scholarly journals Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Sakon Rahong ◽  
Takao Yasui ◽  
Takeshi Yanagida ◽  
Kazuki Nagashima ◽  
Masaki Kanai ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Rna Molecules ◽  
Fast Separation ◽  
Ultra Fast Separation

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anupam Bhattacharya ◽  
Simang Champramary ◽  
Tanya Tripathi ◽  
Debajit Thakur ◽  
Ilya Ioshikhes ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Muscle Development ◽  
Three Dimensional ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics

2005 ◽  
Vol 38 (4) ◽  
pp. 291-301 ◽  
Author(s):  
Carlos Bustamante
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Biological Systems ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Fluctuation Theorems ◽  
Rna Molecules ◽  
The Times ◽  
Non Equilibrium

During the last 15 years, scientists have developed methods that permit the direct mechanical manipulation of individual molecules. Using this approach, they have begun to investigate the effect of force and torque in chemical and biochemical reactions. These studies span from the study of the mechanical properties of macromolecules, to the characterization of molecular motors, to the mechanical unfolding of individual proteins and RNA. Here I present a review of some of our most recent results using mechanical force to unfold individual molecules of RNA. These studies make it possible to follow in real time the trajectory of each molecule as it unfolds and characterize the various intermediates of the reaction. Moreover, if the process takes place reversibly it is possible to extract both kinetic and thermodynamic information from these experiments at the same time that we characterize the forces that maintain the three-dimensional structure of the molecule in solution. These studies bring us closer to the biological unfolding processes in the cell as they simulate in vitro, the mechanical unfolding of RNAs carried out in the cell by helicases. If the unfolding process occurs irreversibly, I show here that single-molecule experiments can still provide equilibrium, thermodynamic information from non-equilibrium data by using recently discovered fluctuation theorems. Such theorems represent a bridge between equilibrium and non-equilibrium statistical mechanics. In fact, first derived in 1997, the first experimental demonstration of the validity of fluctuation theorems was obtained by unfolding mechanically a single molecule of RNA. It is perhaps a sign of the times that important physical results are these days used to extract information about biological systems and that biological systems are being used to test and confirm fundamental new laws in physics.

scholarly journals Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

2018 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Giovanni Pinamonti ◽  
Sabine Reißer ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Molecular Simulations ◽  
Network Models ◽  
Molecular Conformations ◽  
Rna Molecules ◽  
Command Line Tool ◽  
Perform Cluster Analysis ◽  
And Function

AbstractRNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be non-trivial because it requires processing very high-dimensional data that are not easy to visualize and interpret.Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acids structures and molecular simulations. The software consists of a variety of analysis tools that allow the user to i) calculate distances between three-dimensional structures using different metrics, ii) back-calculate experimental data from three-dimensional structures, iii) perform cluster analysis and dimensionality reductions, iv) search three-dimensional motifs in PDB structures and trajectories and v) construct elastic network models (ENM) for nucleic acids and nucleic acids-protein complexes.In addition, Barnaba makes it possible to calculate torsion angles, pucker conformations and to detect base-pairing/base-stacking interactions. Barnaba produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations. The software is available as a command-line tool as well as a library, and supports a variety of 1le formats such as PDB, dcd and xtc 1les. Source code, documentation and examples are freely available at https://github.com/srnas/barnaba under GNU GPLv3 license.

scholarly journals ProLIF: a library to encode molecular interactions as fingerprints

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Cédric Bouysset ◽  
Sébastien Fiorucci
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Data Analysis ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Use Case ◽  
Docking Simulations ◽  
Rna Molecules ◽  
Vector Representations ◽  
Interaction Fingerprints

AbstractInteraction fingerprints are vector representations that summarize the three-dimensional nature of interactions in molecular complexes, typically formed between a protein and a ligand. This kind of encoding has found many applications in drug-discovery projects, from structure-based virtual-screening to machine-learning. Here, we present ProLIF, a Python library designed to generate interaction fingerprints for molecular complexes extracted from molecular dynamics trajectories, experimental structures, and docking simulations. It can handle complexes formed of any combination of ligand, protein, DNA, or RNA molecules. The available interaction types can be fully reparametrized or extended by user-defined ones. Several tutorials that cover typical use-case scenarios are available, and the documentation is accompanied with code snippets showcasing the integration with other data-analysis libraries for a more seamless user-experience. The library can be freely installed from our GitHub repository (https://github.com/chemosim-lab/ProLIF).

