A5066355029- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- RNA Research and Splicing
- Synthesis and Characterization of Heterocyclic Compounds
- Advanced biosensing and bioanalysis techniques
- Protein Structure and Dynamics
- Biochemical and Molecular Research
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Synthesis and Biological Evaluation
- Bacteriophages and microbial interactions
- Fluorine in Organic Chemistry
- Chemical Synthesis and Analysis
- Synthesis and Reactivity of Heterocycles
- Carbohydrate Chemistry and Synthesis
- HIV/AIDS drug development and treatment
- Organophosphorus compounds synthesis
- Synthesis and biological activity
- RNA regulation and disease
- Crystallization and Solubility Studies
- Metal complexes synthesis and properties
- RNA Interference and Gene Delivery
- Photochemistry and Electron Transfer Studies
- Porphyrin and Phthalocyanine Chemistry
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2013-2024
Poznań University of Technology
2012-2022
International Institute of Molecular and Cell Biology
2013
University of Szczecin
2006
Polish Academy of Sciences
1976-2002
Adam Mickiewicz University in Poznań
1988-1995
University of Saskatchewan
1990-1991
Institute of Organic Chemistry
1976-1980
Max Planck Institute of Experimental Medicine
1977-1978
King's College Hospital
1977
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to difficulties experimentally assessing structures large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present novel method fully automated RNA 3D from a user-defined secondary The concept founded machine translation system. engine operates FRABASE database tailored dictionary relating and tertiary...
RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction, freely available at http://rnacomposer.cs.put.poznan.pl/ and http://rnacomposer.ibch.poznan.pl/. Its main components are: manually curated database of elements, highly efficient computational engine user-friendly web application. In this paper, we demonstrate how the latest additions to allow user significantly affect process model composition on several levels. Although in general our method based...
This paper is a report of second round RNA-Puzzles, collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, 10, represented sequences three large structures with limited or no homology previously solved molecules. A lariat-capping ribozyme, as well riboswitches complexed to adenosylcobalamin tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, AMBER refinement. Some derived models...
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures riboswitch aptamers and puzzle 7, ribozyme structure, are included this the experiment. The include biological binding sites for small molecules ( S -adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5′-triphosphate, glutamine) proteins (YbxF), one set describes large conformational...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance field. In this respect, a deeper knowledge complex three-dimensional structures is essential to understand their new biological functions. A number bioinformatic tools been proposed explore two major structural databases (PDB, NDB) in order analyze various aspects tertiary structures. One these FRABASE 1.0, first web-accessible database with an...
In the field of RNA structural biology and bioinformatics, an access to correctly annotated structure is crucial importance, especially in secondary 3D predictions. RNApdbee webserver, introduced 2014, primarily aimed address problem extraction from PDB files. Its new version, 2.0, a highly advanced multifunctional tool for annotation, revealing relationship between given or PDBx/mmCIF format. The upgraded version incorporates algorithms recognition classification high-ordered pseudoknots...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
In RNA structural biology and bioinformatics an access to correct secondary structure its proper representation is of crucial importance. This true especially in the field 3D prediction. Here, we introduce RNApdbee—a new tool that allows extract from pdb file, presents it both textual graphical form. RNApdbee supports processing knotted unknotted structures large RNAs, also within protein complexes. The method works not only for first but high order pseudoknots, gives information about...
The RNA FRABASE is a web-accessible engine with relational database, which allows for the automatic search of user-defined, 3D fragments within set structures. This new tool to and analyse structures, directed at structure modelling. user needs input either sequence(s) and/or secondary structure(s) given in 'dot-bracket' notation. algorithm searching requested very efficient. As August 2007, database contains: (i) sequences notation, derived from 1065 protein data bank (PDB)-deposited...
RNA is a unique biomolecule that involved in variety of fundamental biological functions, all which depend solely on its structure and dynamics. Since the experimental determination crystal structures laborious, computational 3D prediction methods are experiencing an ongoing thriving development. Such can lead to many models; thus, it necessary build comparisons extract common structural motifs for further medical or studies. Here, we introduce pipeline dedicated reference-free...
The intracellular ability of the "10–23" DNAzyme to efficiently inhibit expression targeted proteins has been evidenced by in vitro and vivo studies. However, standard conditions for kinetic measurements catalytic activity include 25 mm Mg2+, a concentration that is very unlikely be achieved intracellularly. To study this discrepancy, we analyzed folding transitions 10–23 induced Mg2+. For purpose, spectroscopic analyzes such as fluorescence resonance energy transfer, anisotropy, circular...
