A5079806827- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- RNA Interference and Gene Delivery
- Plant and Fungal Interactions Research
- Protein Structure and Dynamics
- Biomedical Text Mining and Ontologies
- Various Chemistry Research Topics
- Porphyrin and Phthalocyanine Chemistry
- Plant Disease Resistance and Genetics
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Phytoplasmas and Hemiptera pathogens
- Toxin Mechanisms and Immunotoxins
- Porphyrin Metabolism and Disorders
- Photochemistry and Electron Transfer Studies
- Electron Spin Resonance Studies
- Spectroscopy and Quantum Chemical Studies
Bowling Green State University
2011-2021
University of Colorado Boulder
2011
Czech Academy of Sciences, Institute of Biophysics
2010
Ohio Northern University
2010
Czech Academy of Sciences
2009
Architecture et Réactivité de l'arN
2006
University of Michigan–Ann Arbor
1988
Yale University
1983-1984
Harvard University
1982
Non-Watson–Crick base pairs mediate specific interactions responsible for RNA–RNA self-assembly and RNA–protein recognition. An unambiguous descriptive nomenclature with well-defined nonoverlapping parameters is needed to communicate concisely structural information about RNA pairs. The definitions should reflect underlying molecular structures and, thus, facilitate automated annotation, classification, comparison of new structures. We propose a classification based on the observation that...
RNA molecules exhibit complex structures in which a large fraction of the bases engage non‐Watson–Crick base pairing, forming motifs that mediate long‐range RNA–RNA interactions and create binding sites for proteins small molecule ligands. The rapidly growing number three‐dimensional at atomic resolution requires databases contain annotation such pairs. An unambiguous descriptive nomenclature was proposed recently pairs were classified by edges participating interaction (Watson–Crick,...
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess leading edge techniques; compare existing methods and tools; evaluate their relative strengths, weaknesses, limitations terms sequence length structural complexity. should give potential users insight into suitability available for different applications facilitate efforts community ongoing improve tools. also...
The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D nucleic acid structures and their complexes. In addition primary data, the NDB contains derived geometric classifications of motifs, standards for describing features, as well tools software analysis acids. A variety search capabilities are available, many different types reports. This article describes recent redesign Web site with special emphasis on new RNA-derived data...
Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates individual base pairs or pair collections. A server, RNAview, automatically identifies classifies types that are formed nucleic acid structures by various combinations three edges, Watson–Crick, Hoogsteen Sugar edge. RNAView produces two-dimensional (2D) diagrams secondary tertiary structure either Postscript,...
Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson–Crick base pairs play a central role. Non-Watson–Crick also crucial roles tertiary contacts structured molecules. We previously classified geometrically so as to group together those are structurally similar (isosteric) therefore able substitute for each other by mutation without disrupting structure. Here, we introduce quantitative...
Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of bases in structured Protein Data Bank (PDB) hydrogen-bond with phosphates other nucleotides. By extracting superimposing base-phosphate (BPh) from a reduced-redundancy subset structures PDB, we identified recurrent phosphate-binding sites on bases. Quantum chemical calculations were carried out model systems...
The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, structured by conserved non-Watson–Crick base pairs. Structurally similar define 3D motifs in homologous molecules, but can also occur at nonhomologous sites diverse RNAs, which often vary sequence. To further our understanding motif structure sequence variability to provide a useful resource for modeling prediction, we present new method automated...
The modularity of natural RNA is the basis for design tecto-RNA, modular units capable directed self-assembly. One such association through specific loop–receptor tertiary interactions, which leads to one-dimensional oligomer arrays, demonstrated (see picture).
Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective nanoscience and nanotechnology. ‘RNA tectonics’ design modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- meso-scopic architectures desired size shape. We report three-dimensional tectoRNAs incorporating 4-way junction (4WJ) motifs, hairpin loops their cognate loop–receptors create extended, programmable interaction interfaces....
Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all forms pairs with other two bases triple, providing a natural way to geometrically classify triples. Given 12 geometric pair families defined Leontis–Westhof nomenclature, combinatoric enumeration predicts 108 potential triple families. searched representative atomic-resolution 3D structures and found instances 68 predicted Model building...
Molecular-scale computing has been explored since 1989 owing to the foreseeable limitation of Moore's law for silicon-based computation devices. With potential massive parallelism, low energy consumption and capability working in vivo, molecular-scale promises a new computational paradigm. Inspired by concepts from electronic computer, DNA realized basic Boolean functions progressed into multi-layered circuits. Recently, RNA nanotechnology emerged as an alternative approach. Owing newly...
A significant fraction of the bases in a folded, structured RNA molecule participate noncanonical base pairing interactions, often context internal loops or multi-helix junction loops. The appearance each new high-resolution structure provides welcome data to guide efforts understand and predict 3D structure, especially when question is functionally conserved molecule. recent publication crystal "Loop E" region bacterial 5S ribosomal such an event [Correll CC, Freeborn B, Moore PB, Steitz...
The interaction of 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin (T4MPyP4+) with the oligonucleotide DNA duplex [d(GCACGTGC)]2 was studied by two-dimensional 1H NMR spectroscopy, optical absorbance, circular dichroism, and molecular dynamics simulation employing particle mesh Ewald methods. T4MPyP4+ is one largest aromatic molecules for which intercalative binding to has been proposed, although this called into question recent X-ray crystallographic work [Lipscomb et al. (1996)...