Morphology of escherichia coli ribosomes as obtained by high resolution shadow cast

1978 ◽  
Vol 36 (2) ◽  
pp. 240-241 ◽  
Author(s):  
B. Tesche ◽  
G.W. Tischendorf ◽  
G. Stöffler
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Optical Resolution ◽  
Single Particles ◽  
Three Dimensional Model ◽  
Rna Molecules ◽  
E Coli ◽  
Fine Grained ◽  
Shadow Casting ◽  
Shadow Cast

All components (54 proteins and 3 RNA molecules) of the E. coli ribosome have been identified and characterized by biochemical and biophysical means. The morphology of the ribosome and the structural arrangement of its components, however, is not yet unequivocally known. The reasons for this are that crystal arrangements could not be obtained and that the different preparations of single particles remain invariant; and that holds for different laboratories as well.We applied a preparation which has been demonstrated to be most gentle and hence most structure-preserving; that is, freeze-drying with shadow casting at -150°C. Furthermore, the evaporator is of such design that it produces very little heat and renders a thin, fine-grained tungsten layer. An electron optical resolution of 6 Å can be achieved. Fig. 1 shows a micrograph of a typical shadowgraph obtained with 70S ribosomes from which we attempt to derive a three-dimensional model of the ribosome.

Folding mechanisms of group I ribozymes: role of stability and contact order

2002 ◽  
Vol 30 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
S. A. Woodson
Keyword(s):  
Catalytic Activity ◽  
Rna Folding ◽  
Three Dimensional ◽  
Model System ◽  
Folding Pathway ◽  
Primary Sequence ◽  
Rna Molecules ◽  
Contact Order ◽  
Group I

The mechanism by which RNA molecules assemble into unique three-dimensional conformations is important for understanding their function, regulation and interactions with substrates. The Tetrahymena group I ribozyme is an excellent model system for understanding RNA folding mechanisms, because the catalytic activity of the native RNA is easily measured. Folding of the Tetrahymena ribozyme is dominated by intermediates in which the stable P4-P6 domain is correctly formed, but the P3-P9 domain is partially misfolded. The propensity of the RNA to misfold depends on the relative stability of native and non-native interactions. Circular permutation of the Tetrahymena ribozyme shows that the distance in the primary sequence between native interactions also influences the folding pathway.

A new three-dimensional educational model kit for building DNA and RNA molecules: Development and evaluation

2006 ◽  
Vol 34 (3) ◽  
pp. 187-193 ◽  
Author(s):  
Leila Maria Beltramini ◽  
Ana Paula Ulian Araújo ◽  
Tales Henrique Gonçalves de Oliveira ◽  
Luciano Douglas dos Santos Abel ◽  
Aparecido Rodrigues da Silva ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Educational Model ◽  
Rna Molecules ◽  
Dna And Rna

scholarly journals Structures to the people!

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Nathan J Baird ◽  
Sebastian A Leidel
Keyword(s):  
High Throughput ◽  
3D Modeling ◽  
High Throughput Sequencing ◽  
Three Dimensional ◽  
Rna Molecules ◽  
The People

A combination of 3D modeling and high-throughput sequencing may offer a faster way to determine the three-dimensional structures of RNA molecules.

scholarly journals Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Genomic Region ◽  
Dimensional Structure ◽  
Structure Based Drug Design ◽  
Stem Loop ◽  
Rna Molecules ◽  
Conformational Ensembles ◽  
Dynamics Simulations

The 5' untranslated region (UTR) of SARS-CoV-2 genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structure is not known yet. Here, we predict structure and dynamics of five RNA stem-loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrengements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterisation of these systems, and provide putative three-dimensional models for structure-based drug design studies.

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