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Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics [chapter]

Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
Communications in Computer and Information Science  
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

William Stephenson, Papa Nii Asare-Okai, Scott Tenenbaum, Daniele Fabris, Pan T.X. Li
2014 Biophysical Journal  
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

Kyle A. Cottrell, Hemangi G. Chaudhari, Barak A. Cohen, Sergej Djuranovic
2018 Nature Communications  
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

M.A. Faner, A.L. Feig
2013 Methods  
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]

Hyun-Ju Park, So-Jung Park
2012 Biophysical approaches to translational control of gene expression  
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

K. B. Cook, T. R. Hughes, Q. D. Morris
2014 Briefings in Functional Genomics  
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

Jittrawan Thaiprasit, Boonserm Kaewkamnerdpong, Dujduan Waraho-Zhmayev, Supapon Cheevadhanarak, Asawin Meechai
2016 Entropy  
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]

Caleb Weinreb, Adam J. Riesselman, John B. Ingraham, Torsten Gross, Chris Sander, Debora S. Marks
2016 arXiv   pre-print
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

Laura DiChiacchio, Michael F. Sloma, David H. Mathews
2015 Bioinformatics  
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

Agata Fratczak, Ryszard Kierzek, Elzbieta Kierzek
2011 Biochemistry  
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

Caleb Weinreb, Adam J. Riesselman, John B. Ingraham, Torsten Gross, Chris Sander, Debora S. Marks
2016 Cell  
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

Daria V. Berdnikova, Paolo Carloni, Sybille Krauß, Giulia Rossetti
2021 Molecules  
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

Vinod Scaria, Manoj Hariharan, Souvik Maiti, Beena Pillai, Samir K Brahmachari
2006 Retrovirology  
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]

Andrew X. Li, Manja Marz, Jing Qin, Christian M.Reidys
2010 arXiv   pre-print
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  
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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