C7925 Nucleic acids structure and dynamics

Faculty of Science
Autumn 2010 - only for the accreditation
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. RNDr. Jiří Šponer, DrSc. (lecturer)
Mgr. Naděžda Špačková, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jiří Šponer, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jiří Šponer, DrSc.
Prerequisites
Basic work with operation system UNIX (for ex. C2110 course) is suitable for practical exercise of knowledges obtained in this course.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 10 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should kave knowledges in nucleic acids structure. It is focused on 3D structure and its study by means of theoretical methods and by experiments. First part of the course is focused on detailed description of 3D structure of nucleic acids and their different forms (cannonical forms, triplexes, quadruplexes, complexes...). Next part refers to computational modelling of nucleic acids, especially by means of empirical methods based on molecular mechanics approach. Cooperation with experimental methods and Internet usage in structure study will be discussed.
Syllabus
  • 1. History of structure study, importance of nucleic acids structure and dynamics studies. Terms definition for nucleic acids: bases, nucleosides, nucleotides, DNA x RNA difference. 2. Atom numbering schemes, structure description with help of torsion angles, sugar pucker, glycosidic bond. Internal x cartesian coordinates, helical parameters x torsion angles. 3. Different base-pairint, conformational polymorphism (A, B, Z forms, local structures). Multiple-strand structures. 4. Forces stabilizing nucleic acids: H--bonds, stacking, influence of ions and water. 5. Unusual structures: DNA --- triplexes, quadruplexes, cruci-forms. RNA --- ribozymes, ribozomes. Modified nucleic acids. 6. Interactions: nucleic acids and water, nucleic acids and drugs, nucleic acids and proteins. Higher organization of DNA --- supercoilling, chromatin. 7. Nucleic acids study: X-ray crystallography, NMR spectroscopy, CD spectroscopy. Molecular modelling methods --- overview and comparison. 8. Molecular modelling of nucleic acids: molecular mechanics and dynamics (NMR refinement). Solvent representation (PME, continuum-solvent methods). 9. MD methodology: procedures and outputs. Equilibration, production phases. Analysis of the results. Tips and tricks. 10. Advanced methods: conformational search, quenched dynamics, LES, free energy analysis. 11. Graphical displaying of the molecules, software abilities to describe molecular properties, Internet sources of structure informations. 12. Structure databases: NDB, PDB. Multiple criteria search. Structure analysis based on experimental data.
Literature
  • SAENGER, Wolfram. Principles of nucleic acid structure. New York: Springer-Verlag, 1983, xx, 556 s. ISBN 0-387-90761-0-. info
  • Oxford handbook of nucleic acid structure. Edited by Stephen Neidle. Oxford: Oxford University Press, 1998, xv, 662. ISBN 0198500386. info
Teaching methods
Lectures, class discussion, practical examples.
Assessment methods
2hour lecture. Depending on circunstances exercise with modelling software, internet databases. Exam will have form of a written test with discussion of the results.
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: every week.
Teacher's information
http://www.sci.muni.cz/~evaf/c7925.html
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.