

Phosphate Groups

AbstractThe highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more efficient than monovalent ions in driving them to a compact state although often Mg2+ ions are needed for catalytic activity. Therefore, how ions interact with RNA is relevant in understanding RNA folding. It is often thought that the most of the ions are territorially and non-specifically bound to the RNA, as predicted by the counterion condensation (CIC) theory. Here, we show using simulations of Azoarcus ribozyme, based on an accurate coarse-grained Three Site Interaction (TIS) model, with explicit divalent and monovalent cations, that ion condensation is highly specific and depends on the nucleotide position. The regions with high coordination between the phosphate groups and the divalent cations are discernible at very low concentrations when the ribozyme does not form tertiary interactions. Surprisingly, these regions also contain the secondary structural elements that nucleate subsequently in the self-assembly of RNA, implying that ion condensation is determined by the architecture of the folded state. These results are in sharp contrast to interactions of ions (monovalent and divalent) with rigid charged rods in which ion condensation is uniform and position independent. The differences are explained in terms of the dramatic non-monotonic shape fluctuations in the ribozyme as it folds with increasing Mg2+ or Ca2+ concentration.

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Self-Assembly of Nucleocapsid-Like Particles from Recombinant Hepatitis C Virus Core Protein

Journal of Virology ◽

10.1128/jvi.75.5.2119-2129.2001 ◽

2001 ◽

Vol 75 (5) ◽

pp. 2119-2129 ◽

Cited By ~ 120

Author(s):

Meghan Kunkel ◽

Marta Lorinczi ◽

René Rijnbrand ◽

Stanley M. Lemon ◽

Stanley J. Watowich

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Self Assembly ◽

High Throughput Screening ◽

Core Protein ◽

Rna Molecules ◽

The Core ◽

Assembly Pathway ◽

Core Proteins

ABSTRACT Little is known about the assembly pathway and structure of hepatitis C virus (HCV) since insufficient quantities of purified virus are available for detailed biophysical and structural studies. Here, we show that bacterially expressed HCV core proteins can efficiently self-assemble in vitro into nucleocapsid-like particles. These particles have a regular, spherical morphology with a modal distribution of diameters of approximately 60 nm. Self-assembly of nucleocapsid-like particles requires structured RNA molecules. The 124 N-terminal residues of the core protein are sufficient for self-assembly into nucleocapsid-like particles. Inclusion of the carboxy-terminal domain of the core protein modifies the core assembly pathway such that the resultant particles have an irregular outline. However, these particles are similar in size and shape to those assembled from the 124 N-terminal residues of the core protein. These results provide novel opportunities to delineate protein-protein and protein-RNA interactions critical for HCV assembly, to study the molecular details of HCV assembly, and for performing high-throughput screening of assembly inhibitors.

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Factors Affecting Molecular Self-Assembly and Its Mechanism

Scientific Research Journal ◽

10.24191/srj.v9i1.5385 ◽

2012 ◽

Vol 9 (1) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Hueyling Tan

Keyword(s):

Self Assembly ◽

Building Blocks ◽

Molecular Engineering ◽

Molecular Structures ◽

Polymer Science ◽

New Approach ◽

Factors Affecting ◽

Dna Structures ◽

Self Assembling ◽

Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

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Deemulsification of Water-in-Oil Emulsion with Sludges

Water Quality Research Journal ◽

10.2166/wqrj.1987.034 ◽

1987 ◽

Vol 22 (3) ◽

pp. 437-443 ◽

Cited By ~ 5

Author(s):

N. Kosaric ◽

Z. Duvnjak

Keyword(s):

Activated Sludge ◽

Room Temperature ◽

Petroleum Refinery ◽

Treatment Plant ◽

Granular Sludge ◽

Activated Sludge Process ◽

Sludge Treatment ◽

Oil Emulsion ◽

Water In Oil Emulsion ◽

Aerobic Sludge

Abstract Aerobic sludge from a municipal activated sludge treatment plant, sludge from a conventional municipal anaerobic digester, aerobic sludge from an activated sludge process of a petroleum refinery, and granular sludge from an upflow sludge blanket reactor (USBR) were tested in the deemulsification of a water-in-oil emulsion. All sludges except the last one, showed a good deemulsification capability and could he used for a partial deemulsification of such emulsions. The rate and degree of the deemulsifications increased with an increase in sludge concentrations. The deemulsifications were faster at 85°C and required smaller amounts of sludge than in the case of the deemulsifications at room temperature. An extended stirring (up to a certain limit) in the course of the dispersion of sludge emulsion helped the deemulsification. Too vigorous agitation had an adverse effect. The deemulsification effect of sludge became less visible with an increase in the dilution of emulsion which caused an increase in its spontaneous deemulsification.

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Destruction of water-in-oil emulsions in electromagnetic fields in a dynamic mode

Proceedings of the Mavlyutov Institute of Mechanics ◽

10.21662/uim2012.1.021 ◽

2012 ◽

Vol 9 (1) ◽

pp. 110-115

Author(s):

L.A. Kovaleva ◽

R.R. Zinnatullin ◽

V.N. Blagochinnov ◽

A.A. Musin ◽

Yu.I. Fatkhullina ◽

...

Keyword(s):

Dielectric Properties ◽

Radio Frequency ◽

Electromagnetic Fields ◽

Dynamic Mode ◽

Droplet Dynamics ◽

Oil Emulsion ◽

Numerical Studies ◽

Em Field ◽

Oil Emulsions ◽

Water In Oil Emulsion

Some results of experimental and numerical studies of the influence of radio-frequency (RF) and microwave (MW) electromagnetic (EM) fields on water-in-oil emulsions are presented. A detailed investigation of the dependence of the dielectric properties of emulsions on the frequency of the field makes it possible to establish the most effective frequency range of the EM influence. The results of water-in-oil emulsion stability in the RF EM field depending on their dielectric properties are presented. The effect of the MW EM field on the emulsion in a dynamic mode has been studied experimentally. In an attempt to understand the mechanism of emulsion destruction the mathematical model for a single emulsion droplet dynamics in radio-frequency (RF) and microwave (MW) electromagnetic fields is formulated.

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Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

Protein and Peptide Letters ◽

10.2174/0929866527666200224114627 ◽

2020 ◽

Vol 27 (9) ◽

pp. 923-929

Author(s):

Gaurav Pandey ◽

Prem Prakash Das ◽

Vibin Ramakrishnan

Keyword(s):

Electron Microscopy ◽

Amino Acids ◽

Light Scattering ◽

Chain Length ◽

Self Assembly ◽

The Self ◽

Ionic Charge ◽

Self Assembling ◽

Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

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Self-assembling behaviour of a modified aromatic amino acid in competitive medium

Soft Matter ◽

10.1039/d0sm00584c ◽

2020 ◽

Vol 16 (28) ◽

pp. 6599-6607 ◽

Cited By ~ 1

Author(s):

Pijush Singh ◽

Souvik Misra ◽

Nayim Sepay ◽

Sanjoy Mondal ◽

Debes Ray ◽

...

Keyword(s):

Amino Acid ◽

Self Assembly ◽

Aromatic Amino Acid ◽

Photophysical Properties ◽

Solvent Mixture ◽

The Self ◽

Solvent Ratio ◽

Self Assembling

The self-assembly and photophysical properties of 4-nitrophenylalanine (4NP) are changed with the alteration of solvent and final self-assembly state of 4NP in competitive solvent mixture and are dictated by the solvent ratio.

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