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Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics
[chapter]
Communications in Computer and Information Science
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We show here that both components can be efficiently computed using an improved variant of RNAup. The method is then applied to a set of bacterial small RNAs involved in translational control. ...
The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e. unpaired, and the energy gained from the base pairing of the ...
In the results section, we report how these improvements allow us to more precisely describe translational control by bacterial sRNA. ...
doi:10.1007/978-3-540-70600-7_9
fatcat:wqnxtnnzmnfz5i7su2kbwekaiu
Comparing RNA Kissing Interactions at Single-Molecule and Ensemble Levels
2014
Biophysical Journal
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From a number of crystallographic structures of high molecular weight RNA molecules, we derived a set of effective potentials that describe the interactions between nucleotide centroids. ...
Using this information, we developed a new Force Field that was implemented in a Molecular Dynamics code whose objective is to describe the three-dimensional folding of RNA molecules. ...
RNA II is a primer for replication of the ColE1 plasmid; its function is modulated by interaction with RNA I. Rop is known to bind and stabilize kissing complexes. ...
doi:10.1016/j.bpj.2013.11.1659
fatcat:vupm2yfx6nharltrfe33hbhoy4
PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs
2018
Nature Communications
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The binding sites for these effector molecules influenced different aspects of the RNA lifecycle: RNA stability, translation efficiency, and translation initiation. ...
RNA binding proteins (RBP) and microRNAs (miRNAs) often bind sequences in 3′ untranslated regions (UTRs) of mRNAs, and regulate stability and translation efficiency. ...
H.G.C. and B.A.C. supported by GM092910 and R01-HG008687. This work was funded by NIH GM007067 to K.A.C. and R01-GM112824 to S.D. ...
doi:10.1038/s41467-017-02745-0
pmid:29352242
pmcid:PMC5775260
fatcat:6xrw24jlbbelrfiwo3h5x4t2oi
Identifying and characterizing Hfq–RNA interactions
2013
Methods
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In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions. ...
A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. ...
of Chemistry. ...
doi:10.1016/j.ymeth.2013.04.023
pmid:23707622
pmcid:PMC3787079
fatcat:pwdrh7fgxne4zlilh754uccvri
Virtual Screening for RNA-Interacting Small Molecules
[chapter]
2012
Biophysical approaches to translational control of gene expression
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Many computational docking programs that can automatically dock small molecules into a binding site of a target receptor with minimum input from an operator have been developed and their applicability ...
Computational virtual screening strategy is useful in the very early stage of the drug discovery pipeline and provides a powerful tool for rapid discovery of small biologically active molecules. ...
Thermodynamic or kinetic control of RNA secondary structure folding may be important in regulating the ef fi ciency of −1 FS. ...
doi:10.1007/978-1-4614-3991-2_12
fatcat:kde2gk4effcyvd6xlfe4r37bfm
High-throughput characterization of protein-RNA interactions
2014
Briefings in Functional Genomics
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Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA^protein interactions ...
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. ...
Computational methods for examining protein-RNA interactions The goal of complete understanding of the functions of RBPs in post-transcriptional regulation requires computational analysis of RBP-RNA interactions ...
doi:10.1093/bfgp/elu047
pmid:25504152
pmcid:PMC4303715
fatcat:pe2wybppv5di7n6ijwalr7jqru
iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems
2016
Entropy
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We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. ...
It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. ...
Also, this research was in part supported by the financial budget of fiscal year 2016 from King Mongkut's University of Technology Thonburi. ...
doi:10.3390/e18030083
fatcat:7fwwnrjxvffuvcqsigppeugtn4
3D RNA and functional interactions from evolutionary couplings
[article]
2016
arXiv
pre-print
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Aided by accelerating sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA. ...
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. ...
The binding of both of these RNA elements to an un-charged tRNA induces translation of downstream genes by exposing a Shine-Delgarno (SD) sequence. ...
arXiv:1510.01420v3
fatcat:5vfd6glcrjbkzbzb7rorqopz3a
AccessFold: predicting RNA–RNA interactions with consideration for competing self-structure
2015
Bioinformatics
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Motivation: There are numerous examples of RNA-RNA complexes, including microRNA-mRNA and small RNA-mRNA duplexes for regulation of translation, guide RNA interactions with target RNA for post-transcriptional ...
