Research Topics
| N B LeontisSummaryAffiliation: Bowling Green State University Country: USA Publications
| Collaborators
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Detail Information
Publications
Geometric nomenclature and classification of RNA base pairsN B Leontis
Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
RNA 7:499-512. 2001..Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated...- Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complexEugene Myshkin
Department of Biological Sciences, Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
Biophys J 82:3305-13. 2002..hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs... - The RNA Ontology Consortium: an open invitation to the RNA communityNeocles B Leontis
RNA 12:533-41. 2006.... 
Specific RNA self-assembly with minimal paranemic motifsKirill A Afonin
Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
J Am Chem Soc 130:93-102. 2008..The 3HT motif appears suitable for specific, programmable, and reversible tecto-RNA self-assembly for constructing artificial RNA molecular machines...- Analysis of RNA motifsNeocles B Leontis
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
Curr Opin Struct Biol 13:300-8. 2003..It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically... - The non-Watson-Crick base pairs and their associated isostericity matricesNeocles B Leontis
Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
Nucleic Acids Res 30:3497-531. 2002..This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs... - Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA moleculesN B Leontis
Chemistry Department and Center for Biomolecular Sciences, Overman Hall, Bowling Green State University, Bowling Green, OH 43403, USA
Biochimie 84:961-73. 2002.... - Classification and energetics of the base-phosphate interactions in RNACraig L Zirbel
Department of Mathematics and Statistics, Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
Nucleic Acids Res 37:4898-918. 2009..Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments... - A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAsN B Leontis
Chemistry Department, Bowling Green State University, Bowling Green, OH, 43403, USA
J Mol Biol 283:571-83. 1998..Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in helix P10 of bacterial RNase P, in domain P7 of one sub-group of group I introns, and in domain 3 of one subgroup of group II introns... - Frequency and isostericity of RNA base pairsJesse Stombaugh
Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
Nucleic Acids Res 37:2294-312. 2009..In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments... - Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfoldingK Csaszar
Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
J Mol Biol 313:1073-91. 2001..Sodium cation coordination sites with occupancies above 50 % were also observed... - Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericitiesAli Mokdad
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, OH 43403, USA
Bioinformatics 22:2168-70. 2006..1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform. AVAILABILITY: http://rna.bgsu.edu/ribostral... - Structural and evolutionary classification of G/U wobble basepairs in the ribosomeAli Mokdad
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, OH 43403, USA
Nucleic Acids Res 34:1326-41. 2006..MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments... - FR3D: finding local and composite recurrent structural motifs in RNA 3D structuresMichael Sarver
Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
J Math Biol 56:215-52. 2008..The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes... - The building blocks and motifs of RNA architectureNeocles B Leontis
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
Curr Opin Struct Biol 16:279-87. 2006..This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences... - Controlling RNA self-assembly to form filamentsLorena Nasalean
Department of Chemistry, Bowling Green State University, OH 43402, USA
Nucleic Acids Res 34:1381-92. 2006..This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins... - The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structureN B Leontis
Chemistry Department, Bowling Green State University, Ohio 43403, USA
RNA 4:1134-53. 1998..The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA... - TokenRNA: a new type of sequence-specific, label-free fluorescent biosensor for folded RNA moleculesKirill A Afonin
Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
Chembiochem 9:1902-5. 2008 - Generating new specific RNA interaction interfaces using C-loopsKirill A Afonin
Department of Chemistry and Center for Bimolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43402, USA
J Am Chem Soc 128:16131-7. 2006..Binding affinities for most C-loop-containing molecules were generally equal or higher than those for the parent molecules lacking C-loops... - Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop EKamila Réblová
National Center for Biomolecular Research, Brno, Czech Republic
Biophys J 84:3564-82. 2003..The ordered hydration is intimately connected with RNA local conformational variations... - Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairsJiri Sponer
Institute of Biophysics, Academy of Sciences of the Czech Republic and National Center for Biomolecular Research, Kralovopolska 135, 612 65 Brno, Czech Republic
J Mol Biol 330:967-78. 2003..C. A/G base-pairs requires a detailed analysis of the relation between the molecular structures and the energetics of interactions at a level of single H-bonds and contacts... - Ribosomal RNA kink-turn motif--a flexible molecular hingeFilip Razga
National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic
J Biomol Struct Dyn 22:183-94. 2004..They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome... - Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complexKamila Réblová
National Centre for Biomolecular Research, Faculty of Sciences, Masaryk University, Kotlarska 2, 61137 Brno, Czech Republic
Biophys J 87:3397-412. 2004..Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA... - Recurrent structural RNA motifs, Isostericity Matrices and sequence alignmentsAurelie Lescoute
Institut de Biologie Moleculaire et Cellulaire du CNRS, UPR 9002, Université Louis Pasteur 15 rue René Descartes, F 67084 Strasbourg CEDEX, France
Nucleic Acids Res 33:2395-409. 2005..The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences... - Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired basesFilip Razga
National Centre for Biomolecular Research, Brno, Czech Republic
Biophys J 88:3466-85. 2005..We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle...