Content of lectures: 1. Building blocks and most common modifications of NA and proteins, their conformation, dynamics and physicochemical properties. 2. Primary and secondary structure of NA, Watson Crick base-pairing and its extension (cis, trans, sugar-edge, Hoogsteen), Leontis Westhof nomenclature, Saenger numbering system, A, B, Z form of double helix, G-quadruplex, i-motif, triple-helix. 3. Topology and helical parameters of NA and their analysis on selected motifs, such as nucleosome, hairpins, bulged loops, internal pools, junctions, pseudoknots and kink-turns. Interaction of these motifs with proteins. 4. Primary and secondary structure of proteins. 5. Co-transcriptional folding and folding funnel of molecules. Transitions between conformational states, experimental methods of conformational energy landscape. 6. Thermodynamic properties of DNA, RNA and proteins. 7. Structural insight into DNA repair (O6-alkylguanine or O4 alkylthymine). Ada-regulon. Excision and repair of damaged bases and nucleotides. Corrective function of DNA polymerase III. DNA repair driven by methylation. 8. Influence of epigenetic modifications and environmental conditions such as crowding, hydration, ions on the stability and dynamics of macromolecules and on regulation of gene expression. 9. Pre-tRNA, tRNA and trRNA - influence of posttranscriptional modifications on their structure and function 10. Structure, folding and dynamics of selected structures from IRES, splicesome, editosome and poly(A)sequence. 11. Structures in ribosomal RNA and their interactions with proteins 12. Student project - analysis of structures in pre-mRNA and mRNA Content of practicals: 1) Basic workflow in internet structure databases (PDB, NDB atd - http://www.science.co.il/Biomedical/Structure-Databases.asp). Advanced search and visualisation of structues (VMD, rasmol a pymol). 2) Strukture of most common structural formats (PDB, XYZ, MOL, atd), conversion between formats in Open Babel, extractioin of global structure and helical parameters of NA from these files using biopython, curves+ (https://bisi.ibcp.fr/tools/curves_plus/) and 3DNA (http://dssr.x3dna.org/). 3) Prediction of structure and folding of NA (Gibbs free energy and empirical "nearest-neighbor model", dynamic programming methods - Zuker and Nussinov algorithms, suboptimal structures - mfold, prediction of "pseudoknots" - pknotsRG, Boltzman - sfold, "align and/then fold" algorithms) 4) Bioinformatic tools for prediction of protein structure. Comparison of predicted and experimental structure. 5) Algorithms for searching of structural motifs of NA from sequence and their implementation into programming language python (regular expressions, basic communication with databases, generation of MySQL database of extracted sequences). 6) Design of 3D structure from sequence, "Coarse-grained" molecular dynamics in MMB (https://simtk.org/projects/rnatoolbox) and simple prediction of folding of G-quadruplex, RNA hairpin, tRNA and a short polypeptide. Structural morphing. 7) Detection of change in hydrated radius, induced by structural change or polymerisation of macromolecules by means of FCS. 8) Molecules in equilibrium - analysis of statistical distributions of conformers; structure of i-motif forming sequence as a function of pH investigated by smFRET in diffusion mode. 9) Detection of structural transitions of "Holiday junctions" by means of smFRET on immobilized molecules. 10) Electron transitions in DNA bases, CD of G-quadruplex, i-motif and selected protein. 11) Experimental detection of thermodynamic parameters of molecules (temperature dependence of CD). 12) Evaluation of student's projects.
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Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Demonstration, Laboratory, Individual preparation for exam
- Preparation for classes
- 30 hours per semester
- Class attendance
- 50 hours per semester
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This course will broaden knowledge of students in the fields of dynamics, structure and function of nucleic acids (NA) and proteins. After having completed the course, the students are expected to be able to: 1) Perform common tasks on DNA sequences, such as advanced search in internet databases, identification of putative structural motives in these sequences. 2) Create crude 3D model from sequence. 3) Describe, understand and use most common strategies and methods for biophysical and biochemical characterisation of NA and proteins. 4) Use, understand and interpret advanced biophysical methods and concepts, such as circular dichroism (CD), Foerster Resonance Energy Transfer (FRET), Fluorescence Correlation Spectroscopy (FCS). Write a report in the form of a scientific article.
Students will be introduced into dynamics and function of proteins and nucleic acids.
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