The pseudo-free energy, derived from unimolecular pairing probabilities, is applied per nucleotide in bimolecular pairs, and this approach is able to predict binding sites that are split by unimolecular ...
Funding This work was supported by National Institutes of Health (NIH) grant R01 GM076485 to D.H.M.; NIH grant T32 GM068411 to L.D. and NIH grant T32 GM07356 to L.D. ...
doi:10.1093/bioinformatics/btv682
pmid:26589271
pmcid:PMC4907385
fatcat:uf4br5liwzetpgkpii3mcwkdoe
Isoenergetic Microarrays To Study the Structure and Interactions of DsrA and OxyS RNAs in Two- and Three-Component Complexes
2011
Biochemistry
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Herein, for the first time, isoenergetic microarrays were used to study the binding of RNA to protein or other RNAs, as well as the interactions of two different RNAs and protein in a three-component complex ...
To enhance thermodynamic stability and to make binding of the target RNA to 2′-O-methylated probes sequence independent, locked nucleic acid (LNA) nucleotides, including 2,6-diaminopurine riboside (D) ...
Feig (Wayne State University) for plasmid encoding Hfq protein and Walter Moss (University of Rochester) for comments and suggestions on this manuscript. ...
doi:10.1021/bi200463p
pmid:21793590
pmcid:PMC3312101
fatcat:hbfkas6wpbbyvcw3z6o547hhse
3D RNA and Functional Interactions from Evolutionary Couplings
2016
Cell
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Aided by accelerating sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA. ...
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. ...
AJR is supported by DOE fellowhip DE-FG02-97ER25308. JBI is supported by an NSF Graduate Research Fellowship. DSM, TG and CS are supported by R01 GM106303. ...
doi:10.1016/j.cell.2016.03.030
pmid:27087444
pmcid:PMC5024353
fatcat:52ateosxqrf7xc4mcf2rqo4rcu
Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding
2021
Molecules
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We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy. ...
With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/molecules26113384
fatcat:ct45xpjy5rhtbmwfbrqszz6ahe
Host-virus interaction: a new role for microRNAs
2006
Retrovirology
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These interactions can be further fine-tuned in the host by changes in gene expression, mutations and polymorphisms. ...
MicroRNAs (miRNAs) are a new class of 18-23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes. ...
Authors also acknowledge the Council of Scientific and Industrial Research (CSIR), India for funding through Task Force Project CMM0017. VS acknowledges the Senior Research Fellowship from CSIR. ...
doi:10.1186/1742-4690-3-68
pmid:17032463
pmcid:PMC1626483
fatcat:wqtrioybwnhw5ctfygjukhnpte
RNA-RNA interaction prediction based on multiple sequence alignments
[article]
2010
arXiv
pre-print
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Recently, O(N^6) time and O(N^4) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. ...
Many computerized methods for RNA-RNA interaction structure prediction have been developed. ...
This work was supported by the 973 Project of the Ministry of Science and Technology, the PCSIRT Project of the Ministry of Education, and the National Science Foundation of China to CMR and his lab, grant ...
arXiv:1003.3987v3
fatcat:gqw6yxot55eo3mycsumu4vuune
Protein-Nucleic Acid Interactions - I
2008
Biophysical Journal
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NE hyperpolarized the cell membrane, an effect that was abolished by tolbutamide. The effect of NE on KATP channels was investigated in parallel using outside-out single channel recording. ...
This revealed that NE enhanced the open activities of the KATP channels $2 fold without changing the single channel conductance, demonstrating that NE-induced hyperpolarization was mediated by activation ...
As monitored by protein binding, the assembly process exhibits significant thermodynamic cooperativity. ...
doi:10.1016/s0006-3495(08)79120-3
fatcat:ia4mxic7kzcabgmormzastrl3i
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