C7925 Nucleic acids structure and dynamics

Faculty of Science
Spring 2007
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)
Mgr. Eva Fadrná, Ph.D. (lecturer)
Mgr. Naděžda Špačková, Ph.D. (lecturer)
prof. RNDr. Jiří Šponer, DrSc. (lecturer)
Mgr. Kamila Réblová, Ph.D. (lecturer)
Guaranteed by
Mgr. Eva Fadrná, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Contact Person: Mgr. Eva Fadrná, Ph.D.
Prerequisites
C9530 Structure of biomacromolecules
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
Course objectives
The course extends 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
Assessment methods (in Czech)
2h přednáška. Podle možností praktické ukázky modelovacího software, Internetových zdrojů. Podmínkou pro vykonání zkoušky je zpracování miniprojektu s využitím grafického software a Internetové databáze.
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, Autumn 2010 - only for the accreditation, Spring 2004, Spring 2005, Spring 2006, 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.
  • Enrolment Statistics (Spring 2007, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2007/C7925