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A Study of Accessible Motifs and RNA Folding Complexity [chapter]

Ydo Wexler, Chaya Zilberstein, Michal Ziv-Ukelson
2006 Lecture Notes in Computer Science  
The fast new RNA folding algorithm is utilized for genome-wide discovery of accessible cis-regulatory motifs in data sets of ribosomal densities and decay rates of S. cerevisiae genes and to the mining  ...  The need to apply an accessability criterion to the task of genome-wide mRNA motif discovery raises the challenge of overcoming the core O(n 3 ) factor imposed by the time complexity of the currently best  ...  The research of Michal Ziv-Ukelson was supported in part by the Aly Kaufman Post Doctoral Fellowship.  ... 
doi:10.1007/11732990_40 fatcat:j7urzyagn5c27bm4opo3p2nhm4

A Study of Accessible Motifs and RNA Folding Complexity

Ydo Wexler, Chaya Zilberstein, Michal Ziv-Ukelson
2007 Journal of Computational Biology  
The fast new RNA folding algorithm is utilized for genome-wide discovery of accessible cis-regulatory motifs in data sets of ribosomal densities and decay rates of S. cerevisiae genes and to the mining  ...  The need to apply an accessability criterion to the task of genome-wide mRNA motif discovery raises the challenge of overcoming the core O(n 3 ) factor imposed by the time complexity of the currently best  ...  The research of Michal Ziv-Ukelson was supported in part by the Aly Kaufman Post Doctoral Fellowship.  ... 
doi:10.1089/cmb.2007.r020 pmid:17691898 fatcat:yzz5sna43vb35pan7k7qkcsmqy

Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation

O. FERNANDEZ-MIRAGALL
2005 RNA: A publication of the RNA Society  
Reorganization of domain 3 RNA structure in substitution mutants of motifs A and B. (A) Secondary structure probing of the wild-type IRES using DMS and RNase A, T1, T2, and V1.  ...  (B) RNase T2 and DMS probing of motif A mutant. (C) RNase T2 and DMS probing of motif B mutant. Substituted residues are highlighted in red.  ...  Ló pez de Quinto for early contribution to this work and J. Gó mez and C. Gutierrez for helpful suggestions on the manuscript.  ... 
doi:10.1261/rna.2153206 pmid:16373480 pmcid:PMC1370902 fatcat:qwroid4avneknktv7xzfyfujrm

Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP

Subash C. B. Gopinath, Dhakshnamoorthy Balasundaresan, Thirumananseri Kumarevel, Tomoko S. Misono, Hiroshi Mizuno, Penmetcha K. R. Kumar
2008 Nucleic Acids Research  
On the basis of biochemical, in vivo and X-ray structural analyses, we now report that HutP uses its dual RNA-binding surfaces to access two XAGrich regions (sites I and II) within the terminator RNA to  ...  In this process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first XAG-rich region (site I) and then accesses the second XAG-rich region (site II), located downstream of  ...  Funding to pay the Open Access publication charges for this article was provided by Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.  ... 
doi:10.1093/nar/gkn199 pmid:18445631 pmcid:PMC2425495 fatcat:tqrpimffnngilklebrstuwgfte

In vitro RNA random pools are not structurally diverse: A computational analysis

J. GEVERTZ
2005 RNA: A publication of the RNA Society  
Moreover, we quantify the rise of structural complexity with sequence length and report the dominant class of tree motifs (characterized by vertex number) for each pool.  ...  These analyses show not only that random pools do not lead to a uniform distribution of possible RNA secondary topologies; they point to avenues for designing pools with specific simple and complex structures  ...  the use of graph diameter; Terry McGuire for advisement and support of this project; Uri Laserson for his computing advice and insight; Sabera Asar for her creative ideas; and Daniela Fera for many engaging  ... 
doi:10.1261/rna.7271405 pmid:15923372 pmcid:PMC1370770 fatcat:ovbdpt2e3vbvbksjdt6pbn3tt4

Fuzzy RNA recognition by the Trypanosoma brucei editosome

Wolf-Matthias Leeder, Felix Klaus Geyer, Hans Ulrich Göringer
2022 Nucleic Acids Research  
The assembly of high molecular mass ribonucleoprotein complexes typically relies on the binary interaction of defined RNA sequences or precisely folded RNA motifs with dedicated RNA-binding domains on  ...  Here we describe a new molecular recognition principle of RNA molecules by a high molecular mass protein complex.  ...  ACKNOWLEDGEMENTS We thank Andreas V ölker for trypanosome cell growth, Robert Knieß and Cristian Del Campo for editosomes preparations, and Reza Salavati, Inna Aphasizheva and Ruslan Aphasizhev for transgenic  ... 
doi:10.1093/nar/gkac357 pmid:35580050 pmcid:PMC9178004 fatcat:yf2magkfnjdchmc4qnjbr27ixq

Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment

Barbara Szutkowska, Klaudia Wieczorek, Ryszard Kierzek, Pawel Zmora, Jake M. Peterson, Walter N. Moss, David H. Mathews, Elzbieta Kierzek
2022 International Journal of Molecular Sciences  
These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted.  ...  This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA  ...  The authors of the A/WSN/33 study focused on local folding in virio, forcing a maximum pairing distance of 150 nt.  ... 
doi:10.3390/ijms23052452 pmid:35269600 pmcid:PMC8910647 fatcat:z67wpabuhze4jnlcfdboitui2u

