C7925 Nucleic acids structure and dynamics

Faculty of Science
Autumn 2019
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)
Guaranteed by
prof. RNDr. Jiří Šponer, DrSc.
National Centre for Biomolecular Research - Faculty of Science
Contact Person: prof. RNDr. Jiří Šponer, DrSc.
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Timetable
Wed 14:00–15:50 BFU
Prerequisites
There is prior knowledge that is needed for 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 7 fields of study the course is directly associated with, display
Course objectives
Students will learn the basic knowledge about structure, dynamics and function of nucleic acids (DNA and RNA). The knowledge will be based on explanation of the recent state-of-the art experimental research, namely X-ray crystallography, NMR and structural bioinformatics. Students will also learn basic information about modern theoretical and computational methods. Students will obtain an overall overview of the field and selected case examples will be used to clarify the knowledge of structural dynamics of nucleic acids in biology and chemistry. These include local conformational variability of B-DNA, noncanonical nucleic acids, interactions of DNA with drugs, RNA enzymes, structure and function of the ribosome and regulatory role of RNA and DNA at different levels of genome expression.
Learning outcomes
The main objective of the course is to provide the students with the ability to
- describe structure, dynamics and function of DNA and RNA
- list and characterize various types and structural motifs of DNA and RNA
- explain basic principles of computational methods used in biomolecular studies
- understand the role of nucleic acids in biology and chemistry
Syllabus
  • 1. History of studies of nucleic acids structure and dynamics studies. Bases, nucleosides, nucleotides, DNA x RNA difference.
  • 2. Role of molecular interactions in biomolecules, energy, free energy and kinetics.
  • 3. Atom numbering schemes, torsional space of the sugar phosphate backbone, glycosidic bond. Internal x cartesian coordinates, helical parameters x torsion angles.
  • 4. Different base-pairing, conformational polymorphism (A, B, Z forms, local structures). Multiple-strand structures.
  • 5. Forces stabilizing nucleic acids: H--bonds, stacking, influence of ions and water.
  • 6. Noncanonical structures: DNA --- triplexes, quadruplexes, cruci-forms. RNA --- ribozymes, ribosomes. Modified nucleic acids.
  • 7. Molecular interactions: nucleic acids and water, nucleic acids and drugs, nucleic acids and proteins. Higher organization of DNA --- supercoiling, chromatin.
  • 8. Experimental methods to study Nucleic acids: X-ray crystallography, NMR spectroscopy, CD spectroscopy. Molecular modelling methods --- overview and comparison. Structure databases: NDB, PDB. Multiple criteria search. Structure analysis based on experimental data.
  • 9. Computational methods – molecular simulations and quantum chemistry.
  • 10. Local conformational variability of B-DNA.
  • 11. Structural variability of quadruplex DNA.
  • 12. Developments of drugs interacting with nucleic acids.
  • 13. Structure, dynamics and function of the ribosome.
  • 14. Structure, dynamics and regulatory functions of messenger RNA
  • 15. RNA catalysis.
  • 16. RNA prebiotic chemistry.
Literature
  • VOET, Donald, Judith G. VOET and Charlotte W. PRATT. Principles of biochemistry. 3rd ed. Hoboken, N.J.: John Wiley & Sons, 2008. xxx, 1099. ISBN 9780470233962. info
Teaching methods
Lectures, class discussion, practical examples.
Assessment methods
2hour lecture. Oral exam based on specific thematic questions.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
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, 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 2020.
  • Enrolment Statistics (Autumn 2019, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2019/C7925