Fluorescent N-/purin-6-yl/pyridinium salts are formed in pyridine assisted phosphorylations and arenesulphonations of the hypoxanthine lactam system under various conditions including those used oligonucleotide synthesis. The N1-methyl-N3-/purin-6-yl/imidazolium salt is generated phosphorylation with TPSCl/1-methylimidazole as a coupling system. Both representatives new family ionic side-products synthesis involving residues. Their isolation procedure has been developed. High reactivity...
Abstract Left‐handed double‐helical Z‐RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One‐dimensional proton nmr experiments were used to probe structural details of left‐handed helix in concentrated sodium perchlorate solution. In 1 M NaClO 4 RNA adopts normal A‐form double helix, and 6 it is nearly all Z form. exists as equal parts A form Resonances corresponding both appear spectrum, indicating that duplex exchanges slowly between forms. Spin–spin coupling...
Zinc/acetylacetone/pyridine treatment has been designed as a very efficient method for removal of 2,2,2,-trichloroethyl group from phosphoesters. Internucleotide and terminal 2,2,2-trichloroethylphosphotriesters were transformed to corresponding diesters quantitatively. Much less reactive 2,2,2-trichloroethylphosphodiesters produced monoesters with ca. 90% yield. 31P NMR spectroscopy proposed new tool analysis internucleotide phosphate protecting groups-a crucial step in oligonucleotides...
An improved procedure for the transformation of 5′-0-monomethoxytrityl- 2′-0-acetyl-3′-phosphates uridine la inosine lb and 6-N-benzoyladenosine lc into corresponding 3′/2,2,2-trichloroethyl, 2-cyanoethyl/-phosphates lla-c is reported. 1H NMR characterization nucleoside 3′-phosphotriesters presented. New conditions i. e. anhydrous triethylamine-pyridine treatment have been found selective removal 2-cyanoethyl group from in presence neighbouring 2′-0-acetyl one.
Understanding the formation, architecture and roles of pseudoknots in RNA structures are one most difficult challenges computational biology structural bioinformatics. Methods predicting typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ terms pseudoknots' recognition revealing their nature. A few ways pseudoknot classification exist, common ones refer to a genus or order. Following latter one, we propose new...
Abstract Computational methods to predict RNA 3D structure have more and practical applications in molecular biology medicine. Therefore, it is crucial intensify efforts improve the accuracy quality of predicted three-dimensional structures. A significant role this played by RNA-Puzzles initiative that collects, evaluates, shares RNAs built computationally within currently nearly 30 challenges. datasets, subjected multi-criteria analysis, allow revealing strengths weaknesses computer...
Journal Article New observations concerning the chloroacetaldehyde reaction with some tRNA constituents. Stable intermediates, kinetics and selectivity of Get access J. Biernat, Biernat Department Stereochemistry Natural Products, Institute Organic Chemistry, Polish Academy SciencesNoskowskiego 12/14, 61-704 Poznań, Poland Search for other works by this author on: Oxford Academic PubMed Google Scholar Ciesiolka, Ciesiolka P Górnicki, Górnicki R.W. Adamiak, Adamiak W.J. Krzyzosiak, Krzyzosiak...
In this work, the first example of chemical synthesis oligoribonucleotide containing hypermodified nucleoside N6-/N-threonylcarbonyl/-adenosine /t6A/ is presented. Synthesis heptamer C-C-C-A-U-t6A-A IX, sequence which related to anticodon loop initiator tRNA from yellow lupine, was achieved by: /i/ phosphotriester block suitably protected VI an adenosine unit with a free exo-NH2 group, /ii/ highly effective "one-flask" procedure for transformation group into N,N'-disubstituted urea system...
The function of RNA is strongly dependent on its structure, so an appropriate recognition this every level organization, great importance. One particular concern the assessment base-base interactions, described as secondary knowledge which greatly facilitates interpretation and allows for structure analysis tertiary level. can be predicted from a sequence using in silico methods often adjusted with experimental data, or assessed 3D atom coordinates. Computational approaches typically...
Abstract Matrix metalloproteinase 9 ( MMP ‐9) has recently emerged as a molecule that contributes to pathological synaptic plasticity in schizophrenia, but explanation of the underlying mechanisms been missing. In present study, we performed phenotype‐based genetic association study PGAS ) > 1,000 schizophrenia patients from Göttingen Research Association for Schizophrenia GRAS data collection and found an between ‐9 rs20544 C/T single‐nucleotide polymorphism SNP located 3′untranslated...