Defining the syntax for self-assembling RNA tertiary architectures

L. Jaeger
2009 Nucleic Acids Symposium Series  
Using comparative sequence and structural analysis of known X-ray structures of RNAs, folding and assembly principles of RNA can presently be gathered to generate the syntax of a proto-language for rational  ...  Stable RNAs are modular and hierarchical three-dimensional (3D) architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions (1,2).  ...  More recently, as a proof of concept, we have demonstrated that structurally complex RNA structures based on a syntax involving a repertoire of several different RNA motifs can self-assemble into complex  ... 
doi:10.1093/nass/nrp042 pmid:19749271 pmcid:PMC2823629 fatcat:nnvdr2k6ivbw3dv6krl2u5fnji

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function

Daniel Herschlag, Benjamin E Allred, Seshadri Gowrishankar
2015 Current Opinion in Structural Biology  
to a small region of the ensemble, that this region is highly dependent on the junction's topology, and that the correct alignment of tertiary motifs may be a rare conformation on the overall folding  ...  An incisive approach to understanding the function and folding of biological RNA systems involves characterizing small, simple components that are largely responsible for the behavior of complex systems  ...  Acknowledgements We thank Steve Bonilla, Xuesong Shi, and Shan Yang for helpful discussions. We thank members of the Herschlag laboratory for comments and suggestions.  ... 
doi:10.1016/j.sbi.2015.02.006 pmid:25744941 pmcid:PMC4416989 fatcat:k5bzcer4nzhflcep27vsctwew4

Improving the odds: Influence of starting pools on in vitro selection outcomes

Kelsey Pobanz, Andrej Lupták
2016 Methods  
Longer randomized regions support the formation of more complex structures and presumably allow formation of more intricate tertiary interactions, but they also tend to misfold and aggregate, whereas shorter  ...  In vitro selections isolate functional nucleic acids that fold into specific structures and form unique binding and catalytic sites.  ...  Acknowledgements Support of our research by the Pew Charitable Trusts, NIH EUREKA Program (R01GM094929), NSF (MCB-1330606), and the John Templeton Foundation/Foundation for Applied Molecular Evolution  ... 
doi:10.1016/j.ymeth.2016.04.021 pmid:27109058 pmcid:PMC5775183 fatcat:nivawp7sbjhy5ois72xbl3k36y

MeRNA: a database of metal ion binding sites in RNA structures

L. R. Stefan
2006 Nucleic Acids Research  
To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA 3D structures available  ...  Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes.  ...  ., S.E.B. and S.R.H. were supported by National Institutes of Health (NIGMS) grant  ... 
doi:10.1093/nar/gkj058 pmid:16381830 pmcid:PMC1347421 fatcat:eppdsd4etjh3tfuf375tx6sg7m

Recognition of duplex DNA by RNA polynucleotides

Claudia D. McDonald, L. James Maher
1995 Nucleic Acids Research  
The affinity of a polymeric RNA with three copies of the recognition sequence was greater than that of a polymeric RNA with a single copy of the sequence.  ...  Enzymatic probing of folded RNAs suggests that reduced affinity arises from unfavorable electrostatic, structural and topological considerations.  ...  LJM is a recipient of a Junior Faculty Research Award from the American Cancer Society and a Young Investigator's Award from Abbott Laboratories.  ... 
doi:10.1093/nar/23.3.500 pmid:7533903 pmcid:PMC306703 fatcat:5pld5hkcsrhntjinw2tye7yzgu

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Vincent B Chu, Daniel Herschlag
2008 Current Opinion in Structural Biology  
Next, we focus on advances in understanding, and characterizing the basic biophysical forces that govern the folding of complex RNAs.  ...  Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.  ...  Our work on RNA folding is supported by NIH grant PO1 GM066275. VBC is supported by a Pfizer Bio-X Graduate fellowship.  ... 
doi:10.1016/j.sbi.2008.05.002 pmid:18555681 pmcid:PMC2574980 fatcat:ju2zjgp4brd2ffczm2uak2tsli

Identification and Structural Aspects of G-Quadruplex-Forming Sequences from the Influenza A Virus Genome

Maria Tomaszewska, Marta Szabat, Karolina Zielińska, Ryszard Kierzek
2021 International Journal of Molecular Sciences  
Therefore, conserved structural motifs of vRNA can represent a novel therapeutic target.  ...  Here, we focused on the presence of G-rich sequences within the influenza A/California/07/2009(H1N1) genome and their ability to form RNA G-quadruplex structures (G4s).  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.  ... 
doi:10.3390/ijms22116031 pmid:34199658 pmcid:PMC8199785 fatcat:udrgonlu4zgk5lhroeiilwhcye

Substrate Dependence of Conformational Changes in the RNA-Binding Domain of Tristetraprolin Assessed by Fluorescence Spectroscopy of Tryptophan Mutants†

Brandy Y. Brewer, Jeff D. Ballin, Elizabeth J. Fialcowitz-White, Perry J. Blackshear, Gerald M. Wilson
2006 Biochemistry  
Studies with mutant ARE ligands revealed that a single UUAU half-site was sufficient to induce structural modulation of the N-terminal finger.  ...  Fluorescence methods demonstrate that the Nterminal, but not C-terminal zinc finger domain adopts a stably folded conformation in the presence of Zn 2+ .  ...  Kristin Varney for assistance with the molecular modeling of the TIS11d: RNA complex.  ... 
doi:10.1021/bi061320j pmid:17105199 pmcid:PMC1640280 fatcat:6zqa4cxgjfeltlckzckj36pxii
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